51
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Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. Am J Physiol Lung Cell Mol Physiol 2022; 322:L822-L841. [PMID: 35438006 PMCID: PMC9142163 DOI: 10.1152/ajplung.00254.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown. To elucidate the role of EMT in the development of aberrant basaloid cells from the bronchial epithelium, we mapped EMT-induced transcriptional changes at the population and single-cell levels. Human bronchial epithelial cells grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing. Comparison of submerged and ALI cultures revealed differential expression of 8,247 protein coding (PC) and 1,621 long noncoding RNA (lncRNA) genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,020 PC and 907 lncRNA genes. Although there was no evidence for fibroblast/myofibroblast conversion following EMT induction, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype. The substantial transcriptional differences between submerged and ALI cultures highlight that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and an interactive browser (https://bronc-epi-in-vitro.cells.ucsc.edu/) of single-cell RNA-Seq data for further exploration of potential roles in the lung epithelium in health and lung disease.
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Affiliation(s)
- Dinesh Babu Uthaya Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
| | - Efthymios Motakis
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Johad Khoury
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jessica Grassmann
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, Massachusetts
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jonathan L Koff
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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52
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Moshkelgosha S, Duong A, Wilson G, Andrews T, Berra G, Renaud-Picard B, Liu M, Keshavjee S, MacParland S, Yeung J, Martinu T, Juvet S. Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation. J Heart Lung Transplant 2022; 41:1556-1569. [DOI: 10.1016/j.healun.2022.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/27/2022] Open
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53
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Role of Respiratory Epithelial Cells in Allergic Diseases. Cells 2022; 11:cells11091387. [PMID: 35563693 PMCID: PMC9105716 DOI: 10.3390/cells11091387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
The airway epithelium provides the first line of defense to the surrounding environment. However, dysfunctions of this physical barrier are frequently observed in allergic diseases, which are tightly connected with pro- or anti-inflammatory processes. When the epithelial cells are confronted with allergens or pathogens, specific response mechanisms are set in motion, which in homeostasis, lead to the elimination of the invaders and leave permanent traces on the respiratory epithelium. However, allergens can also cause damage in the sensitized organism, which can be ascribed to the excessive immune reactions. The tight interaction of epithelial cells of the upper and lower airways with local and systemic immune cells can leave an imprint that may mirror the pathophysiology. The interaction with effector T cells, along with the macrophages, play an important role in this response, as reflected in the gene expression profiles (transcriptomes) of the epithelial cells, as well as in the secretory pattern (secretomes). Further, the storage of information from past exposures as memories within discrete cell types may allow a tissue to inform and fundamentally alter its future responses. Recently, several lines of evidence have highlighted the contributions from myeloid cells, lymphoid cells, stromal cells, mast cells, and epithelial cells to the emerging concepts of inflammatory memory and trained immunity.
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Abstract
Cell type assignment is a major challenge for all types of high throughput single cell data. In many cases such assignment requires the repeated manual use of external and complementary data sources. To improve the ability to uniformly assign cell types across large consortia, platforms and modalities, we developed Cellar, a software tool that provides interactive support to all the different steps involved in the assignment and dataset comparison process. We discuss the different methods implemented by Cellar, how these can be used with different data types, how to combine complementary data types and how to analyze and visualize spatial data. We demonstrate the advantages of Cellar by using it to annotate several HuBMAP datasets from multi-omics single-cell sequencing and spatial proteomics studies. Cellar is open-source and includes several annotated HuBMAP datasets.
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55
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Secretory Immunoglobulin A Immunity in Chronic Obstructive Respiratory Diseases. Cells 2022; 11:cells11081324. [PMID: 35456002 PMCID: PMC9027823 DOI: 10.3390/cells11081324] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD), asthma and cystic fibrosis (CF) are distinct respiratory diseases that share features such as the obstruction of small airways and disease flare-ups that are called exacerbations and are often caused by infections. Along the airway epithelium, immunoglobulin (Ig) A contributes to first line mucosal protection against inhaled particles and pathogens. Dimeric IgA produced by mucosal plasma cells is transported towards the apical pole of airway epithelial cells by the polymeric Ig receptor (pIgR), where it is released as secretory IgA. Secretory IgA mediates immune exclusion and promotes the clearance of pathogens from the airway surface by inhibiting their adherence to the epithelium. In this review, we summarize the current knowledge regarding alterations of the IgA/pIgR system observed in those major obstructive airway diseases and discuss their implication for disease pathogenesis.
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56
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Toth A, Steinmeyer S, Kannan P, Gray J, Jackson CM, Mukherjee S, Demmert M, Sheak JR, Benson D, Kitzmiller J, Wayman JA, Presicce P, Cates C, Rubin R, Chetal K, Du Y, Miao Y, Gu M, Guo M, Kalinichenko VV, Kallapur SG, Miraldi ER, Xu Y, Swarr D, Lewkowich I, Salomonis N, Miller L, Sucre JS, Whitsett JA, Chougnet CA, Jobe AH, Deshmukh H, Zacharias WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Sci Transl Med 2022; 14:eabl8574. [PMID: 35353543 PMCID: PMC9082785 DOI: 10.1126/scitranslmed.abl8574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Perinatal inflammatory stress is associated with early life morbidity and lifelong consequences for pulmonary health. Chorioamnionitis, an inflammatory condition affecting the placenta and fluid surrounding the developing fetus, affects 25 to 40% of preterm births. Severe chorioamnionitis with preterm birth is associated with significantly increased risk of pulmonary disease and secondary infections in childhood, suggesting that fetal inflammation may markedly alter the development of the lung. Here, we used intra-amniotic lipopolysaccharide (LPS) challenge to induce experimental chorioamnionitis in a prenatal rhesus macaque (Macaca mulatta) model that mirrors structural and temporal aspects of human lung development. Inflammatory injury directly disrupted the developing gas exchange surface of the primate lung, with extensive damage to alveolar structure, particularly the close association and coordinated differentiation of alveolar type 1 pneumocytes and specialized alveolar capillary endothelium. Single-cell RNA sequencing analysis defined a multicellular alveolar signaling niche driving alveologenesis that was extensively disrupted by perinatal inflammation, leading to a loss of gas exchange surface and alveolar simplification, with notable resemblance to chronic lung disease in newborns. Blockade of the inflammatory cytokines interleukin-1β and tumor necrosis factor-α ameliorated LPS-induced inflammatory lung injury by blunting stromal responses to inflammation and modulating innate immune activation in myeloid cells, restoring structural integrity and key signaling networks in the developing alveolus. These data provide new insight into the pathophysiology of developmental lung injury and suggest that modulating inflammation is a promising therapeutic approach to prevent fetal consequences of chorioamnionitis.
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Affiliation(s)
- Andrea Toth
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Shelby Steinmeyer
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Paranthaman Kannan
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Jerilyn Gray
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Courtney M. Jackson
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Department of Pediatrics, Division of Allergy and Immunology, University of Rochester, Rochester, NY USA
| | - Shibabrata Mukherjee
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Martin Demmert
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, Institute for Systemic Inflammation Research, University of Lϋbeck, Lϋbeck, Germany
| | - Joshua R. Sheak
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Daniel Benson
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Joseph Kitzmiller
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Joseph A. Wayman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Pietro Presicce
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA USA
| | - Christopher Cates
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Rhea Rubin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Yina Du
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Yifei Miao
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Mingxia Gu
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Minzhe Guo
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Vladimir V. Kalinichenko
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Suhas G. Kallapur
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA USA
| | - Emily R. Miraldi
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Yan Xu
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Daniel Swarr
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Ian Lewkowich
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Nathan Salomonis
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Lisa Miller
- California National Primate Research Center, University of California Davis, Davis, CA USA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA USA
| | - Jennifer S. Sucre
- Division of Neonatology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Jeffrey A. Whitsett
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Claire A. Chougnet
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Alan H. Jobe
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Hitesh Deshmukh
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - William J. Zacharias
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
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57
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Duong TE, Wu Y, Sos BC, Dong W, Limaye S, Rivier LH, Myers G, Hagood JS, Zhang K. A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. CELL GENOMICS 2022; 2:100108. [PMID: 35434692 PMCID: PMC9012447 DOI: 10.1016/j.xgen.2022.100108] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 05/05/2021] [Accepted: 02/02/2022] [Indexed: 04/14/2023]
Abstract
Ex-utero regulation of the lungs' responses to breathing air and continued alveolar development shape adult respiratory health. Applying single-cell transposome hypersensitive site sequencing (scTHS-seq) to over 80,000 cells, we assembled the first regulatory atlas of postnatal human and mouse lung alveolar development. We defined regulatory modules and elucidated new mechanistic insights directing alveolar septation, including alveolar type 1 and myofibroblast cell signaling and differentiation, and a unique human matrix fibroblast population. Incorporating GWAS, we mapped lung function causal variants to myofibroblasts and identified a pathogenic regulatory unit linked to lineage marker FGF18, demonstrating the utility of chromatin accessibility data to uncover disease mechanism targets. Our regulatory map and analysis model provide valuable new resources to investigate age-dependent and species-specific control of critical developmental processes. Furthermore, these resources complement existing atlas efforts to advance our understanding of lung health and disease across the human lifespan.
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Affiliation(s)
- Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yan Wu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Brandon Chin Sos
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Weixiu Dong
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Siddharth Limaye
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Lauraine H. Rivier
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Greg Myers
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James S. Hagood
- Department of Pediatrics, Division of Pediatric Pulmonology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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58
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Ding J, Sharon N, Bar-Joseph Z. Temporal modelling using single-cell transcriptomics. Nat Rev Genet 2022; 23:355-368. [PMID: 35102309 DOI: 10.1038/s41576-021-00444-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/16/2022]
Abstract
Methods for profiling genes at the single-cell level have revolutionized our ability to study several biological processes and systems including development, differentiation, response programmes and disease progression. In many of these studies, cells are profiled over time in order to infer dynamic changes in cell states and types, sets of expressed genes, active pathways and key regulators. However, time-series single-cell RNA sequencing (scRNA-seq) also raises several new analysis and modelling issues. These issues range from determining when and how deep to profile cells, linking cells within and between time points, learning continuous trajectories, and integrating bulk and single-cell data for reconstructing models of dynamic networks. In this Review, we discuss several approaches for the analysis and modelling of time-series scRNA-seq, highlighting their steps, key assumptions, and the types of data and biological questions they are most appropriate for.
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59
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Teng H, Yuan Y, Bar-Joseph Z. Clustering spatial transcriptomics data. Bioinformatics 2022; 38:997-1004. [PMID: 34623423 PMCID: PMC8796363 DOI: 10.1093/bioinformatics/btab704] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/28/2021] [Accepted: 10/06/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Recent advancements in fluorescence in situ hybridization (FISH) techniques enable them to concurrently obtain information on the location and gene expression of single cells. A key question in the initial analysis of such spatial transcriptomics data is the assignment of cell types. To date, most studies used methods that only rely on the expression levels of the genes in each cell for such assignments. To fully utilize the data and to improve the ability to identify novel sub-types, we developed a new method, FICT, which combines both expression and neighborhood information when assigning cell types. RESULTS FICT optimizes a probabilistic function that we formalize and for which we provide learning and inference algorithms. We used FICT to analyze both simulated and several real spatial transcriptomics data. As we show, FICT can accurately identify cell types and sub-types, improving on expression only methods and other methods proposed for clustering spatial transcriptomics data. Some of the spatial sub-types identified by FICT provide novel hypotheses about the new functions for excitatory and inhibitory neurons. AVAILABILITY AND IMPLEMENTATION FICT is available at: https://github.com/haotianteng/FICT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haotian Teng
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, 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
| | - Ziv Bar-Joseph
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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60
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Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J 2022; 60:13993003.02057-2021. [PMID: 35086829 PMCID: PMC9386332 DOI: 10.1183/13993003.02057-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions. The discovAIR project contributes to the Human Cell Atlas Lung Biological Network by establishing a first draft of the Human Lung Cell Atlas, advancing our insight into the cellular complexity and spatial organisation of the lung in health and diseasehttps://bit.ly/3zX4cad
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Affiliation(s)
- Malte D Luecken
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Laure-Emmanuelle Zaragozi
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.,These authors made an equal contribution to this manuscript
| | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,These authors made an equal contribution to this manuscript
| | - Lisa Sikkema
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Alexandra B Firsova
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Louis Kümmerle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Janine Schniering
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Christoph H Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Sarah Teichmann
- Wellcome Sanger Institute, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK
| | - Karen van Eunen
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,UMCG Research BV, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Sylvie Leroy
- Département de Pneumologie, Université Côte d'Azur and CHU Nice, FHU-OncoAge, Nice, France
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Maarten van den Berge
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Peter Horváth
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Joachim Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Herbert B Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Pascal Barbry
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Ilya Petoukhov
- A Beta World (former Principal at MIcompany), Amsterdam, the Netherlands
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ian Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Christos Samakovlis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands .,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
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61
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Guntur VP, Manka LA, Moore CM, Wynn E, Vladar EK, Alam R, Pham TH, Fingerlin TE, Martin RJ. Refractory neutrophilic asthma and ciliary genes. J Allergy Clin Immunol 2022; 149:1970-1980. [PMID: 35034774 DOI: 10.1016/j.jaci.2021.12.761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/12/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Refractory asthma (RA) remains poorly controlled, resulting in high health care utilization despite guideline-based therapies. Patients with RA manifest higher neutrophilia as a result of increased airway inflammation and subclinical infection, the underlying mechanisms of which remain unclear. OBJECTIVE We sought to characterize and clinically correlate gene expression differences between refractory and nonrefractory (NR) asthma to uncover molecular mechanisms driving group distinctions. METHODS Microarray gene expression of paired airway epithelial brush and endobronchial biopsy samples was compared between 60 RA and 30 NR subjects. Subjects were hierarchically clustered to identify subgroups of RA, and biochemical and clinical traits (airway inflammatory molecules, respiratory pathogens, chest imaging) were compared between groups. Weighted gene correlation network analysis was used to identify coexpressed gene modules. Module expression scores were compared between groups using linear regression, controlling for age, sex, and body mass index. RESULTS Differential gene expression analysis showed upregulation of proneutrophilic and downregulation of ciliary function genes/pathways in RA compared to NR. A subgroup of RA with downregulated ciliary gene expression had increased levels of subclinical infections, airway neutrophilia, and eosinophilia as well as higher chest imaging mucus burden compared to other RA, the dominant differences between RA and NR. Weighted gene correlation network analysis identified gene modules related to ciliary function, which were downregulated in RA and were associated with lower pulmonary function and higher airway wall thickness/inflammation, markers of poorer asthma control. CONCLUSIONS Identification of a novel ciliary-deficient subgroup of RA suggests that diminished mucociliary clearance may underlie repeated asthma exacerbations despite adequate treatment, necessitating further exploration of function, mechanism, and therapeutics.
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Affiliation(s)
- Vamsi P Guntur
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo.
| | - Laurie A Manka
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo
| | - Camille M Moore
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colo
| | - Elizabeth Wynn
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Eszter K Vladar
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, and the Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colo
| | - Rafeul Alam
- The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo; Division of Allergy and Immunology, National Jewish Health, Denver, Colo
| | - Tuyet-Hang Pham
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colo; Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Richard J Martin
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo
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62
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Wasnick RM, Shalashova I, Wilhelm J, Khadim A, Schmidt N, Hackstein H, Hecker A, Hoetzenecker K, Seeger W, Bellusci S, El Agha E, Ruppert C, Guenther A. Differential LysoTracker Uptake Defines Two Populations of Distal Epithelial Cells in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:235. [PMID: 35053350 PMCID: PMC8773634 DOI: 10.3390/cells11020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 12/18/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal degenerative lung disease of unknown etiology. Although in its final stages it implicates, in a reactive manner, all lung cell types, the initial damage involves the alveolar epithelial compartment, in particular the alveolar epithelial type 2 cells (AEC2s). AEC2s serve dual progenitor and surfactant secreting functions, both of which are deeply impacted in IPF. Thus, we hypothesize that the size of the surfactant processing compartment, as measured by LysoTracker incorporation, allows the identification of different epithelial states in the IPF lung. Flow cytometry analysis of epithelial LysoTracker incorporation delineates two populations (Lysohigh and Lysolow) of AEC2s that behave in a compensatory manner during bleomycin injury and in the donor/IPF lung. Employing flow cytometry and transcriptomic analysis of cells isolated from donor and IPF lungs, we demonstrate that the Lysohigh population expresses all classical AEC2 markers and is drastically diminished in IPF. The Lysolow population, which is increased in proportion in IPF, co-expressed AEC2 and basal cell markers, resembling the phenotype of the previously identified intermediate AEC2 population in the IPF lung. In that regard, we provide an in-depth flow-cytometry characterization of LysoTracker uptake, HTII-280, proSP-C, mature SP-B, NGFR, KRT5, and CD24 expression in human lung epithelial cells. Combining functional analysis with extracellular and intracellular marker expression and transcriptomic analysis, we advance the current understanding of epithelial cell behavior and fate in lung fibrosis.
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Affiliation(s)
- Roxana Maria Wasnick
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
| | - Irina Shalashova
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
| | - Jochen Wilhelm
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Excellence Cluster Cardiopulmonary Institute (CPI), 35392 Giessen, Germany
- Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Ali Khadim
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Nicolai Schmidt
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
| | - Holger Hackstein
- Department of Clinical Immunology and Transfusion Medicine, 35392 Giessen, Germany;
| | - Andreas Hecker
- Department of General and Thoracic Surgery, University Hospital Giessen, 35392 Giessen, Germany;
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, 1090 Vienna, Austria;
| | - Werner Seeger
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Excellence Cluster Cardiopulmonary Institute (CPI), 35392 Giessen, Germany
- Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Saverio Bellusci
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Excellence Cluster Cardiopulmonary Institute (CPI), 35392 Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Elie El Agha
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Clemens Ruppert
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Excellence Cluster Cardiopulmonary Institute (CPI), 35392 Giessen, Germany
- European IPF Registry/UGLMC Giessen Biobank, 35392 Giessen, Germany
| | - Andreas Guenther
- Universities of Giessen and Marburg Lung Center (UGMLC), The German Center for Lung Research (DZL), 35392 Giessen, Germany; (I.S.); (J.W.); (A.K.); (N.S.); (W.S.); (S.B.); (E.E.A.); (C.R.); (A.G.)
- Excellence Cluster Cardiopulmonary Institute (CPI), 35392 Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
- Department of General and Thoracic Surgery, University Hospital Giessen, 35392 Giessen, Germany;
- European IPF Registry/UGLMC Giessen Biobank, 35392 Giessen, Germany
- Lung Clinic Waldhof-Elgershausen, 35753 Greifenstein, Germany
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63
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Chen WW, Liu W, Li Y, Wang J, Ren Y, Wang G, Chen C, Li H. Deciphering the Immune-Tumor Interplay During Early-Stage Lung Cancer Development via Single-Cell Technology. Front Oncol 2022; 11:716042. [PMID: 35047383 PMCID: PMC8761635 DOI: 10.3389/fonc.2021.716042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/08/2021] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Cancer immunotherapy has shown great success in treating advanced-stage lung cancer but has yet been used to treat early-stage lung cancer, mostly due to lack of understanding of the tumor immune microenvironment in early-stage lung cancer. The immune system could both constrain and promote tumorigenesis in a process termed immune editing that can be divided into three phases, namely, elimination, equilibrium, and escape. Current understanding of the immune response toward tumor is mainly on the "escape" phase when the tumor is clinically detectable. The detailed mechanism by which tumor progenitor lesions was modulated by the immune system during early stage of lung cancer development remains elusive. The advent of single-cell sequencing technology enables tumor immunologists to address those fundamental questions. In this perspective, we will summarize our current understanding and big gaps about the immune response during early lung tumorigenesis. We will then present the state of the art of single-cell technology and then envision how single-cell technology could be used to address those questions. Advances in the understanding of the immune response and its dynamics during malignant transformation of pre-malignant lesion will shed light on how malignant cells interact with the immune system and evolve under immune selection. Such knowledge could then contribute to the development of precision and early intervention strategies toward lung malignancy.
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Affiliation(s)
- Wei-Wei Chen
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wei Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingze Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guangsuo Wang
- Department of Thoracic Surgery, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hanjie Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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64
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Ibañez-Solé O, Ascensión AM, Araúzo-Bravo MJ, Izeta A. Lack of evidence for increased transcriptional noise in aged tissues. eLife 2022; 11:80380. [PMID: 36576247 PMCID: PMC9934862 DOI: 10.7554/elife.80380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Aging is often associated with a loss of cell type identity that results in an increase in transcriptional noise in aged tissues. If this phenomenon reflects a fundamental property of aging remains an open question. Transcriptional changes at the cellular level are best detected by single-cell RNA sequencing (scRNAseq). However, the diverse computational methods used for the quantification of age-related loss of cellular identity have prevented reaching meaningful conclusions by direct comparison of existing scRNAseq datasets. To address these issues we created Decibel, a Python toolkit that implements side-to-side four commonly used methods for the quantification of age-related transcriptional noise in scRNAseq data. Additionally, we developed Scallop, a novel computational method for the quantification of membership of single cells to their assigned cell type cluster. Cells with a greater Scallop membership score are transcriptionally more stable. Application of these computational tools to seven aging datasets showed large variability between tissues and datasets, suggesting that increased transcriptional noise is not a universal hallmark of aging. To understand the source of apparent loss of cell type identity associated with aging, we analyzed cell type-specific changes in transcriptional noise and the changes in cell type composition of the mammalian lung. No robust pattern of cell type-specific transcriptional noise alteration was found across aging lung datasets. In contrast, age-associated changes in cell type composition of the lung were consistently found, particularly of immune cells. These results suggest that claims of increased transcriptional noise of aged tissues should be reformulated.
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Affiliation(s)
- Olga Ibañez-Solé
- Biodonostia Health Research Institute, Computational Biology and Systems Biomedicine GroupDonostia-San SebastiánSpain,Biodonostia Health Research Institute, Tissue Engineering groupDonostia-San SebastiánSpain
| | - Alex M Ascensión
- Biodonostia Health Research Institute, Computational Biology and Systems Biomedicine GroupDonostia-San SebastiánSpain,Biodonostia Health Research Institute, Tissue Engineering groupDonostia-San SebastiánSpain
| | - Marcos J Araúzo-Bravo
- Biodonostia Health Research Institute, Computational Biology and Systems Biomedicine GroupDonostia-San SebastiánSpain,Biodonostia Health Research Institute, Computational Biomedicine Data Analysis PlatformDonostia-San SebastiánSpain,CIBER of Frailty and Healthy Aging (CIBERfes)MadridSpain,IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | - Ander Izeta
- Biodonostia Health Research Institute, Tissue Engineering groupDonostia-San SebastiánSpain,Tecnun-University of NavarraDonostia-San SebastiánSpain
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65
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Bascom R, Dhingra R, Francomano CA. Respiratory manifestations in the Ehlers-Danlos syndromes. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2021; 187:533-548. [PMID: 34811894 DOI: 10.1002/ajmg.c.31953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Persons with the Ehlers-Danlos syndromes (EDS) report a wide range of respiratory symptoms, most commonly shortness of breath, exercise limitation, and cough. Also reported are noisy breathing attributed to asthma, difficulty with deep inhalation, and inspiratory thoracic pain. The literature consists of case reports and small cross-sectional and cohort studies. One case-control study estimated twofold to threefold greater respiratory disease burden among persons with EDS as compared to controls. The differential diagnosis for symptoms is broad. Structural alterations include pectus deformities, scoliosis, recurrent rib subluxations, and tracheobronchomalacia, associated with varying degrees of physiologic impairment. Those with vascular EDS have an increased risk of pneumothorax, intrapulmonary bleeding, cysts, and nonmalignant fibrous nodules. Functional aerodigestive manifestations such as inducible laryngeal obstruction may be misdiagnosed as asthma, with gastro-esophageal dysmotility and reflux as common contributing factors. Inflammatory manifestations include costochondritis, bronchiectasis, and localized respiratory allergic and nonallergic mast cell activation. Cranio-cervical instability can dysregulate respiratory control pathways. There is a need for careful phenotyping using standardized clinical tools and patient-reported outcomes and continuing collaboration with aerodigestive specialists including otolaryngologists and gastroenterologists. Also needed is further evaluation of respiratory symptoms in persons with hypermobility spectrum disorders. Personalized monitoring strategies are invaluable for interpretation and long-term management of respiratory symptoms.
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Affiliation(s)
- Rebecca Bascom
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Penn State College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Radha Dhingra
- Division of Epidemiology, Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Clair A Francomano
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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66
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McKellar DW, Walter LD, Song LT, Mantri M, Wang MFZ, De Vlaminck I, Cosgrove BD. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol 2021; 4:1280. [PMID: 34773081 PMCID: PMC8589952 DOI: 10.1038/s42003-021-02810-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. We created a single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 88 publicly available single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting dataset includes more than 365,000 cells and spans a wide range of ages, injury, and repair conditions. Together, these data enabled identification of the predominant cell types in skeletal muscle, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro-adipogenic progenitors defined by functional roles, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem cell quiescence to myofiber maturation, and identified rare, transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. We also used the integrated dataset to explore ligand-receptor co-expression patterns and identify dynamic cell-cell interactions in muscle injury response. We provide a public web tool to enable interactive exploration and visualization of the data. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.
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Affiliation(s)
- David W McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Lauren D Walter
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Leo T Song
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Madhav Mantri
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael F Z Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Benjamin D Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
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67
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Conte E. Targeting monocytes/macrophages in fibrosis and cancer diseases: Therapeutic approaches. Pharmacol Ther 2021; 234:108031. [PMID: 34774879 DOI: 10.1016/j.pharmthera.2021.108031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/19/2021] [Accepted: 11/02/2021] [Indexed: 02/08/2023]
Abstract
Over almost 140 years since their identification, the knowledge about macrophages has unbelievably evolved. The 'big eaters' from being thought of as simple phagocytic cells have been recognized as master regulators in immunity, homeostasis, healing/repair and organ development. Long considered to originate exclusively from bone marrow-derived circulating monocytes, macrophages have been also demonstrated to be the first immune cells colonizing tissues in the developing embryo and persisting in adult life by self-renewal, as long-lived tissue resident macrophages. Therefore, heterogeneous populations of macrophages with different ontogeny and functions co-exist in tissues. Macrophages act as sentinels of homeostasis and are intrinsically programmed to lead the wound healing and repair processes that occur after injury. However, in certain pathological circumstances macrophages get dysfunctional, and impaired or aberrant macrophage activities become key features of diseases. For instance, in both fibrosis and cancer, that have been defined 'wounds that do not heal', dysfunctional monocyte-derived macrophages overall play a key detrimental role. On the other hand, due to their plasticity these cells can be 're-educated' and exert anti-fibrotic and anti-cancer functions. Therefore macrophages represent an important therapeutic target in both fibrosis and cancer diseases. The current review will illustrate new insights into the role of monocytes/macrophages in these devastating diseases and summarize new therapeutic strategies and applications of macrophage-targeted drug development in their clinical setting.
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68
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Pouwels SD, Burgess JK, Verschuuren E, Slebos DJ. The cellular composition of the lung lining fluid gradually changes from bronchus to alveolus. Respir Res 2021; 22:285. [PMID: 34736473 PMCID: PMC8570005 DOI: 10.1186/s12931-021-01882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Although large advances have recently been made mapping out the cellular composition of lung tissue using single cell sequencing, the composition and distribution of the cellular elements within the lining fluid of the lung has not been extensively studied. Here, we assessed the cellular composition of the lung lining fluid by performing a differential cell analysis on bronchoalveolar lavage fluid (BALF) and epithelial lining fluid (ELF) at four different locations within the lung in post-lung transplantation patients. The percentage of neutrophils and lymphocytes is reduced in more distal regions of the lungs, while the percentage of macrophages increases in these more distal regions. These data provide valuable information to determine which lung lining fluid sampling technique and location is best to use for measuring specific factors and biomarkers, and to increase the understanding of different cell populations in specific lung regions.
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Affiliation(s)
- S D Pouwels
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands. .,Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. .,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, The Netherlands.
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Verschuuren
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dirk-Jan Slebos
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, The Netherlands
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69
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Aevermann B, Zhang Y, Novotny M, Keshk M, Bakken T, Miller J, Hodge R, Lelieveldt B, Lein E, Scheuermann RH. A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing. Genome Res 2021; 31:1767-1780. [PMID: 34088715 PMCID: PMC8494219 DOI: 10.1101/gr.275569.121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022]
Abstract
Single-cell genomics is rapidly advancing our knowledge of the diversity of cell phenotypes, including both cell types and cell states. Driven by single-cell/-nucleus RNA sequencing (scRNA-seq), comprehensive cell atlas projects characterizing a wide range of organisms and tissues are currently underway. As a result, it is critical that the transcriptional phenotypes discovered are defined and disseminated in a consistent and concise manner. Molecular biomarkers have historically played an important role in biological research, from defining immune cell types by surface protein expression to defining diseases by their molecular drivers. Here, we describe a machine learning-based marker gene selection algorithm, NS-Forest version 2.0, which leverages the nonlinear attributes of random forest feature selection and a binary expression scoring approach to discover the minimal marker gene expression combinations that optimally capture the cell type identity represented in complete scRNA-seq transcriptional profiles. The marker genes selected provide an expression barcode that serves as both a useful tool for downstream biological investigation and the necessary and sufficient characteristics for semantic cell type definition. The use of NS-Forest to identify marker genes for human brain middle temporal gyrus cell types reveals the importance of cell signaling and noncoding RNAs in neuronal cell type identity.
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Affiliation(s)
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Mohamed Keshk
- J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Boudewijn Lelieveldt
- Department of Radiology, Leiden University Medical Center, 2300 Leiden, The Netherlands
- Department of Intelligent Systems, Delft University of Technology, 2628 Delft, The Netherlands
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, California 92037, USA
- University of California San Diego, La Jolla, California 92093, USA
- La Jolla Institute for Immunology, La Jolla, California 92037, USA
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70
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Affiliation(s)
- Christian Martin
- University Hospital Aachen, RWTH, Aachen, Institute of Pharmacology and Toxicology, Aachen, Germany;
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71
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Cho HJ, Ha JG, Lee SN, Kim CH, Wang DY, Yoon JH. Differences and similarities between the upper and lower airway: focusing on innate immunity. Rhinology 2021; 59:441-450. [PMID: 34339483 DOI: 10.4193/rhin21.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The nose is the first respiratory barrier to external pathogens, allergens, pollutants, or cigarette smoke, and vigorous immune responses are triggered when external pathogens come in contact with the nasal epithelium. The mucosal epithelial cells of the nose are essential to the innate immune response against external pathogens and transmit signals that modulate the adaptive immune response. The upper and lower airways share many physiological and immunological features, but there are also numerous differences. It is crucial to understand these differences and their contribution to pathophysiology in order to optimize treatments for inflammatory diseases of the respiratory tract. This review summarizes important differences in the embryological development, histological features, microbiota, immune responses, and cellular subtypes of mucosal epithelial cells of the nose and lungs.
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Affiliation(s)
- H-J Cho
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - J G Ha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - S N Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea 2 Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea
| | - C-H Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - D-Y Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J-H Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
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72
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Forno E, Abman SH, Singh J, Robbins ME, Selvadurai H, Schumacker PT, Robinson PD. Update in Pediatrics 2020. Am J Respir Crit Care Med 2021; 204:274-284. [PMID: 34126039 DOI: 10.1164/rccm.202103-0605up] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Erick Forno
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Steven H Abman
- Department of Pediatrics, Children's Hospital Colorado, Denver, Colorado.,University of Colorado Anschutz School of Medicine, Denver, Colorado
| | - Jagdev Singh
- Department of Respiratory Medicine, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Pediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Mary E Robbins
- Division of Neonatology, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois; and.,Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hiran Selvadurai
- Department of Respiratory Medicine, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Pediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Paul T Schumacker
- Division of Neonatology, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois; and.,Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Paul D Robinson
- Department of Respiratory Medicine, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Pediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
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73
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Barbry P, Marcet B, Caballero I. Where Is the Cystic Fibrosis Transmembrane Conductance Regulator? Am J Respir Crit Care Med 2021; 203:1214-1216. [PMID: 33428551 PMCID: PMC8456474 DOI: 10.1164/rccm.202012-4434ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire Université Côte d'Azur-CNRS Sophia Antipolis, France
| | - Brice Marcet
- Institut de Pharmacologie Moléculaire et Cellulaire Université Côte d'Azur-CNRS Sophia Antipolis, France
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74
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Adegunsoye A, Ryerson CJ. Diagnostic Classification of Interstitial Lung Disease in Clinical Practice. Clin Chest Med 2021; 42:251-261. [PMID: 34024401 DOI: 10.1016/j.ccm.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Interstitial lung diseases (ILDs) are challenging to diagnose, requiring integration of multiple complex features that are often difficult to interpret. This article reviews a pragmatic approach to ILD diagnosis and classification, focusing on diagnostic tools and strategies that are used to separate different subtypes and identify the most appropriate management. We discuss the evolution of ILD classification and the contemporary approach that integrates routinely used diagnostic tools in a multidisciplinary discussion. We highlight the increasing importance of taking a multipronged approach to ILD classification that reflects the recent emphasis on disease behavior while also considering etiopathogenesis and morphologic features.
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Affiliation(s)
- Ayodeji Adegunsoye
- Section of Pulmonary & Critical Care, The University of Chicago Medicine, 5841 South Maryland Avenue - MC6076
- M662, Chicago, IL 60637, USA
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia, Centre for Heart Lung Innovation, St. Paul's Hospital, Ward 8B, 1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada.
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75
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021; 595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 461] [Impact Index Per Article: 153.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.
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Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Harvard Medical School, Boston, MA 02115, USA,Massachusetts Institute of Technology, Cambridge, MA
02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public
Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Division of Infectious Diseases, Department of Medicine,
Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki,
Finland,Analytical & Translational Genetics Unit,
Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA,FAS Center for Systems Biology, Department of Organismic
and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical
Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Genetics and BASE Initiative, Stanford
University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki,
Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115,Harvard-MIT Division of Health Sciences and Technology,
Cambridge MA,Department of Pathology, Harvard Medical School, Boston,
MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA,Center for Regenerative Medicine, Massachusetts General
Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine,
Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public
Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of
MIT and Harvard, Cambridge, MA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston,
MA 02115, USA,Department of Molecular Biology and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA,Department of Immunology and Infectious Diseases, Harvard
T.H. Chan School of Public Health, Harvard University, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Massachusetts Consortium on Pathogen Readiness, Boston,
MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering,
Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138,Wyss Institute for Biologically Inspired Engineering,
Harvard University,Vascular Biology Program and Department of Surgery,
Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY,Herbert Irving Comprehensive Cancer Center, Columbia
University Irving Medical Center, New York, NY,Program for Mathematical Genomics, Columbia University
Irving Medical Center, New York, NY
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA,Harvard Medical School, Boston, MA 02115, USA,Harvard Stem Cell Institute, Cambridge, MA, USA,Program in Computational & Systems Biology,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Program in Immunology, Harvard Medical School, Boston, MA
02115, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
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76
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Curras-Alonso S, Soulier J, Walter T, Mueller F, Londoño-Vallejo A, Fouillade C. Spatial transcriptomics for respiratory research and medicine. Eur Respir J 2021; 58:13993003.04314-2020. [PMID: 33833036 DOI: 10.1183/13993003.04314-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Sandra Curras-Alonso
- Institut Curie, CNRS UMR 3244, PSL Research University, Paris Cedex 05, France.,Institut Curie, Inserm U1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay Cedex, France
| | - Juliette Soulier
- Institut Curie, CNRS UMR 3244, PSL Research University, Paris Cedex 05, France
| | - Thomas Walter
- Centre for Computational Biology (CBIO), MINES ParisTech, PSL University, Paris Cedex 06, France.,Institut Curie, Paris Cedex, France.,INSERM, U900, Paris Cedex, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, Paris, France.,C3BI, USR 3756 IP CNRS, Paris, France
| | - Arturo Londoño-Vallejo
- Institut Curie, CNRS UMR 3244, PSL Research University, Paris Cedex 05, France.,A. Londoño-Vallejo and C. Fouillade contributed equally to this article as lead authors and supervised the work
| | - Charles Fouillade
- Institut Curie, Inserm U1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay Cedex, France .,A. Londoño-Vallejo and C. Fouillade contributed equally to this article as lead authors and supervised the work
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77
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Hynds RE, Zacharias WJ, Nikolić MZ, Königshoff M, Eickelberg O, Gosens R, de Coppi P, Janes SM, Morrisey E, Clevers H, Ryan AL, Stripp BR, Sun X, Kim CF, Lin QS. National Heart, Lung, and Blood Institute and Building Respiratory Epithelium and Tissue for Health (BREATH) Consortium Workshop Report: Moving Forward in Lung Regeneration. Am J Respir Cell Mol Biol 2021; 65:22-29. [PMID: 33625958 PMCID: PMC8320125 DOI: 10.1165/rcmb.2020-0397ws] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The National Heart, Lung, and Blood Institute of the National Institutes of Health, together with the Longfonds BREATH consortium, convened a working group to review the field of lung regeneration and suggest avenues for future research. The meeting took place on May 22, 2019, at the American Thoracic Society 2019 conference in Dallas, Texas, United States, and brought together investigators studying lung development, adult stem-cell biology, induced pluripotent stem cells, biomaterials, and respiratory disease. The purpose of the working group was 1) to examine the present status of basic science approaches to tackling lung disease and promoting lung regeneration in patients and 2) to determine priorities for future research in the field.
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Affiliation(s)
- Robert E. Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, and
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - William J. Zacharias
- Division of Pulmonary Biology, Department of Pediatrics, Cincinnati Children’s Hospital–College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Marko Z. Nikolić
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Melanie Königshoff
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lung Repair and Regeneration Research Unit, Comprehensive Pneumology Center, Helmholtz Zentrum München, Munich, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Reinoud Gosens
- Department of Molecular Pharmacology and
- Groningen Research Institute for Asthma and Chronic Obstructive Pulmonary Disease, University of Groningen, Groningen, the Netherlands
| | - Paolo de Coppi
- Stem Cell and Regenerative Medicine Section, National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre–University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Sam M. Janes
- Division of Medicine, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Edward Morrisey
- Department of Medicine
- Department of Cell and Developmental Biology
- Lung Biology Institute, University of Pennsylvania–Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences–University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Amy L. Ryan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Hastings Center for Pulmonary Research, and
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California
| | - Barry R. Stripp
- Lung Institute and
- Board of Governors Regenerative Medicine Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Xin Sun
- Department of Pediatrics and
- Department of Biological Sciences, University of California San Diego, San Diego, California
| | - Carla F. Kim
- Division of Hematology/Oncology and
- Division of Respiratory Disease, Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Harvard University, Boston, Massachusetts
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; and
| | - Qing S. Lin
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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78
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Huang KY, Petretto E. Cross-species integration of single-cell RNA-seq resolved alveolar-epithelial transitional states in idiopathic pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol 2021; 321:L491-L506. [PMID: 34132117 DOI: 10.1152/ajplung.00594.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Single-cell transcriptomics analyses of the fibrotic lung uncovered two cell states critical to lung injury recovery in the alveolar epithelium-a reparative transitional cell state in the mouse and a disease-specific cell state (KRT5-/KRT17+) in human idiopathic pulmonary fibrosis (IPF). The murine transitional cell state lies between the differentiation from type 2 (AT2) to type 1 pneumocyte (AT1), and the human KRT5-/KRT17+ cell state may arise from the dysregulation of this differentiation process. We review major findings of single-cell transcriptomics analyses of the fibrotic lung and reanalyzed data from seven single-cell RNA sequencing studies of human and murine models of IPF, focusing on the alveolar epithelium. Our comparative and cross-species single-cell transcriptomics analyses allowed us to further delineate the differentiation trajectories from AT2 to AT1 and AT2 to the KRT5-/KRT17+ cell state. We observed AT1 cells in human IPF retain the transcriptional signature of the murine transitional cell state. Using pseudotime analysis, we recapitulated the differentiation trajectories from AT2 to AT1 and from AT2 to KRT5-/KRT17+ cell state in multiple human IPF studies. We further delineated transcriptional programs underlying cell-state transitions and determined the molecular phenotypes at terminal differentiation. We hypothesize that in addition to the reactivation of developmental programs (SOX4, SOX9), senescence (TP63, SOX4) and the Notch pathway (HES1) are predicted to steer intermediate progenitors to the KRT5-/KRT17+ cell state. Our analyses suggest that activation of SMAD3 later in the differentiation process may explain the fibrotic molecular phenotype typical of KRT5-/KRT17+ cells.
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Affiliation(s)
- Kevin Y Huang
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore
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79
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Ward RA, Thompson GR, Villani AC, Li B, Mansour MK, Wuethrich M, Tam JM, Klein BS, Vyas JM. The Known Unknowns of the Immune Response to Coccidioides. J Fungi (Basel) 2021; 7:jof7050377. [PMID: 34065016 PMCID: PMC8151481 DOI: 10.3390/jof7050377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
Coccidioidomycosis, otherwise known as Valley Fever, is caused by the dimorphic fungi Coccidioides immitis and C. posadasii. While most clinical cases present with self-limiting pulmonary infection, dissemination of Coccidioides spp. results in prolonged treatment and portends higher mortality rates. While the structure, genome, and niches for Coccidioides have provided some insight into the pathogenesis of disease, the underlying immunological mechanisms of clearance or inability to contain the infection in the lung are poorly understood. This review focuses on the known innate and adaptive immune responses to Coccidioides and highlights three important areas of uncertainty and potential approaches to address them. Closing these gaps in knowledge may enable new preventative and therapeutic strategies to be pursued.
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Affiliation(s)
- Rebecca A. Ward
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
| | - George R. Thompson
- Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA 96817, USA;
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Bo Li
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Michael K. Mansour
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
| | - Marcel Wuethrich
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
| | - Jenny M. Tam
- Harvard Medical School, Boston, MA 02115, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bruce S. Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jatin M. Vyas
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
- Correspondence: ; Tel.: +1-617-643-6444
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80
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Kanagaki S, Suezawa T, Moriguchi K, Nakao K, Toyomoto M, Yamamoto Y, Murakami K, Hagiwara M, Gotoh S. Hydroxypropyl Cyclodextrin Improves Amiodarone-induced Aberrant Lipid Homeostasis of Alveolar Cells. Am J Respir Cell Mol Biol 2021; 64:504-514. [PMID: 33493427 DOI: 10.1165/rcmb.2020-0119oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alveolar epithelial type II (AT2) cells secrete pulmonary surfactant via lamellar bodies (LBs). Abnormalities in LBs are associated with pulmonary disorders, including fibrosis. However, high-content screening (HCS) for LB abnormalities is limited by the lack of understanding of AT2 cell functions. In the present study, we have developed LB cells harboring LB-like organelles that secrete surfactant proteins. These cells were more similar to AT2 cells than to parental A549 cells. LB cells recapitulated amiodarone (AMD)-induced LB enlargement, similar to AT2 cells of patients exposed to AMD. To reverse AMD-induced LB abnormalities, we performed HCS of approved drugs and identified 2-hydroxypropyl-β-cyclodextrin (HPβCD), a cyclic oligosaccharide, as a potential therapeutic agent. A transcriptome analysis revealed that HPβCD modulates lipid homeostasis. In addition, HPβCD inhibited AMD-induced LB abnormalities in human induced pluripotent stem cell-derived AT2 cells. Our results demonstrate that LB cells are useful for HCS and suggest that HPβCD is a candidate therapeutic agent for AMD-induced interstitial pneumonia.
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Affiliation(s)
- Shuhei Kanagaki
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Takahiro Suezawa
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Keita Moriguchi
- Department of Drug Discovery for Lung Diseases and.,Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Kazuhisa Nakao
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Masayasu Toyomoto
- Department of Drug Discovery for Lung Diseases and.,Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; and
| | | | - Koji Murakami
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; and
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81
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van der Vaart J, Clevers H. Airway organoids as models of human disease. J Intern Med 2021; 289:604-613. [PMID: 32350962 DOI: 10.1111/joim.13075] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
Studies developing and applying organoid technology have greatly increased in volume and visibility over the past decade. Organoids are three-dimensional structures that are established from pluripotent stem cells (PSCs) or adult tissue stem cells (ASCs). They consist of organ-specific cell types that self-organize through cell sorting and spatially restricted lineage commitment to generate architectural and functional characteristics of the tissue of interest. The field of respiratory development and disease has been particularly productive in this regard. Starting from human cells (PSCs or ASCs), models of the two segments of the lung, the airways and the alveoli, can be built. Such organoids allow the study of development, physiology and disease and thus bridge the gap between animal models and clinical studies. This review discusses current developments in the pulmonary organoid field, highlighting the potential and limitations of current models.
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Affiliation(s)
- J van der Vaart
- From the, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - H Clevers
- From the, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Centre Utrecht, Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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82
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Zhang L, Zhu J, Wang H, Xia J, Liu P, Chen F, Jiang H, Miao Q, Wu W, Zhang L, Luo L, Jiang X, Bai Y, Sun C, Chen D, Zhang X. A high-resolution cell atlas of the domestic pig lung and an online platform for exploring lung single-cell data. J Genet Genomics 2021; 48:411-425. [PMID: 34144929 DOI: 10.1016/j.jgg.2021.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/01/2021] [Accepted: 03/16/2021] [Indexed: 12/28/2022]
Abstract
The genetically engineered pig is regarded as an optimal source of organ transplantation for humans and an excellent model for human disease research, given its comparable physiology to human beings. A myriad of single-cell RNA sequencing (scRNA-seq) data on humans has been reported, but such data on pigs are scarce. Here, we apply scRNA-seq technology to study the cellular heterogeneity of 3-month-old pig lungs, generating the single-cell atlas of 13,580 cells covering 16 major cell types. Based on these data, we systematically characterize the similarities and differences in the cellular cross-talk and expression patterns of respiratory virus receptors in each cell type of pig lungs compared with human lungs. Furthermore, we analyze pig lung xenotransplantation barriers and reported the cell-type expression patterns of 10 genes associated with pig-to-human immunobiological incompatibility and coagulation dysregulation. We also investigate the conserved transcription factors (TFs) and their candidate target genes and constructed five conserved TF regulatory networks in the main cell types shared by pig and human lungs. Finally, we present a comprehensive and openly accessible online platform, ScdbLung. Our scRNA-seq atlas of the domestic pig lung and ScdbLung database can guide pig lung research and clinical applicability.
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Affiliation(s)
- Lijing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiacheng Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Xia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- MGI, BGI-Shenzhen, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuling Miao
- Department of Pathology, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Weiying Wu
- Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310031, China
| | - Lingli Zhang
- Department of Pathophysiology, School of Basic Medicine, Guilin Medical University, Guilin 541199, China
| | - Lihua Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Bai
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chengcheng Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xingliang Zhang
- Institute of Pediatrics, Department of Pediatric Surgery, Shenzhen Children's Hospital, Shenzhen 518038, China; Department of Pediatrics, The Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
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83
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Teschendorff AE, Feinberg AP. Statistical mechanics meets single-cell biology. Nat Rev Genet 2021; 22:459-476. [PMID: 33875884 PMCID: PMC10152720 DOI: 10.1038/s41576-021-00341-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,UCL Cancer Institute, University College London, London, UK.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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84
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Schneider JL, Rowe JH, Garcia-de-Alba C, Kim CF, Sharpe AH, Haigis MC. The aging lung: Physiology, disease, and immunity. Cell 2021; 184:1990-2019. [PMID: 33811810 PMCID: PMC8052295 DOI: 10.1016/j.cell.2021.03.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023]
Abstract
The population is aging at a rate never seen before in human history. As the number of elderly adults grows, it is imperative we expand our understanding of the underpinnings of aging biology. Human lungs are composed of a unique panoply of cell types that face ongoing chemical, mechanical, biological, immunological, and xenobiotic stress over a lifetime. Yet, we do not fully appreciate the mechanistic drivers of lung aging and why age increases the risk of parenchymal lung disease, fatal respiratory infection, and primary lung cancer. Here, we review the molecular and cellular aspects of lung aging, local stress response pathways, and how the aging process predisposes to the pathogenesis of pulmonary disease. We place these insights into context of the COVID-19 pandemic and discuss how innate and adaptive immunity within the lung is altered with age.
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Affiliation(s)
- Jaime L Schneider
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Jared H Rowe
- Division of Hematology Boston Children's Hospital and Division of Pediatric Oncology Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Disease, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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85
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Wanczyk H, Jensen T, Weiss DJ, Finck C. Advanced single-cell technologies to guide the development of bioengineered lungs. Am J Physiol Lung Cell Mol Physiol 2021; 320:L1101-L1117. [PMID: 33851545 DOI: 10.1152/ajplung.00089.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lung transplantation remains the only viable option for individuals suffering from end-stage lung failure. However, a number of current limitations exist including a continuing shortage of suitable donor lungs and immune rejection following transplantation. To address these concerns, engineering a decellularized biocompatible lung scaffold from cadavers reseeded with autologous lung cells to promote tissue regeneration is being explored. Proof-of-concept transplantation of these bioengineered lungs into animal models has been accomplished. However, these lungs were incompletely recellularized with resulting epithelial and endothelial leakage and insufficient basement membrane integrity. Failure to repopulate lung scaffolds with all of the distinct cell populations necessary for proper function remains a significant hurdle for the progression of current engineering approaches and precludes clinical translation. Advancements in 3D bioprinting, lung organoid models, and microfluidic device and bioreactor development have enhanced our knowledge of pulmonary lung development, as well as important cell-cell and cell-matrix interactions, all of which will help in the path to a bioengineered transplantable lung. However, a significant gap in knowledge of the spatiotemporal interactions between cell populations as well as relative quantities and localization within each compartment of the lung necessary for its proper growth and function remains. This review will provide an update on cells currently used for reseeding decellularized scaffolds with outcomes of recent lung engineering attempts. Focus will then be on how data obtained from advanced single-cell analyses, coupled with multiomics approaches and high-resolution 3D imaging, can guide current lung bioengineering efforts for the development of fully functional, transplantable lungs.
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Affiliation(s)
- Heather Wanczyk
- Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut
| | - Todd Jensen
- Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut
| | - Daniel J Weiss
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Christine Finck
- Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut.,Department of Surgery, Connecticut Children's Medical Center, Hartford, Connecticut
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86
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Mayr CH, Simon LM, Leuschner G, Ansari M, Schniering J, Geyer PE, Angelidis I, Strunz M, Singh P, Kneidinger N, Reichenberger F, Silbernagel E, Böhm S, Adler H, Lindner M, Maurer B, Hilgendorff A, Prasse A, Behr J, Mann M, Eickelberg O, Theis FJ, Schiller HB. Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers. EMBO Mol Med 2021; 13:e12871. [PMID: 33650774 PMCID: PMC8033531 DOI: 10.15252/emmm.202012871] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
The correspondence of cell state changes in diseased organs to peripheral protein signatures is currently unknown. Here, we generated and integrated single-cell transcriptomic and proteomic data from multiple large pulmonary fibrosis patient cohorts. Integration of 233,638 single-cell transcriptomes (n = 61) across three independent cohorts enabled us to derive shifts in cell type proportions and a robust core set of genes altered in lung fibrosis for 45 cell types. Mass spectrometry analysis of lung lavage fluid (n = 124) and plasma (n = 141) proteomes identified distinct protein signatures correlated with diagnosis, lung function, and injury status. A novel SSTR2+ pericyte state correlated with disease severity and was reflected in lavage fluid by increased levels of the complement regulatory factor CFHR1. We further discovered CRTAC1 as a biomarker of alveolar type-2 epithelial cell health status in lavage fluid and plasma. Using cross-modal analysis and machine learning, we identified the cellular source of biomarkers and demonstrated that information transfer between modalities correctly predicts disease status, suggesting feasibility of clinical cell state monitoring through longitudinal sampling of body fluid proteomes.
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Affiliation(s)
- Christoph H Mayr
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Lukas M Simon
- Institute of Computational BiologyHelmholtz Zentrum MünchenMunichGermany
| | - Gabriela Leuschner
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
- Department of Internal Medicine VLudwig‐Maximilians University (LMU) MunichMember of the German Center for Lung Research (DZL), CPC‐M bioArchiveMunichGermany
| | - Meshal Ansari
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
- Institute of Computational BiologyHelmholtz Zentrum MünchenMunichGermany
| | - Janine Schniering
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
- Department of RheumatologyCenter of Experimental RheumatologyUniversity & University Hospital ZurichZurichSwitzerland
| | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Ilias Angelidis
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Maximilian Strunz
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Pawandeep Singh
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Nikolaus Kneidinger
- Department of Internal Medicine VLudwig‐Maximilians University (LMU) MunichMember of the German Center for Lung Research (DZL), CPC‐M bioArchiveMunichGermany
| | - Frank Reichenberger
- Asklepios Fachkliniken Munich‐GautingCPC‐M bioArchive, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Edith Silbernagel
- Asklepios Fachkliniken Munich‐GautingCPC‐M bioArchive, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Stephan Böhm
- Faculty of MedicineMax von Pettenkofer‐Institute, VirologyNational Reference Center for RetrovirusesLMU MünchenMunichGermany
| | - Heiko Adler
- Helmholtz Zentrum MünchenResearch Unit Lung Repair and Regeneration, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Michael Lindner
- Asklepios Fachkliniken Munich‐GautingCPC‐M bioArchive, Member of the German Center for Lung Research (DZL)MunichGermany
- University Department of Visceral and Thoracic Surgery SalzburgParacelsus Medical UniversitySalzburgAustria
| | - Britta Maurer
- Department of RheumatologyCenter of Experimental RheumatologyUniversity & University Hospital ZurichZurichSwitzerland
| | - Anne Hilgendorff
- Center for Comprehensive Developmental Care (CDeCLMU)Member of the German Center for Lung Research (DZL)Hospital of the Ludwig‐Maximilians University (LMU)CPC‐M bioArchiveMunichGermany
| | - Antje Prasse
- Department of PneumologyHannover Medical School, Member of the German Center for Lung Research (DZL)HannoverGermany
| | - Jürgen Behr
- Department of Internal Medicine VLudwig‐Maximilians University (LMU) MunichMember of the German Center for Lung Research (DZL), CPC‐M bioArchiveMunichGermany
- Asklepios Fachkliniken Munich‐GautingCPC‐M bioArchive, Member of the German Center for Lung Research (DZL)MunichGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care MedicineDepartment of MedicineUniversity of PittsburghPittsburghPAUSA
| | - Fabian J Theis
- Institute of Computational BiologyHelmholtz Zentrum MünchenMunichGermany
| | - Herbert B Schiller
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC–M bioArchiveHelmholtz Zentrum München, Member of the German Center for Lung Research (DZL)MunichGermany
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87
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Garcia-de-Alba C. Repurposing A549 Adenocarcinoma Cells: New Options for Drug Discovery. Am J Respir Cell Mol Biol 2021; 64:405-406. [PMID: 33596392 PMCID: PMC8008800 DOI: 10.1165/rcmb.2021-0048ed] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Carolina Garcia-de-Alba
- Stem Cell Program
- Division of Hematology/Oncology and
- Division of Pulmonary Medicine Boston Children's Hospital Boston, Massachusetts
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88
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Harker JA, Lloyd CM. Overlapping and distinct features of viral and allergen immunity in the human lung. Immunity 2021; 54:617-631. [PMID: 33852829 DOI: 10.1016/j.immuni.2021.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/28/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022]
Abstract
Immunity in the human respiratory tract is provided by a diverse range of tissue-resident cells, including specialized epithelial and macrophage populations and a network of innate and innate-like lymphocytes, such as natural killer cells, innate lymphoid cells, and invariant T cells. Lung-resident memory T and B cells contribute to this network following initial exposure to antigenic stimuli. This review explores how advances in the study of human immunology have shaped our understanding of this resident immune network and its response to two of the most commonly encountered inflammatory stimuli in the airways: viruses and allergens. It discusses the many ways in which pathogenic infection and allergic inflammation mirror each other, highlighting the key checkpoints at which they diverge and how this can result in a lifetime of allergic exacerbation versus protective anti-viral immunity.
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Affiliation(s)
- James A Harker
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK.
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Llamazares-Prada M, Espinet E, Mijošek V, Schwartz U, Lutsik P, Tamas R, Richter M, Behrendt A, Pohl ST, Benz NP, Muley T, Warth A, Heußel CP, Winter H, Landry JJM, Herth FJ, Mertens TC, Karmouty-Quintana H, Koch I, Benes V, Korbel JO, Waszak SM, Trumpp A, Wyatt DM, Stahl HF, Plass C, Jurkowska RZ. Versatile workflow for cell type-resolved transcriptional and epigenetic profiles from cryopreserved human lung. JCI Insight 2021; 6:140443. [PMID: 33630765 PMCID: PMC8026197 DOI: 10.1172/jci.insight.140443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Complexity of lung microenvironment and changes in cellular composition during disease make it exceptionally hard to understand molecular mechanisms driving development of chronic lung diseases. Although recent advances in cell type-resolved approaches hold great promise for studying complex diseases, their implementation relies on local access to fresh tissue, as traditional tissue storage methods do not allow viable cell isolation. To overcome these hurdles, we developed a versatile workflow that allows storage of lung tissue with high viability, permits thorough sample quality check before cell isolation, and befits sequencing-based profiling. We demonstrate that cryopreservation enables isolation of multiple cell types from both healthy and diseased lungs. Basal cells from cryopreserved airways retain their differentiation ability, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing and EPIC Array, we show that gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for omics profiling of lung cells. Moreover, we obtained high-quality single-cell RNA-sequencing data of cells from cryopreserved human lungs, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our workflow is well suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to viable human tissue.
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Affiliation(s)
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | | | | | - Pavlo Lutsik
- Division of Cancer Epigenomics, DKFZ, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | | | | | | | | | | | - Thomas Muley
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
| | - Arne Warth
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Claus Peter Heußel
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
- Department of Surgery, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Felix J.F. Herth
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine and Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Tinne C.J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, DZL, Gauting, Germany
| | | | | | | | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | | | - Heiko F. Stahl
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, DKFZ, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Renata Z. Jurkowska
- BioMed X Institute, Heidelberg, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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90
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Payen VL, Lavergne A, Alevra Sarika N, Colonval M, Karim L, Deckers M, Najimi M, Coppieters W, Charloteaux B, Sokal EM, El Taghdouini A. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity. JHEP Rep 2021; 3:100278. [PMID: 34027339 PMCID: PMC8121977 DOI: 10.1016/j.jhepr.2021.100278] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/11/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Background & Aims The multiple vital functions of the human liver are performed by highly specialised parenchymal and non-parenchymal cells organised in complex collaborative sinusoidal units. Although crucial for homeostasis, the cellular make-up of the human liver remains to be fully elucidated. Here, single-cell RNA-sequencing was used to unravel the heterogeneity of human liver cells, in particular of hepatocytes (HEPs) and hepatic stellate cells (HSCs). Method The transcriptome of ~25,000 freshly isolated human liver cells was profiled using droplet-based RNA-sequencing. Recently published data sets and RNA in situ hybridisation were integrated to validate and locate newly identified cell populations. Results In total, 22 cell populations were annotated that reflected the heterogeneity of human parenchymal and non-parenchymal liver cells. More than 20,000 HEPs were ordered along the portocentral axis to confirm known, and reveal previously undescribed, zonated liver functions. The existence of 2 subpopulations of human HSCs with unique gene expression signatures and distinct intralobular localisation was revealed (i.e. portal and central vein-concentrated GPC3+ HSCs and perisinusoidally located DBH+ HSCs). In particular, these data suggest that, although both subpopulations collaborate in the production and organisation of extracellular matrix, GPC3+ HSCs specifically express genes involved in the metabolism of glycosaminoglycans, whereas DBH+ HSCs display a gene signature that is reminiscent of antigen-presenting cells. Conclusions This study highlights metabolic zonation as a key determinant of HEP transcriptomic heterogeneity and, for the first time, outlines the existence of heterogeneous HSC subpopulations in the human liver. These findings call for further research on the functional implications of liver cell heterogeneity in health and disease. Lay summary This study resolves the cellular landscape of the human liver in an unbiased manner and at high resolution to provide new insights into human liver cell biology. The results highlight the physiological heterogeneity of human hepatic stellate cells. A cell atlas from the near-native transcriptome of >25,000 human liver cells is presented. Hepatocytes were ordered along the portocentral axis to reveal previously undescribed gene expression patterns and zonated liver functions. Two subpopulations of human hepatic stellate cells (HSCs) are reported, characterised by different spatial distribution in the native tissue. Characteristic gene signatures of HSC subpopulations are suggestive of far-reaching functional differences.
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Key Words
- BSA, bovine serum albumin
- CC, cholangiocyte
- CV, central vein
- DEG, differentially expressed gene
- EC, endothelial cell
- ECM, extracellular matrix
- Extracellular matrix
- FFPE, formaldehyde-fixed paraffin embedded
- GAG, glycosaminoglycan
- GEO, Gene Expression Omnibus
- GO, gene ontology
- HEP, hepatocyte
- HLA, human leukocyte antigen
- HRP, horseradish peroxidase
- HSC, hepatic stellate cell
- Hepatocyte
- ISH, in situ hybridisation
- KLR, killer lectin-like receptor
- LP, lymphoid cell
- Liver cell atlas
- MP, macrophage
- MZ, midzonal
- PC, pericentral
- PP, periportal
- PV, portal vein
- TBS, Tris buffered saline
- TSA, tyramide signal amplification
- UMAP, uniform manifold approximation and projection
- UMI, unique molecular identifier
- VIM, vimentin
- Zonation
- scRNA-seq, single-cell RNA-sequencing
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Affiliation(s)
- Valéry L. Payen
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Arnaud Lavergne
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Niki Alevra Sarika
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Megan Colonval
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | | | - Etienne M. Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
| | - Adil El Taghdouini
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
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Singh K, Chen YC, Hassanzadeh S, Han K, Judy JT, Seifuddin F, Tunc I, Sack MN, Pirooznia M. Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection. Front Genet 2021; 12:599261. [PMID: 33796130 PMCID: PMC8008150 DOI: 10.3389/fgene.2021.599261] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
Analyzing host cells' transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help delineate biological processes underlying viral pathogenesis. First, analysis of expression profiles of lung cell lines A549 and Calu3 revealed upregulation of antiviral interferon signaling genes in response to all three SARS-CoV-2, MERS-CoV, or influenza A virus (IAV) infections. However, perturbations in expression of genes involved in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2-infected cells. Next, a validation study in infected human nasopharyngeal samples also revealed perturbations in autophagy and mitochondrial processes. Specifically, mTOR expression, mitochondrial ribosomal, mitochondrial complex I, lysosome acidification, and mitochondrial fission promoting genes were concurrently downregulated in both infected cell lines and human samples. SARS-CoV-2 infection impeded autophagic flux either by upregulating GSK3B in lung cell lines or by downregulating autophagy genes, SNAP29, and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Finally, age-stratified SARS-CoV-2-positive human data revealed impaired upregulation of chemokines, interferon-stimulated genes, and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2-infected host cells.
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Affiliation(s)
- Komudi Singh
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shahin Hassanzadeh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer T. Judy
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ilker Tunc
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael N. Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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Perotin JM, Polette M, Deslée G, Dormoy V. CiliOPD: a ciliopathy-associated COPD endotype. Respir Res 2021; 22:74. [PMID: 33639936 PMCID: PMC7912836 DOI: 10.1186/s12931-021-01665-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/11/2021] [Indexed: 12/18/2022] Open
Abstract
The pathophysiology of chronic obstructive pulmonary disease (COPD) relies on airway remodelling and inflammation. Alterations of mucociliary clearance are a major hallmark of COPD caused by structural and functional cilia abnormalities. Using transcriptomic databases of whole lung tissues and isolated small airway epithelial cells (SAEC), we comparatively analysed cilia-associated and ciliopathy-associated gene signatures from a set of 495 genes in 7 datasets including 538 non-COPD and 508 COPD patients. This bio-informatics approach unveils yet undescribed cilia and ciliopathy genes associated with COPD including NEK6 and PROM2 that may contribute to the pathology, and suggests a COPD endotype exhibiting ciliopathy features (CiliOPD).
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Affiliation(s)
- Jeanne-Marie Perotin
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Respiratory Diseases, CHU of Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Myriam Polette
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Biopathology, CHU Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Gaëtan Deslée
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Respiratory Diseases, CHU of Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Valérian Dormoy
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.25.430130. [PMID: 33655247 PMCID: PMC7924267 DOI: 10.1101/2021.02.25.430130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.
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Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Asa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Zohar Bloom-Ackerman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics and BASE Initiative, Stanford University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Judit Jane-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Cambridge MA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109, USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
- Wyss Institute for Biologically Inspired Engineering, Harvard University
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
- Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
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94
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Croasdell Lucchini A, Gachanja NN, Rossi AG, Dorward DA, Lucas CD. Epithelial Cells and Inflammation in Pulmonary Wound Repair. Cells 2021; 10:339. [PMID: 33562816 PMCID: PMC7914803 DOI: 10.3390/cells10020339] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/15/2021] [Accepted: 01/30/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory diseases are frequently characterised by epithelial injury, airway inflammation, defective tissue repair, and airway remodelling. This may occur in a subacute or chronic context, such as asthma and chronic obstructive pulmonary disease, or occur acutely as in pathogen challenge and acute respiratory distress syndrome (ARDS). Despite the frequent challenge of lung homeostasis, not all pulmonary insults lead to disease. Traditionally thought of as a quiescent organ, emerging evidence highlights that the lung has significant capacity to respond to injury by repairing and replacing damaged cells. This occurs with the appropriate and timely resolution of inflammation and concurrent initiation of tissue repair programmes. Airway epithelial cells are key effectors in lung homeostasis and host defence; continual exposure to pathogens, toxins, and particulate matter challenge homeostasis, requiring robust defence and repair mechanisms. As such, the epithelium is critically involved in the return to homeostasis, orchestrating the resolution of inflammation and initiating tissue repair. This review examines the pivotal role of pulmonary airway epithelial cells in initiating and moderating tissue repair and restitution. We discuss emerging evidence of the interactions between airway epithelial cells and candidate stem or progenitor cells to initiate tissue repair as well as with cells of the innate and adaptive immune systems in driving successful tissue regeneration. Understanding the mechanisms of intercellular communication is rapidly increasing, and a major focus of this review includes the various mediators involved, including growth factors, extracellular vesicles, soluble lipid mediators, cytokines, and chemokines. Understanding these areas will ultimately identify potential cells, mediators, and interactions for therapeutic targeting.
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Affiliation(s)
| | | | | | | | - Christopher D. Lucas
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh EH16 4TJ, UK; (A.C.L.); (N.N.G.); (A.G.R.); (D.A.D.)
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95
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Wu X, Verschut V, Woest ME, Ng-Blichfeldt JP, Matias A, Villetti G, Accetta A, Facchinetti F, Gosens R, Kistemaker LEM. Rho-Kinase 1/2 Inhibition Prevents Transforming Growth Factor-β-Induced Effects on Pulmonary Remodeling and Repair. Front Pharmacol 2021; 11:609509. [PMID: 33551810 PMCID: PMC7855981 DOI: 10.3389/fphar.2020.609509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
Transforming growth factor (TGF)-β-induced myofibroblast transformation and alterations in mesenchymal-epithelial interactions contribute to chronic lung diseases such as chronic obstructive pulmonary disease (COPD), asthma and pulmonary fibrosis. Rho-associated coiled-coil-forming protein kinase (ROCK) consists as two isoforms, ROCK1 and ROCK2, and both are playing critical roles in many cellular responses to injury. In this study, we aimed to elucidate the differential role of ROCK isoforms on TGF-β signaling in lung fibrosis and repair. For this purpose, we tested the effect of a non-selective ROCK 1 and 2 inhibitor (compound 31) and a selective ROCK2 inhibitor (compound A11) in inhibiting TGF-β-induced remodeling in lung fibroblasts and slices; and dysfunctional epithelial-progenitor interactions in lung organoids. Here, we demonstrated that the inhibition of ROCK1/2 with compound 31 represses TGF-β-driven actin remodeling as well as extracellular matrix deposition in lung fibroblasts and PCLS, whereas selective ROCK2 inhibition with compound A11 did not. Furthermore, the TGF-β induced inhibition of organoid formation was functionally restored in a concentration-dependent manner by both dual ROCK 1 and 2 inhibition and selective ROCK2 inhibition. We conclude that dual pharmacological inhibition of ROCK 1 and 2 counteracts TGF-β induced effects on remodeling and alveolar epithelial progenitor function, suggesting this to be a promising therapeutic approach for respiratory diseases associated with fibrosis and defective lung repair.
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Affiliation(s)
- Xinhui Wu
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Manon E. Woest
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- AQUILO BV, Groningen, Netherlands
| | - John-Poul Ng-Blichfeldt
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ana Matias
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Gino Villetti
- Corporate Pre-Clinical R and D, Chiesi Farmaceutici S.p.A., Parma, Italy
| | - Alessandro Accetta
- Corporate Pre-Clinical R and D, Chiesi Farmaceutici S.p.A., Parma, Italy
| | | | - Reinoud Gosens
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Loes E. M. Kistemaker
- Department of Molecular Pharmacology, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- AQUILO BV, Groningen, Netherlands
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96
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Royer DJ, Cook DN. Regulation of Immune Responses by Nonhematopoietic Cells in Asthma. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:292-301. [PMID: 33397743 PMCID: PMC8581969 DOI: 10.4049/jimmunol.2000885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Nonhematopoietic cells are emerging as important contributors to many inflammatory diseases, including allergic asthma. Recent advances have led to a deeper understanding of how these cells interact with traditional immune cells, thereby modulating their activities in both homeostasis and disease. In addition to their well-established roles in gas exchange and barrier function, lung epithelial cells express an armament of innate sensors that can be triggered by various inhaled environmental agents, leading to the production of proinflammatory molecules. Advances in cell lineage tracing and single-cell RNA sequencing have expanded our knowledge of rare, but immunologically important nonhematopoietic cell populations. In parallel with these advances, novel reverse genetic approaches are revealing how individual genes in different lung-resident nonhematopoietic cell populations contribute to the initiation and maintenance of asthma. This knowledge is already revealing new pathways that can be selectively targeted to treat distinct forms of asthma.
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Affiliation(s)
- Derek J Royer
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Donald N Cook
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
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Zhang Z, Guo L, Huang L, Zhang C, Luo R, Zeng L, Liang H, Li Q, Lu X, Wang X, Yan Ma C, Shao J, Luo W, Li L, Liu L, Li Z, Zhou X, Zhang X, Liu J, Yang J, Kwan KY, Liu W, Xu Y, Jiang H, Liu H, Du H, Wu Y, Yu G, Chen J, Wu J, Zhang J, Liao C, Chen HJ, Chen Z, Tse HF, Xia H, Lian Q. Distinct disease severity between children and older adults with COVID-19: Impacts of ACE2 expression, distribution, and lung progenitor cells. Clin Infect Dis 2021; 73:e4154-e4165. [PMID: 33388749 PMCID: PMC7799282 DOI: 10.1093/cid/ciaa1911] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Children and older adults with coronavirus disease 2019 (COVID-19) display a distinct spectrum of disease severity yet the risk factors aren't well understood. We sought to examine the expression pattern of angiotensin-converting enzyme 2 (ACE2), the cell-entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the role of lung progenitor cells in children and older patients. METHODS We retrospectively analysed clinical features in a cohort of 299 patients with COVID-19. The expression and distribution of ACE2 and lung progenitor cells were systematically examined using a combination of public single-cell RNA-seq datasets, lung biopsies, and ex vivo infection of lung tissues with SARS-CoV-2 pseudovirus in children and older adults. We also followed up patients who had recovered from COVID-19. RESULTS Compared with children, older patients (> 50 yrs.) were more likely to develop into serious pneumonia with reduced lymphocytes and aberrant inflammatory response (p = 0.001). The expression level of ACE2 and lung progenitor cell markers were generally decreased in older patients. Notably, ACE2 positive cells were mainly distributed in the alveolar region, including SFTPC positive cells, but rarely in airway regions in the older adults (p < 0.01). The follow-up of discharged patients revealed a prolonged recovery from pneumonia in the older (p < 0.025). CONCLUSION Compared to children, ACE2 positive cells are generally decreased in older adults and mainly presented in the lower pulmonary tract. The lung progenitor cells are also decreased. These risk factors may impact disease severity and recovery from pneumonia caused by SARS-Cov-2 infection in older patients.
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Affiliation(s)
- Zhao Zhang
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Medicine
| | - Liyan Guo
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Huang
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Institute of Drug Clinical Trial
| | - Che Zhang
- Department of Pediatrics, Affiliated Taihe Hospital of Hubei University of Medicine, Shiyan, Hubei, China
| | - Ruibang Luo
- Department of Computer Science, the University of Hong Kong, Hong Kong SAR, China
| | - Liang Zeng
- Department of Pathology; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huiying Liang
- Guangdong Provincial Children's Medical Research Center; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuhui Li
- Department of Computer Science, the University of Hong Kong, Hong Kong SAR, China
| | | | - Xianfeng Wang
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | | | - Jianbo Shao
- Department of Haematology; Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weiren Luo
- Department of Pediatrics, Third People's Hospital of Shenzhen, Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Le Li
- Department of Haematology; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Liu
- AIDS Institute and Department of Microbiology, Li Ka Shing Faculty of Medicine
| | - Ziyue Li
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaoya Zhou
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaoxian Zhang
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jie Liu
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinjian Yang
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ka Yi Kwan
- AIDS Institute and Department of Microbiology, Li Ka Shing Faculty of Medicine
| | - Wei Liu
- Department of Surgery; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yi Xu
- Department of Emergency Medicine; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hua Jiang
- Department of Haematology; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hongsheng Liu
- Department of Radiology; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hui Du
- Department of Haematology; Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanheng Wu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Guangyin Yu
- Department of Pathology; Intervention and Cell Therapy Centre, Peking University Shenzhen Hospital, Shenzhen, China
| | - Junhui Chen
- Department of Pathology; Intervention and Cell Therapy Centre, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jieying Wu
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinqiu Zhang
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huanhuan Joyce Chen
- The Pritzker school of Molecular Engineering, the Ben May department of Cancer Research, the University of Chicago, Chicago, Illinois, USA
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, Li Ka Shing Faculty of Medicine
| | | | - Huimin Xia
- Guangdong Provincial Children's Medical Research Center; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qizhou Lian
- Prenatal Diagnostic Centre and Cord Blood Bank; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Medicine.,Lead Contact
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Du Y, Ouyang W, Kitzmiller JA, Guo M, Zhao S, Whitsett JA, Xu Y. Lung Gene Expression Analysis Web Portal Version 3: Lung-at-a-Glance. Am J Respir Cell Mol Biol 2021; 64:146-149. [PMID: 33385216 PMCID: PMC7781007 DOI: 10.1165/rcmb.2020-0308le] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Yina Du
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
| | - Weichen Ouyang
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
| | | | - Minzhe Guo
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
| | - Shuyang Zhao
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
| | - Jeffrey A. Whitsett
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
- University of Cincinnati School of MedicineCincinnati, Ohio
| | - Yan Xu
- Cincinnati Children’s Hospital Medical CenterCincinnati, Ohioand
- University of Cincinnati School of MedicineCincinnati, Ohio
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Abstract
The community of cells lining our airways plays a collaborative role in the preservation of immune homeostasis in the lung and provides protection from the pathogens and pollutants in the air we breathe. In addition to its structural attributes that provide effective mucociliary clearance of the lower airspace, the airway epithelium is an immunologically active barrier surface that senses changes in the airway environment and interacts with resident and recruited immune cells. Single-cell RNA-sequencing is illuminating the cellular heterogeneity that exists in the airway wall and has identified novel cell populations with unique molecular signatures, trajectories of differentiation and diverse functions in health and disease. In this Review, we discuss how our view of the airway epithelial landscape has evolved with the advent of transcriptomic approaches to cellular phenotyping, with a focus on epithelial interactions with the local neuronal and immune systems.
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100
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Affiliation(s)
- Jonas Christian Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine Yale University School of Medicine New Haven, Connecticut and
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine Yale University School of Medicine New Haven, Connecticut and
- Department of Biostatistics Yale School of Public Health New Haven, Connecticut
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine Yale University School of Medicine New Haven, Connecticut and
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