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Chandran RR, Adams TS, Kabir I, Gallardo-Vara E, Kaminski N, Gomperts BN, Greif DM. Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease. Front Cell Dev Biol 2024; 12:1335061. [PMID: 38572485 PMCID: PMC10987733 DOI: 10.3389/fcell.2024.1335061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Alveolarization ensures sufficient lung surface area for gas exchange, and during bulk alveolarization in mice (postnatal day [P] 4.5-14.5), alpha-smooth muscle actin (SMA)+ myofibroblasts accumulate, secrete elastin, and lay down alveolar septum. Herein, we delineate the dynamics of the lineage of early postnatal SMA+ myofibroblasts during and after bulk alveolarization and in response to lung injury. SMA+ lung myofibroblasts first appear at ∼ P2.5 and proliferate robustly. Lineage tracing shows that, at P14.5 and over the next few days, the vast majority of SMA+ myofibroblasts downregulate smooth muscle cell markers and undergo apoptosis. Of note, ∼8% of these dedifferentiated cells and another ∼1% of SMA+ myofibroblasts persist to adulthood. Single cell RNA sequencing analysis of the persistent SMA- cells and SMA+ myofibroblasts in the adult lung reveals distinct gene expression profiles. For instance, dedifferentiated SMA- cells exhibit higher levels of tissue remodeling genes. Most interestingly, these dedifferentiated early postnatal myofibroblasts re-express SMA upon exposure of the adult lung to hypoxia or the pro-fibrotic drug bleomycin. However, unlike during alveolarization, these cells that re-express SMA do not proliferate with hypoxia. In sum, dedifferentiated early postnatal myofibroblasts are a previously undescribed cell type in the adult lung and redifferentiate in response to injury.
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Affiliation(s)
- Rachana R. Chandran
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Inamul Kabir
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Eunate Gallardo-Vara
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Brigitte N. Gomperts
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Children’s Discovery and Innovation Institute, Mattel Children’s Hospital, Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Daniel M. Greif
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
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2
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Carter H, Costa RM, Adams TS, Gilchrist T, Emch CE, Bame M, Oldham JM, Linderholm AL, Noth I, Kaminski N, Moore BB, Gurczynski SJ. Dendritic Cell - Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis. bioRxiv 2024:2024.03.15.584457. [PMID: 38559175 PMCID: PMC10980010 DOI: 10.1101/2024.03.15.584457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring and loss of lung function. With limited treatment options, patients succumb to the disease within 2-5 years. The molecular pathogenesis of IPF regarding the immunologic changes that occur is poorly understood. We characterize a role for non-canonical aryl-hydrocarbon receptor signaling (ncAHR) in dendritic cells (DCs) that leads to production of IL-6 and IL-17, promoting fibrosis. TLR9 signaling in myofibroblasts is shown to regulate production of TDO2 which converts tryptophan into the endogenous AHR ligand kynurenine. Mice with augmented ncAHR signaling were created by crossing floxed AHR exon-2 deletion mice (AHR Δex2 ) with mice harboring a CD11c-Cre. Bleomycin was used to study fibrotic pathogenesis. Isolated CD11c+ cells and primary fibroblasts were treated ex-vivo with relevant TLR agonists and AHR modulating compounds to study how AHR signaling influenced inflammatory cytokine production. Human datasets were also interrogated. Inhibition of all AHR signaling rescued fibrosis, however, AHR Δex2 mice treated with bleomycin developed more fibrosis and DCs from these mice were hyperinflammatory and profibrotic upon adoptive transfer. Treatment of fibrotic fibroblasts with TLR9 agonist increased expression of TDO2. Study of human samples corroborate the relevance of these findings in IPF patients. We also, for the first time, identify that AHR exon-2 floxed mice retain capacity for ncAHR signaling.
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Obacz J, Valer JA, Nibhani R, Adams TS, Schupp JC, Veale N, Lewis-Wade A, Flint J, Hogan J, Aresu G, Coonar AS, Peryt A, Biffi G, Kaminski N, Francies H, Rassl DM, Garnett MJ, Rintoul RC, Marciniak SJ. Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma. Eur Respir J 2024; 63:2300143. [PMID: 38212075 PMCID: PMC10809128 DOI: 10.1183/13993003.00143-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/30/2023] [Indexed: 01/13/2024]
Abstract
The pleural lining of the thorax regulates local immunity, inflammation and repair. A variety of conditions, both benign and malignant, including pleural mesothelioma, can affect this tissue. A lack of knowledge concerning the mesothelial and stromal cells comprising the pleura has hampered the development of targeted therapies. Here, we present the first comprehensive single-cell transcriptomic atlas of the human parietal pleura and demonstrate its utility in elucidating pleural biology. We confirm the presence of known universal fibroblasts and describe novel, potentially pleural-specific, fibroblast subtypes. We also present transcriptomic characterisation of multiple in vitro models of benign and malignant mesothelial cells, and characterise these through comparison with in vivo transcriptomic data. While bulk pleural transcriptomes have been reported previously, this is the first study to provide resolution at the single-cell level. We expect our pleural cell atlas will prove invaluable to those studying pleural biology and disease. It has already enabled us to shed light on the transdifferentiation of mesothelial cells, allowing us to develop a simple method for prolonging mesothelial cell differentiation in vitro.
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Affiliation(s)
- Joanna Obacz
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- Joint first authors
| | - Jose Antonio Valer
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- Joint first authors
| | - Reshma Nibhani
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Department of Respiratory Medicine, Hannover Medical School, German Center for Lung Research (DZL), Hannover, Germany
| | - Niki Veale
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Amanah Lewis-Wade
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jasper Flint
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Hogan
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Giuseppe Aresu
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Aman S Coonar
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Adam Peryt
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Giulia Biffi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hayley Francies
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Doris M Rassl
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Joint senior authors
| | - Robert C Rintoul
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Joint senior authors
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
- Joint senior authors
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Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023; 24:394. [PMID: 37858060 PMCID: PMC10588114 DOI: 10.1186/s12859-023-05523-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Affiliation(s)
- Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jiayi Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ningya Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, German Center for Lung Research (DZL), Hannover, Germany
| | - Weimiao Wu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
- Meta Platforms, Inc, Cambridge, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geoffrey L Chupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
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5
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Zhao AY, Unterman A, Abu Hussein N, Sharma P, Flint J, Yan X, Adams TS, Justet A, Sumida TS, Zhao J, Schupp JC, Raredon MSB, Ahangari F, Zhang Y, Buendia-Roldan I, Adegunsoye A, Sperling AI, Prasse A, Ryu C, Herzog E, Selman M, Pardo A, Kaminski N. Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases. bioRxiv 2023:2023.09.20.558301. [PMID: 37786685 PMCID: PMC10541583 DOI: 10.1101/2023.09.20.558301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Rationale and Objectives The extent and commonality of peripheral blood immune aberrations in fibrotic interstitial lung diseases are not well characterized. In this study, we aimed to identify common and distinct immune aberrations in patients with idiopathic pulmonary fibrosis (IPF) and fibrotic hypersensitivity pneumonitis (FHP) using cutting-edge single-cell profiling technologies. Methods Single-cell RNA sequencing was performed on patients and healthy controls' peripheral blood and bronchoalveolar lavage samples using 10X Genomics 5' gene expression and V(D)J profiling. Cell type composition, transcriptional profiles, cellular trajectories and signaling, and T and B cell receptor repertoires were studied. The standard Seurat R pipeline was followed for cell type composition and differential gene expression analyses. Transcription factor activity was imputed using the DoRothEA-VIPER algorithm. Pseudotime analyses were conducted using Monocle3, while RNA velocity analyses were performed with Velocyto, scVelo, and CellRank. Cell-cell connectomics were assessed using the Connectome R package. V(D)J analyses were conducted using CellRanger and Immcantation frameworks. Across all analyses, disease group differences were assessed using the Wilcoxon rank-sum test. Measurements and Main Results 327,990 cells from 83 samples were profiled. Overall, changes in monocytes were common to IPF and FHP, whereas lymphocytes exhibited disease-specific aberrations. Both diseases displayed enrichment of CCL3 hi /CCL4 hi CD14+ monocytes (p<2.2e-16) and S100A hi CD14+ monocytes (p<2.2e-16) versus controls. Trajectory and RNA velocity analysis suggested that pro-fibrotic macrophages observed in BAL originated from peripheral blood monocytes. Lymphocytes exhibited disease-specific aberrations, with CD8+ GZMK hi T cells and activated B cells primarily enriched in FHP patients. V(D)J analyses revealed unique T and B cell receptor complementarity-determining region 3 (CDR3) amino acid compositions (p<0.05) in FHP and significant IgA enrichment in IPF (p<5.2e-7). Conclusions We identified common and disease-specific immune mechanisms in IPF and FHP; S100A hi monocytes and SPP1 hi macrophages are common to IPF and FHP, whereas GMZK hi T lymphocytes and T and B cell receptor repertoires were unique in FHP. Our findings open novel strategies for the diagnosis and treatment of IPF and FHP.
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Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Justet A, Adams TS, Homer R, Amei A, Rosas IO, Kaminski N, Wang Z, Yan X. A hybrid machine learning and regression method for cell type deconvolution of spatial barcoding-based transcriptomic data. bioRxiv 2023:2023.08.24.554722. [PMID: 37662370 PMCID: PMC10473707 DOI: 10.1101/2023.08.24.554722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Spatial barcoding-based transcriptomic (ST) data require cell type deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method, to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER uses a machine learning approach to remove the systematic difference between ST and scRNA-seq data (platform effects) explicitly and efficiently to ensure the linear relationship between ST data and cell type-specific expression profile. It also considers sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. Based on the estimated cell type proportions, SDePER imputes cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution. Applications to coarse-grained simulated data and four real datasets showed that SDePER achieved more accurate and robust results than existing methods, suggesting the importance of considering platform effects, sparsity and spatial correlation in cell type deconvolution.
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Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023; 24:318. [PMID: 37608264 PMCID: PMC10463720 DOI: 10.1186/s12859-023-05432-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due to the heterogeneity in environmental exposure and genetic background across subjects, subject effect contributes to the major source of variation in scRNA-seq data with multiple subjects, which severely confounds cell type specific differential expression (DE) analysis. Moreover, dropout events are prevalent in scRNA-seq data, leading to excessive number of zeroes in the data, which further aggravates the challenge in DE analysis. RESULTS We developed iDESC to detect cell type specific DE genes between two groups of subjects in scRNA-seq data. iDESC uses a zero-inflated negative binomial mixed model to consider both subject effect and dropouts. The prevalence of dropout events (dropout rate) was demonstrated to be dependent on gene expression level, which is modeled by pooling information across genes. Subject effect is modeled as a random effect in the log-mean of the negative binomial component. We evaluated and compared the performance of iDESC with eleven existing DE analysis methods. Using simulated data, we demonstrated that iDESC had well-controlled type I error and higher power compared to the existing methods. Applications of those methods with well-controlled type I error to three real scRNA-seq datasets from the same tissue and disease showed that the results of iDESC achieved the best consistency between datasets and the best disease relevance. CONCLUSIONS iDESC was able to achieve more accurate and robust DE analysis results by separating subject effect from disease effect with consideration of dropouts to identify DE genes, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.
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Affiliation(s)
- Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jiayi Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ningya Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, German Center for Lung Research (DZL), Hannover, Germany
| | - Weimiao Wu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
- Meta Platforms, Inc, Cambridge, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geoffrey L Chupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
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Kim SH, Adams TS, Hu Q, Shin HJ, Chae G, Lee SE, Sharma L, Kwon HK, Lee FY, Park HJ, Huh WJ, Manning E, Kaminski N, Sauler M, Chen L, Song JW, Kim TK, Kang MJ. VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2023; 69:22-33. [PMID: 36450109 PMCID: PMC10324045 DOI: 10.1165/rcmb.2022-0219oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/30/2022] [Indexed: 09/09/2023] Open
Abstract
VISTA (V domain immunoglobulin suppressor of T cell activation, also called PD-1H [programmed death-1 homolog]), a novel immune regulator expressed on myeloid and T lymphocyte lineages, is upregulated in mouse and human idiopathic pulmonary fibrosis (IPF). However, the significance of VISTA and its therapeutic potential in regulating IPF has yet to be defined. To determine the role of VISTA and its therapeutic potential in IPF, the expression profile of VISTA was evaluated from human single-cell RNA sequencing data (IPF Cell Atlas). Inflammatory response and lung fibrosis were assessed in bleomycin-induced experimental pulmonary fibrosis models in VISTA-deficient mice compared with wild-type littermates. In addition, these outcomes were evaluated after VISTA agonistic antibody treatment in the wild-type pulmonary fibrosis mice. VISTA expression was increased in lung tissue-infiltrating monocytes of patients with IPF. VISTA was induced in the myeloid population, mainly circulating monocyte-derived macrophages, during bleomycin-induced pulmonary fibrosis. Genetic ablation of VISTA drastically promoted pulmonary fibrosis, and bleomycin-induced fibroblast activation was dependent on the interaction between VISTA-expressing myeloid cells and fibroblasts. Treatment with VISTA agonistic antibody reduced fibrotic phenotypes accompanied by the suppression of lung innate immune and fibrotic mediators. In conclusion, these results suggest that VISTA upregulation in pulmonary fibrosis may be a compensatory mechanism to limit inflammation and fibrosis, and stimulation of VISTA signaling using VISTA agonists effectively limits the fibrotic innate immune landscape and consequent tissue fibrosis. Further studies are warranted to test VISTA as a novel therapeutic target for the IPF treatment.
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Affiliation(s)
- Sang-Hun Kim
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | | | - Qianni Hu
- Division of Hematology and Oncology, Department of Medicine at Vanderbilt University Medical Center, Nashville, Tennessee; and
| | | | - Ganghee Chae
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang Eun Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | | | | | - Hong-Jai Park
- Section of Rheumatology, Allergy, and Immunology, Department of Internal Medicine
| | | | | | | | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | - Lieping Chen
- Department of Immunobiology, and
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Jin Woo Song
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Tae Kon Kim
- Division of Hematology and Oncology, Department of Medicine at Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Min-Jong Kang
- Section of Pulmonary, Critical Care, and Sleep Medicine
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Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, Kaminski N, Macosko EZ, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Rep 2023; 42:112412. [PMID: 37086403 PMCID: PMC10242439 DOI: 10.1016/j.celrep.2023.112412] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/26/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at the cell population level, where cells divide labor and specialize in different functions. Division of labor can arise due to instruction by tissue environment or through self-organization. Here, we develop a computational framework to investigate the contribution of these mechanisms to division of labor within a cell-type population. By optimizing collective cellular task performance under trade-offs, we find that distinguishable expression patterns can emerge from cell-cell interactions versus instructive signals. We propose a method to construct ligand-receptor networks between specialist cells and use it to infer division-of-labor mechanisms from single-cell RNA sequencing (RNA-seq) and spatial transcriptomics data of stromal, epithelial, and immune cells. Our framework can be used to characterize the complexity of cell interactions within tissues.
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Affiliation(s)
- Miri Adler
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Noa Moriel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aleksandrina Goeva
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Inbal Avraham-Davidi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon Mages
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Evan Z Macosko
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ruslan Medzhitov
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA; Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel; Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Leiby KL, Yuan Y, Ng R, Raredon MSB, Adams TS, Baevova P, Greaney AM, Hirschi KK, Campbell SG, Kaminski N, Herzog EL, Niklason LE. Rational engineering of lung alveolar epithelium. NPJ Regen Med 2023; 8:22. [PMID: 37117221 PMCID: PMC10147714 DOI: 10.1038/s41536-023-00295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/06/2023] [Indexed: 04/30/2023] Open
Abstract
Engineered whole lungs may one day expand therapeutic options for patients with end-stage lung disease. However, the feasibility of ex vivo lung regeneration remains limited by the inability to recapitulate mature, functional alveolar epithelium. Here, we modulate multimodal components of the alveolar epithelial type 2 cell (AEC2) niche in decellularized lung scaffolds in order to guide AEC2 behavior for epithelial regeneration. First, endothelial cells coordinate with fibroblasts, in the presence of soluble growth and maturation factors, to promote alveolar scaffold population with surfactant-secreting AEC2s. Subsequent withdrawal of Wnt and FGF agonism synergizes with tidal-magnitude mechanical strain to induce the differentiation of AEC2s to squamous type 1 AECs (AEC1s) in cultured alveoli, in situ. These results outline a rational strategy to engineer an epithelium of AEC2s and AEC1s contained within epithelial-mesenchymal-endothelial alveolar-like units, and highlight the critical interplay amongst cellular, biochemical, and mechanical niche cues within the reconstituting alveolus.
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Affiliation(s)
- Katherine L Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Yifan Yuan
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Ronald Ng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Pavlina Baevova
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Karen K Hirschi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
- Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Stuart G Campbell
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.
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11
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De Man R, McDonough JE, Adams TS, Manning EP, Myers G, Vos R, Ceulemans L, Dupont L, Vanaudenaerde BM, Wuyts WA, Rosas IO, Hagood JS, Ambalavanan N, Niklason L, Hansen KC, Yan X, Kaminski N. A Multi-omic Analysis of the Human Lung Reveals Distinct Cell Specific Aging and Senescence Molecular Programs. bioRxiv 2023:2023.04.19.536722. [PMID: 37131739 PMCID: PMC10153177 DOI: 10.1101/2023.04.19.536722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Age is a major risk factor for lung disease. To understand the mechanisms underlying this association, we characterized the changing cellular, genomic, transcriptional, and epigenetic landscape of lung aging using bulk and single-cell RNAseq (scRNAseq) data. Our analysis revealed age-associated gene networks that reflected hallmarks of aging, including mitochondrial dysfunction, inflammation, and cellular senescence. Cell type deconvolution revealed age-associated changes in the cellular composition of the lung: decreased alveolar epithelial cells and increased fibroblasts and endothelial cells. In the alveolar microenvironment, aging is characterized by decreased AT2B cells and reduced surfactant production, a finding that was validated by scRNAseq and IHC. We showed that a previously reported senescence signature, SenMayo, captures cells expressing canonical senescence markers. SenMayo signature also identified cell-type specific senescence-associated co-expression modules that have distinct molecular functions, including ECM regulation, cell signaling, and damage response pathways. Analysis of somatic mutations showed that burden was highest in lymphocytes and endothelial cells and was associated with high expression of senescence signature. Finally, aging and senescence gene expression modules were associated with differentially methylated regions, with inflammatory markers such as IL1B, IL6R, and TNF being significantly regulated with age. Our findings provide new insights into the mechanisms underlying lung aging and may have implications for the development of interventions to prevent or treat age-related lung diseases.
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Affiliation(s)
- Ruben De Man
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Edward P Manning
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Greg Myers
- Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill
| | - Robin Vos
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | | | - Lieven Dupont
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | | | - Wim A Wuyts
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - James S. Hagood
- Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill
| | | | - Laura Niklason
- Department of Anesthesiology, Yale School of Medicine; and Humacyte Global Inc
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
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12
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Ahangari F, Price NL, Malik S, Chioccioli M, Bärnthaler T, Adams TS, Kim J, Pradeep SP, Ding S, Cosmos C, Rose KAS, McDonough JE, Aurelien NR, Ibarra G, Omote N, Schupp JC, DeIuliis G, Villalba Nunez JA, Sharma L, Ryu C, Dela Cruz CS, Liu X, Prasse A, Rosas I, Bahal R, Fernández-Hernando C, Kaminski N. microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis. JCI Insight 2023; 8:e158100. [PMID: 36626225 PMCID: PMC9977502 DOI: 10.1172/jci.insight.158100] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and ultimately fatal disease. Recent findings have shown a marked metabolic reprogramming associated with changes in mitochondrial homeostasis and autophagy during pulmonary fibrosis. The microRNA-33 (miR-33) family of microRNAs (miRNAs) encoded within the introns of sterol regulatory element binding protein (SREBP) genes are master regulators of sterol and fatty acid (FA) metabolism. miR-33 controls macrophage immunometabolic response and enhances mitochondrial biogenesis, FA oxidation, and cholesterol efflux. Here, we show that miR-33 levels are increased in bronchoalveolar lavage (BAL) cells isolated from patients with IPF compared with healthy controls. We demonstrate that specific genetic ablation of miR-33 in macrophages protects against bleomycin-induced pulmonary fibrosis. The absence of miR-33 in macrophages improves mitochondrial homeostasis and increases autophagy while decreasing inflammatory response after bleomycin injury. Notably, pharmacological inhibition of miR-33 in macrophages via administration of anti-miR-33 peptide nucleic acids (PNA-33) attenuates fibrosis in different in vivo and ex vivo mice and human models of pulmonary fibrosis. These studies elucidate a major role of miR-33 in macrophages in the regulation of pulmonary fibrosis and uncover a potentially novel therapeutic approach to treat this disease.
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Affiliation(s)
- Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan L. Price
- Vascular Biology and Therapeutics Program, Yale Center for Molecular and System Metabolism, Department of Comparative Medicine, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas Bärnthaler
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jooyoung Kim
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Shuizi Ding
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carlos Cosmos
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kadi-Ann S. Rose
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - John E. McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nachelle R. Aurelien
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Internal Medicine, Weill Cornell Hospital Medicine, New York, New York, USA
| | - Gabriel Ibarra
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Life Span Medical Group, Department of Internal Medicine, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Norihito Omote
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julian A. Villalba Nunez
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Changwan Ryu
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Charles S. Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Xinran Liu
- Center for Cellular and Molecular Imaging (CCMI), Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Antje Prasse
- Department of Pneumology, University of Hannover, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Ivan Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale Center for Molecular and System Metabolism, Department of Comparative Medicine, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Abstract
The human lung cellular portfolio, traditionally characterized by cellular morphology and individual markers, is highly diverse, with over 40 cell types and a complex branching structure highly adapted for agile airflow and gas exchange. While constant during adulthood, lung cellular content changes in response to exposure, injury, and infection. Some changes are temporary, but others are persistent, leading to structural changes and progressive lung disease. The recent advance of single-cell profiling technologies allows an unprecedented level of detail and scale to cellular measurements, leading to the rise of comprehensive cell atlas styles of reporting. In this review, we chronical the rise of cell atlases and explore their contributions to human lung biology in health and disease.
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Affiliation(s)
- Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
| | - Arnaud Marlier
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
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14
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Cortese R, Adams TS, Cataldo KH, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea. Eur Respir J 2023; 61:13993003.01465-2022. [PMID: 36356973 DOI: 10.1183/13993003.01465-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Obstructive sleep apnoea (OSA) is a highly prevalent disease and a major cause of systemic inflammation leading to neurocognitive, behavioural, metabolic and cardiovascular dysfunction in children and adults. However, the impact of OSA on the heterogeneity of circulating immune cells remains to be determined. METHODS We applied single-cell transcriptomics analysis (scRNA-seq) to identify OSA-induced changes in transcriptional landscape in peripheral blood mononuclear cell (PBMC) composition, which uncovered severity-dependent differences in several cell lineages. Furthermore, a machine-learning approach was used to combine scRNAs-seq cell-specific markers with those differentially expressed in OSA. RESULTS scRNA-seq demonstrated OSA-induced heterogeneity in cellular composition and enabled the identification of previously undescribed cell types in PBMCs. We identified a molecular signature consisting of 32 genes, which distinguished OSA patients from various controls with high precision (area under the curve 0.96) and accuracy (93% positive predictive value and 95% negative predictive value) in an independent PBMC bulk RNA expression dataset. CONCLUSION OSA deregulates systemic immune function and displays a molecular signature that can be assessed in standard cellular RNA without the need for pre-analytical cell separation, thereby making the assay amenable to application in a molecular diagnostic setting.
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Affiliation(s)
- Rene Cortese
- Department of Child Health, Child Health Research Institute, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Kylie H Cataldo
- Department of Child Health, Child Health Research Institute, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Justin Hummel
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Leila Kheirandish-Gozal
- Department of Child Health, Child Health Research Institute, School of Medicine, University of Missouri, Columbia, MO, USA
| | - David Gozal
- Department of Child Health, Child Health Research Institute, School of Medicine, University of Missouri, Columbia, MO, USA
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15
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Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. Am J Respir Crit Care Med 2022; 206:459-475. [PMID: 35687485 DOI: 10.1164/rccm.202109-2151oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/06/2022] [Indexed: 01/10/2023] Open
Abstract
Rationale: A prevailing paradigm recognizes idiopathic pulmonary fibrosis (IPF) originating from various alveolar epithelial cell (AEC) injuries, and there is a growing appreciation of AEC aging as a key driver of the pathogenesis. Despite this progress, it is incompletely understood what main factor(s) contribute to the worsened alveolar epithelial aging in lung fibrosis. It remains a challenge how to dampen AEC aging and thereby mitigate the disease progression. Objectives: To determine the role of AEC CD38 (cluster of differentiation 38) in promoting cellular aging and lung fibrosis. Methods: We used single-cell RNA sequencing, real-time PCR, flow cytometry, and Western blotting. Measurements and Main Results: We discovered a pivotal role of CD38, a cardinal nicotinamide adenine dinucleotide (NAD) hydrolase, in AEC aging and its promotion of lung fibrosis. We found increased CD38 expression in IPF lungs that inversely correlated with the lung functions of patients. CD38 was primarily located in the AECs of human lung parenchyma and was markedly induced in IPF AECs. Similarly, CD38 expression was elevated in the AECs of fibrotic lungs of young mice and further augmented in those of old mice, which was in accordance with a worsened AEC aging phenotype and an aggravated lung fibrosis in the old animals. Mechanistically, we found that CD38 elevation downregulated intracellular NAD, which likely led to the aging promoting impairment of the NAD-dependent cellular and molecular activities. Furthermore, we demonstrated that genetic and pharmacological inactivation of CD38 improved these NAD dependent events and ameliorated bleomycin-induced lung fibrosis. Conclusions: Our study suggests targeting alveolar CD38 as a novel and effective therapeutic strategy to treat this pathology.
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Affiliation(s)
- Huachun Cui
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Na Xie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sami Banerjee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tapan Dey
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rui-Ming Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Veena B Antony
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Victor J Thannickal
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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16
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Zhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Microenvironmental sensing by fibroblasts controls macrophage population size. Proc Natl Acad Sci U S A 2022; 119:e2205360119. [PMID: 35930670 PMCID: PMC9371703 DOI: 10.1073/pnas.2205360119] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Animal tissues comprise diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF-β target genes are both regulated by cell density. We found YAP1, the transcriptional coactivator of the Hippo signaling pathway, directly regulates expression of Csf1, the lineage-specific growth factor for macrophages, through an enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition.
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Affiliation(s)
- Xu Zhou
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Ruth A. Franklin
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Miri Adler
- bBroad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Trevor S. Carter
- cDepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Emily Condiff
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Taylor S. Adams
- dPulmonary Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT 06510
| | - Scott D. Pope
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
- eHHMI, Yale University School of Medicine, New Haven, CT 06510
| | - Naomi H. Philip
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Matthew L. Meizlish
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Naftali Kaminski
- dPulmonary Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT 06510
| | - Ruslan Medzhitov
- aDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
- eHHMI, Yale University School of Medicine, New Haven, CT 06510
- 5To whom correspondence may be addressed.
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17
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Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome. Sci Rep 2022; 12:4187. [PMID: 35264704 PMCID: PMC8906120 DOI: 10.1038/s41598-022-07959-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which signaling networks are compared between tissue systems. Connectome focuses on computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets and reveal biologic insight. We present approaches to quantify focused network topologies and discuss some of the biologic theory leading to their design.
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Affiliation(s)
- Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA.
| | - Junchen Yang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - James Garritano
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Meng Wang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Dan Kushnir
- NOKIA Bell-Laboratories, Murray Hill, NJ, USA
| | - Jonas Christian Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Katherine L Leiby
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Applied Mathematics Program, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.
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18
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Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 2022; 13:494. [PMID: 35078977 PMCID: PMC8789871 DOI: 10.1038/s41467-022-28062-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, however our understanding of cell specific mechanisms underlying COPD pathobiology remains incomplete. Here, we analyze single-cell RNA sequencing profiles of explanted lung tissue from subjects with advanced COPD or control lungs, and we validate findings using single-cell RNA sequencing of lungs from mice exposed to 10 months of cigarette smoke, RNA sequencing of isolated human alveolar epithelial cells, functional in vitro models, and in situ hybridization and immunostaining of human lung tissue samples. We identify a subpopulation of alveolar epithelial type II cells with transcriptional evidence for aberrant cellular metabolism and reduced cellular stress tolerance in COPD. Using transcriptomic network analyses, we predict capillary endothelial cells are inflamed in COPD, particularly through increased CXCL-motif chemokine signaling. Finally, we detect a high-metallothionein expressing macrophage subpopulation enriched in advanced COPD. Collectively, these findings highlight cell-specific mechanisms involved in the pathobiology of advanced COPD.
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Affiliation(s)
- Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - John E McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Neeharika Kothapalli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Thomas Barnthaler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Jessica Nouws
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Matthew J Robertson
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Tao Yang
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Department of Internal Medicine, Mount Sinai Medical Center, Miami, FL, USA
| | - Ehab A Ayaub
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah G Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Clemente J Britto
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Micha Sam B Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
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19
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Yuan Y, Leiby KL, Greaney AM, Raredon MSB, Qian H, Schupp JC, Engler AJ, Baevova P, Adams TS, Kural MH, Wang J, Obata T, Yoder MC, Kaminski N, Niklason LE. A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds. Front Bioeng Biotechnol 2021; 9:760309. [PMID: 34869270 PMCID: PMC8640093 DOI: 10.3389/fbioe.2021.760309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
The development of an in vitro system for the study of lung vascular disease is critical to understanding human pathologies. Conventional culture systems fail to fully recapitulate native microenvironmental conditions and are typically limited in their ability to represent human pathophysiology for the study of disease and drug mechanisms. Whole organ decellularization provides a means to developing a construct that recapitulates structural, mechanical, and biological features of a complete vascular structure. Here, we developed a culture protocol to improve endothelial cell coverage in whole lung scaffolds and used single-cell RNA-sequencing analysis to explore the impact of decellularized whole lung scaffolds on endothelial phenotypes and functions in a biomimetic bioreactor system. Intriguingly, we found that the phenotype and functional signals of primary pulmonary microvascular revert back—at least partially—toward native lung endothelium. Additionally, human induced pluripotent stem cell-derived endothelium cultured in decellularized lung systems start to gain various native human endothelial phenotypes. Vascular barrier function was partially restored, while small capillaries remained patent in endothelial cell-repopulated lungs. To evaluate the ability of the engineered endothelium to modulate permeability in response to exogenous stimuli, lipopolysaccharide (LPS) was introduced into repopulated lungs to simulate acute lung injury. After LPS treatment, proinflammatory signals were significantly increased and the vascular barrier was impaired. Taken together, these results demonstrate a novel platform that recapitulates some pulmonary microvascular functions and phenotypes at a whole organ level. This development may help pave the way for using the whole organ engineering approach to model vascular diseases.
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Affiliation(s)
- Yifan Yuan
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Katherine L Leiby
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Medical Scientist Training Program, Yale University, New Haven, CT, United States
| | - Allison M Greaney
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Micha Sam Brickman Raredon
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Medical Scientist Training Program, Yale University, New Haven, CT, United States
| | - Hong Qian
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States.,Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Alexander J Engler
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Pavlina Baevova
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Mehmet H Kural
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Juan Wang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Tomohiro Obata
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States
| | - Mervin C Yoder
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Laura E Niklason
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States.,Department of Anesthesiology, Yale University, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States
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20
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Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J 2021; 58:2002950. [PMID: 34083402 PMCID: PMC9759791 DOI: 10.1183/13993003.02950-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. METHODS RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50). RESULTS Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg. CONCLUSION Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada
- Equally contributing authors
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Equally contributing authors
| | - Kevin F Gibson
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Mridu Gulati
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Buqu Hu
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Antun Mihaljinec
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tony N Woolard
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Heather Lynn
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- University of Arizona Health Sciences, Tucson, AZ, USA
| | - Nkiruka Emeagwali
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Alison Morris
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Joseph K Leader
- Dept of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | | | | | | | | | - Michael J Becich
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Harry Hochheiser
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven R Wisniewski
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Panayiotis V Benos
- Dept of Computational and Systems Biology and Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Antje Prasse
- Hannover Medical School (MHH), Hannover, Germany
- Fraunhofer ITEM, Hannover, Germany
| | - Laura L Koth
- University of California San Francisco, San Francisco, CA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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21
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Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021; 144:286-302. [PMID: 34030460 PMCID: PMC8300155 DOI: 10.1161/circulationaha.120.052318] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cellular diversity of the lung endothelium has not been systematically characterized in humans. We provide a reference atlas of human lung endothelial cells (ECs) to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium. METHODS We reprocessed human control single-cell RNA sequencing (scRNAseq) data from 6 datasets. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by fluorescent microscopy and in situ hybridization. scRNAseq of primary lung ECs cultured in vitro was performed. The signaling network between different lung cell types was studied. For cross-species analysis or disease relevance, we applied the same methods to scRNAseq data obtained from mouse lungs or from human lungs with pulmonary hypertension. RESULTS Six lung scRNAseq datasets were reanalyzed and annotated to identify >15 000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including panendothelial, panvascular, and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial, and venous ECs, we found previously indistinguishable subpopulations; among venous EC, we identified 2 previously indistinguishable populations: pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary ECs, we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1, and TBX2 and general capillary EC. We confirmed that all 6 endothelial cell types, including the systemic-venous ECs and aerocytes, are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. scRNAseq of commercially available primary lung ECs demonstrated a loss of their native lung phenotype in culture. scRNAseq revealed that endothelial diversity is maintained in pulmonary hypertension. Our article is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). CONCLUSIONS Our integrated analysis provides a comprehensive and well-crafted reference atlas of ECs in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.
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Affiliation(s)
- Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Yifan Yuan
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Sergio Poli
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
- Division of Internal Medicine, Mount Sinai Medical Center, Miami Beach, FL (S.P.)
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Kadi-Ann Rose
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Edward P. Manning
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
- VA Connecticut Healthcare System (E.P.M.), West Haven
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Nir Neumark
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
| | - Austin J. Gutierrez
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, PA (R.L.)
| | - Richard W. Pierce
- Department of Pediatrics (R.W.P.), Yale University School of Medicine, New Haven, CT
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, UK (S.A.T.)
| | | | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
- Department of Veterans Affairs Medical Center, Nashville, TN (J.A.K.)
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN (J.A.K.)
| | - Laura E. Niklason
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Dana Pe’er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (D.P.)
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology (R.J.H.), Yale University School of Medicine, New Haven, CT
- Pathology and Laboratory Medicine Service (R.J.H.), West Haven
| | - Ivan O. Rosas
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
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22
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Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nat Commun 2021; 12:4314. [PMID: 34262047 PMCID: PMC8280215 DOI: 10.1038/s41467-021-24467-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/04/2021] [Indexed: 02/08/2023] Open
Abstract
Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
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Affiliation(s)
- Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nichelle I Winters
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chitra Joseph
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | - Arun C Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lance M Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica B Blackburn
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley W Richmond
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Andrew G Nicholson
- National Heart and Lung Institute, Imperial College, London, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - William A Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Pathology, Edinburgh University Medical School, Edinburgh, UK
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - R Gisli Jenkins
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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23
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Nakahara Y, Hashimoto N, Sakamoto K, Enomoto A, Adams TS, Yokoi T, Omote N, Poli S, Ando A, Wakahara K, Suzuki A, Inoue M, Hara A, Mizutani Y, Imaizumi K, Kawabe T, Rosas IO, Takahashi M, Kaminski N, Hasegawa Y. Fibroblasts positive for meflin have anti-fibrotic property in pulmonary fibrosis. Eur Respir J 2021; 58:13993003.03397-2020. [PMID: 34049947 DOI: 10.1183/13993003.03397-2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/07/2021] [Indexed: 11/05/2022]
Abstract
The prognosis of elderly individuals with idiopathic pulmonary fibrosis (IPF) remains poor. Fibroblastic foci, in which aggregates of proliferating fibroblasts and myofibroblasts are involved, are the pathological hallmark lesions in IPF to represent focal areas of active fibrogenesis. Fibroblast heterogeneity in fibrotic lesions hampers the discovery of the pathogenesis of pulmonary fibrosis. Therefore, to determine of the pathogenesis of IPF, identification of functional fibroblasts is warranted. This study was aimed to determine the role of fibroblasts positive for meflin, identified as a potential marker for mesenchymal stromal cells, during the development of pulmonary fibrosis. We characterised meflin-positive cells in a single cell atlas established by single-cell RNA sequencing (scRNA-seq)-based profiling of 243 472 cells from 32 IPF lungs and 29 normal lung samples. scRNA-seq combined with in situ RNA hybridisation identified proliferating fibroblasts positive for meflin in fibroblastic foci, not dense fibrosis, of fibrotic lungs in IPF patients. We determined the role of fibroblasts positive for meflin using bleomycin (BLM)-induced pulmonary fibrosis. A BLM-induced lung fibrosis model for meflin-deficient mice showed that fibroblasts positive for meflin had anti-fibrotic property to prevent pulmonary fibrosis. Although transforming growth factor-β-induced fibrogenesis and cell senescence with senescence-associated secretory phenotype were exacerbated in fibroblasts via the repression or lack of meflin, these were inhibited in meflin-deficient fibroblasts with meflin reconstitution. These findings provide evidence to show the biological importance of meflin expression on fibroblasts and myofibroblasts in the active fibrotic region of pulmonary fibrosis.
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Affiliation(s)
- Yoshio Nakahara
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan.,These authors contributed equally to this work
| | - Naozumi Hashimoto
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan .,These authors contributed equally to this work
| | - Koji Sakamoto
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan.,These authors contributed equally to this work
| | - Atsushi Enomoto
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | | | - Norihito Omote
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Sergio Poli
- Department of Medicine, Mount Sinai Medical Center, Miami Beach, FL, USA
| | - Akira Ando
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Wakahara
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Suzuki
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahide Inoue
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akitoshi Hara
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuyuki Mizutani
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Gastroenterology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuyoshi Imaizumi
- Department of Respiratory Medicine and Allergy, Fujita Health University, Toyoake, Japan
| | - Tsutomu Kawabe
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ivan O Rosas
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Masahide Takahashi
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States
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24
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Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams TS, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo AS, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CG. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med 2021; 27:546-559. [PMID: 33654293 PMCID: PMC9469728 DOI: 10.1038/s41591-020-01227-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/23/2020] [Indexed: 02/01/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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Affiliation(s)
- Christoph Muus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard, University, Cambridge, MA 02138
| | - Malte D. Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, , Neuherberg, Germany
| | - Gokcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lisa Sikkema
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Eeshit Dhaval Vaishnav
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elizabeth Thu Duong
- University of California San Diego, Department of Pediatrics, Division of Respiratory Medicine
| | - Evgenij Fiskin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Peiwen Cai
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital,Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sijia Chen
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Jian Shu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Adam L. Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA. Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hattie Chung
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel T. Montoro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Samuel J. Allon
- Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Zaneta Andrusivova
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | - Ilias Angelidis
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bassler
- Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | | | - Inbal Benhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Emelie Braun
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ
| | - Steven Callori
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Evgeny Chichelnitskiy
- Institute of Transplant Immunology, Hannover Medical School, MHH, Carl-Neuberg Str. 1, 30625 Hannover, Germany, phone +40 511 532 9745; fax +40 511 532 8090; German Center for Infectious Diseases DZIF, TTU-IICH 07.801
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA, 92093
| | - Thomas M. Conlon
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anna S.E. Cuomo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Marie Deprez
- Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, 06560, France
| | - Grant Duclos
- Boston University School of Medicine, Boston, MA 02118, USA
| | | | - David S. Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Astrid Gillich
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Bruno Giotti
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Minzhe Guo
- Divisions of Pulmonary Biology; Perinatal Institute, Cincinnati Children's Hospital Medical Center
| | | | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Peng He
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Xiaomeng Hou
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Yan Hu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Aurora, CO, USA 80045
| | - Alok Jaiswal
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lu Ji
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Theodoro S. Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Christin S. Kuo
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Ludvig Larsson
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | | | - Kyungtae Lim
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Monika Litviňuková
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Leif S. Ludwig
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Division of Hematology / Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Soeren Lukassen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wendy Luo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Elo Madissoon
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK; Wellcome Sanger Institute, Cellular Genetics Programme Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Kasidet Manakongtreecheep
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sylvie Leroy
- Université Côte d’Azur, Pulmonology Department, CHU Nice, NICE, France; Institut de Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Christoph H. Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ian M. Mbano
- Africa Health Research Institute,Durban, South Africa. School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of Kwazulu Natal, Durban, South Africa
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
| | - Ahmad N. Nabhan
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Sarah K. Nyquist
- Computational and Systems Biology, CSAIL, Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Lolita Penland
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Olivier B. Poirion
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sergio Poli
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - CanCan Qi
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rachel Queen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne NE1 3 BZ, UK
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, United States.; Department of Cardiology, University Heart & Vascular Center, University of Hamburg, Hamburg, Germany
| | - Ivan Rosas
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Conor V. Shea
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Xingyi Shi
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Rene V. Sit
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Kamil Slowikowski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Neal P. Smith
- Massachusetts General Hospital Center for Immunology and Inflammatory Diseases
| | - Alex Sountoulidis
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute
| | - Maximilian Strunz
- Comprehensive Pneumology Center (CPC) and Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Dawei Sun
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Carlos Talavera-López
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peng Tan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jessica Tantivit
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Nathan R. Tucker
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142; Masonic Medical Research Institute, Utica, NY, USA 13501
| | - Katherine A. Vernon
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marc H. Wadsworth
- Institute for Medical Engineering and Science, Department of Chemistry & Koch Institute for Integrative Cancer Research, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xiuting Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Ke Xu
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - William Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Carly G.K. Ziegler
- Harvard-MIT Health Sciences and Technology, Institute for Medical Engineering and Science, Koch Institute for Integrative Cancer Research, MIT; Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard
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25
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Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. bioRxiv 2021:2020.10.20.347187. [PMID: 33106805 PMCID: PMC7587778 DOI: 10.1101/2020.10.20.347187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyzed the transcriptomes of 605,904 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observed a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD epithelial cells expressed higher levels of genes linked directly to the efficiency of viral replication and innate immune response. Additionally, we identified basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
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Affiliation(s)
- Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nichelle I. Winters
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chitra Joseph
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lance M. Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J. Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica B. Blackburn
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley W. Richmond
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Andrew G. Nicholson
- National Heart and Lung Institute, Imperial College, London, SW3 6LY, UK
- Royal Brompton and Harefield NHS Foundation Trust, Department of Histopathology, Sydney Street, London, SW3 6NP, UK
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - William A. Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Pathology, Edinburgh University Medical School, Edinburgh, UK
| | - Ivan O. Rosas
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - R. Gisli Jenkins
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis. Am J Respir Crit Care Med 2020; 202:1419-1429. [PMID: 32603604 DOI: 10.1164/rccm.202004-0991oc] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rationale: Cystic fibrosis (CF) is a life-shortening, multisystem hereditary disease caused by abnormal chloride transport. CF lung disease is driven by innate immune dysfunction and exaggerated inflammatory responses that contribute to tissue injury. To define the transcriptional profile of this airway immune dysfunction, we performed the first single-cell transcriptome characterization of CF sputum.Objectives: To define the transcriptional profile of sputum cells and its implication in the pathogenesis of immune function and the development of CF lung disease.Methods: We performed single-cell RNA sequencing of sputum cells from nine subjects with CF and five healthy control subjects. We applied novel computational approaches to define expression-based cell function and maturity profiles, herein called transcriptional archetypes.Measurements and Main Results: The airway immune cell repertoire shifted from alveolar macrophages in healthy control subjects to a predominance of recruited monocytes and neutrophils in CF. Recruited lung mononuclear phagocytes were abundant in CF and were separated into the following three archetypes: activated monocytes, monocyte-derived macrophages, and heat shock-activated monocytes. Neutrophils were the most prevalent in CF, with a dominant immature proinflammatory archetype. Although CF monocytes exhibited proinflammatory features, both monocytes and neutrophils showed transcriptional evidence of abnormal phagocytic and cell-survival programs.Conclusions: Our findings offer an opportunity to understand subject-specific immune dysfunction and its contribution to divergent clinical courses in CF. As we progress toward personalized applications of therapeutic and genomic developments, we hope this inflammation-profiling approach will enable further discoveries that change the natural history of CF lung disease.
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Affiliation(s)
| | - Sara Khanal
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | - Jose L Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | | | | | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine
| | - Sergio Poli
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; and.,Division of Internal Medicine, Mount Sinai Medical Center, Miami, Florida
| | | | | | - Ivan O Rosas
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; and
| | | | - Emanuela M Bruscia
- Division of Pediatric Pulmonology, Allergy, Immunology, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Marie E Egan
- Division of Pediatric Pulmonology, Allergy, Immunology, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
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Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci Adv 2020; 6:eaba1983. [PMID: 32832599 PMCID: PMC7439502 DOI: 10.1126/sciadv.aba1983] [Citation(s) in RCA: 556] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/01/2020] [Indexed: 05/20/2023]
Abstract
We provide a single-cell atlas of idiopathic pulmonary fibrosis (IPF), a fatal interstitial lung disease, by profiling 312,928 cells from 32 IPF, 28 smoker and nonsmoker controls, and 18 chronic obstructive pulmonary disease (COPD) lungs. Among epithelial cells enriched in IPF, we identify a previously unidentified population of aberrant basaloid cells that coexpress basal epithelial, mesenchymal, senescence, and developmental markers and are located at the edge of myofibroblast foci in the IPF lung. Among vascular endothelial cells, we identify an ectopically expanded cell population transcriptomically identical to bronchial restricted vascular endothelial cells in IPF. We confirm the presence of both populations by immunohistochemistry and independent datasets. Among stromal cells, we identify IPF myofibroblasts and invasive fibroblasts with partially overlapping cells in control and COPD lungs. Last, we confirm previous findings of profibrotic macrophage populations in the IPF lung. Our comprehensive catalog reveals the complexity and diversity of aberrant cellular populations in IPF.
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Affiliation(s)
- Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ehab A. Ayaub
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nir Neumark
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sarah G. Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin A. Raby
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary Medicine, Boston’s Children Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | | | - George R. Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Pathology and Laboratory Medicine Service and VA CT HealthCare System, West Haven, CT, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ivan O. Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
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Tsukui T, Sun KH, Wetter JB, Wilson-Kanamori JR, Hazelwood LA, Henderson NC, Adams TS, Schupp JC, Poli SD, Rosas IO, Kaminski N, Matthay MA, Wolters PJ, Sheppard D. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis. Nat Commun 2020; 11:1920. [PMID: 32317643 PMCID: PMC7174390 DOI: 10.1038/s41467-020-15647-5] [Citation(s) in RCA: 271] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/20/2020] [Indexed: 01/18/2023] Open
Abstract
Collagen-producing cells maintain the complex architecture of the lung and drive pathologic scarring in pulmonary fibrosis. Here we perform single-cell RNA-sequencing to identify all collagen-producing cells in normal and fibrotic lungs. We characterize multiple collagen-producing subpopulations with distinct anatomical localizations in different compartments of murine lungs. One subpopulation, characterized by expression of Cthrc1 (collagen triple helix repeat containing 1), emerges in fibrotic lungs and expresses the highest levels of collagens. Single-cell RNA-sequencing of human lungs, including those from idiopathic pulmonary fibrosis and scleroderma patients, demonstrate similar heterogeneity and CTHRC1-expressing fibroblasts present uniquely in fibrotic lungs. Immunostaining and in situ hybridization show that these cells are concentrated within fibroblastic foci. We purify collagen-producing subpopulations and find disease-relevant phenotypes of Cthrc1-expressing fibroblasts in in vitro and adoptive transfer experiments. Our atlas of collagen-producing cells provides a roadmap for studying the roles of these unique populations in homeostasis and pathologic fibrosis.
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Affiliation(s)
- Tatsuya Tsukui
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kai-Hui Sun
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - John R Wilson-Kanamori
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio D Poli
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivan O Rosas
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Michael A Matthay
- Departments of Medicine and Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Paul J Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dean Sheppard
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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Greaney AM, Adams TS, Brickman Raredon MS, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing. Cell Rep 2020; 30:4250-4265.e6. [PMID: 32209482 PMCID: PMC7175071 DOI: 10.1016/j.celrep.2020.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/24/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, here, we isolate and culture a population of pharmacologically expanded basal cells (peBCs) from rat tracheas. At peak basal marker expression, we simultaneously split peBCs into four in vitro platforms: organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples are evaluated using single-cell RNA sequencing (scRNA-seq) and computational pipelines are developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium is also evaluated by scRNA-seq as a control for engineered epithelium. Overall, this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.
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Affiliation(s)
- Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA.
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Medical Scientist Training Program, Yale University, New Haven, CT 06511, USA
| | - Elise Gubbins
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Alexander J Engler
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA
| | - Mahboobe Ghaedi
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Yifan Yuan
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
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Adams TS, Mbatani NH. Clinical management of women presenting with field effect of HPV and intraepithelial disease. Best Pract Res Clin Obstet Gynaecol 2017; 47:86-94. [PMID: 29030149 DOI: 10.1016/j.bpobgyn.2017.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 01/26/2023]
Abstract
Anogenital human papillomavirus is the most common sexually transmitted infection acquired through skin-to-skin contact. Most infections are cleared by an intact immune system. Persistence of these infections results in precancerous lesions and, eventually, to cancers of the cervix, vagina, vulva, and perianal area. The introduction of the prophylactic human papilloma virus (HPV) vaccinations may reduce the incidence of these infections, but the effect of these vaccinations will be seen only in the decades that follow. In the meantime, multiple therapies such as immune modulators, ablative modalities, and surgical excision are used in an attempt to treat precancerous lesions and hence prevent cancer. There is an increase in multicentric disease in young women, especially with the HIV epidemic and in women who are immune compromised. This article aims to address the challenges and management options in women who have a field effect of HPV-associated disease.
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Affiliation(s)
- T S Adams
- Department of Obstetrics and Gynaecology, H Floor, Old Main Building, Groote Schuur Hospital, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa; SAMRC Gynaecological Cancer Research Centre (SAMRC GCR), Cape Town, South Africa.
| | - N H Mbatani
- Department of Obstetrics and Gynaecology, H Floor, Old Main Building, Groote Schuur Hospital, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa; SAMRC Gynaecological Cancer Research Centre (SAMRC GCR), Cape Town, South Africa.
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Adams TS, Murphy JV, Gillespie PH, Roberts AH. The use of high frequency ultrasonography in the prediction of burn depth. J Burn Care Rehabil 2001; 22:261-2. [PMID: 11403252 DOI: 10.1097/00004630-200105000-00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yi SX, Adams TS. Age- and diapause-related acid and alkaline phosphatase activities in the intestine and malpighian tubules of the Colorado potato beetle, Leptinotarsa decemlineata (Say). Arch Insect Biochem Physiol 2001; 46:152-163. [PMID: 11276072 DOI: 10.1002/arch.1025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Specific activities for soluble (s) and membrane (m)-bound acid (ACP) and alkaline phosphatases (ALP) were determined in the midgut, hindgut, and Malpighian tubules for developing, prediapausing, and diapausing adult Colorado potato beetles, Leptinotarsa decemlineata (Say). High ACP activities were found in the hindgut and Malpighian tubules while high ALP activities were found in the Malpighian tubules. Variation in both ACP and ALP activities in each tissue reflects fluctuation in protein synthesis and secretion involved with digestion, excretion, and other unknown functions. Phosphatase activities in the tissues examined show the dynamic nature of diapause in this insect. Diapausing beetles showed increases in phosphatase activity after hormone treatments. JHA treatments increased s-ACP and m-ACP activities in all tissues but 20-HE did not increase activity in any tissue. Allatotropin tended to mimic the effects of JHA treatment. The s-ALP activity was also increased in all tissues whereas m-ALP was increased in the midgut and hindgut by JHA treatment. Malpighian tubule m-ALP activity was only increased by 20-HE treatments. Allatotropin was not as effective in increasing ALP activities as it was with ACP activities.
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Affiliation(s)
- S X Yi
- Biosciences Research Laboratory, USDA-ARS, State University Station, Fargo, North Dakota 58105-5674, USA
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Yi S, Adams TS. Effect of pyriproxyfen and photoperiod on free amino acid concentrations and proteins in the hemolymph of the Colorado potato beetle, Leptinotarsa decemlineata (Say). J Insect Physiol 2000; 46:1341-1353. [PMID: 10878261 DOI: 10.1016/s0022-1910(00)00062-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A North Dakota strain of the Colorado potato beetle, Leptinotarsa decemlineata (Say), was reared under both short- (8L:16D) and long-day (17L:7D) conditions. Age-related and pyriproxyfen- (JHA-) induced changes in hemolymph free amino acids and proteins were examined. Under a short-day photoperiod, the total free amino acid concentration in the hemolymph increased gradually up to 20 days of adult life, but the long-day beetles showed marked increases during the first 10 days and then decreased afterwards. Proline, glutamine and valine were the most abundant free amino acids in both sexes of beetles held under either short- or long-day photoregims. JHA treatment of diapausing adults, held under either short- or long-day conditions after treatment, terminated diapause as indicated by re-emergence from the vermiculite, feeding, mating, changes in free amino acid levels, the disappearance of diapause protein 1 and appearance of vitellogenin in the hemolymph. Furthermore, most of the JHA-treated females held under long-day conditions also matured oocytes and oviposited, but those held under short-day conditions did not.
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Affiliation(s)
- S Yi
- Biosciences Research Laboratory, USDA-ARS, State University Station, 58105-5674, Fargo, ND, USA
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Abstract
Ovaries from house flies maintained on sucrose secrete large amounts of ecdysteroid when they are cultured with ovarian ecdysteroidogenic hormone, OEH. However, ovarian ecdysteroid secretion is reduced by incubation with both OEH and the ovarian ecdysteroidostatin (OES). A partially purified OES fraction from a semi-preparative reverse phase HPLC C18 column caused a 98% inhibition of ovarian ecdysteroid secretion in vitro at a concentration of 0.8 equivalents per microliter. Ovaries can be activated to produce ecdysteroid in vivo by feeding diet containing protein to flies maintained on sucrose. Ecdysteroid secretion was inhibited when the in vivo stimulated ovaries were cultured with OES. This suggests that OES does not interfere with the OEH activation mechanism, but blocks ovarian ecdysteroid synthesis or release. Furthermore, OES inhibition is reversible and ecdysteroid secretion resumes when OES is removed. Musca OES could explain the decrease in ecdysteroid levels found in flies after mid-vitellogenesis. Both adult male and female abdomens contain OES, but OES was not transferred to females during mating. Evidence is presented that OES is not a trypsin modulating oostatic factor.
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Affiliation(s)
- T S Adams
- Biosciences Research Laboratory, USDA-ARS, State University Station, Fargo, North Dakota 58105-5674, USA.
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Talas G, Adams TS, Eastwood M, Rubio G, Brown RA. Phenytoin reduces the contraction of recessive dystrophic epidermolysis bullosa fibroblast populated collagen gels. Int J Biochem Cell Biol 1997; 29:261-70. [PMID: 9076961 DOI: 10.1016/s1357-2725(96)00132-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a group of genetic disorders in which blistering occurs below the basement membrane, in many cases resulting in extensive scar formation, contractures and mitten deformities. Our aim was to compare quantitatively the contraction forces generated by normal and RDEB fibroblats and to investigate the effect of Phenytoin (5,5-diphenyl-2,4-imidazolidinedione, sodium salt; PHT). PHT is an anticonvulsant agent, that causes fibrosis as a side effect. This study utilised conventional untethered fibroblast populated collagen lattice contraction and a quantitative force measurement instrument, the culture force monitor (CFM). The RDEB cell lines were hypercontractile, generating 2.5 times the force of normal fibroblasts, though they appeared morphologically normal. In untethered collagen gels PHT (20 micrograms/ml) significantly reduced contraction of both normal and RDEB fibroblasts over 7 days. Pre-treatment of RDEB cells for 5 days also produced a 40% reduction in contraction as measured in the CFM. One suggested mechanism of PHT action is through inhibition of matrix metalloproteinase activity, but the similar effects of PHT and Colchicine (an inhibitor of microtubule polymerisation) in the CFM, indicate that it may act on contraction through disruption of microfilaments and changes to cell shape. These findings show that isolated RDEB fibroblasts retain the hypercontractile features of many of the patient's lesion sites and imply that local application of PHT may have a therapeutic effect in controlling contraction.
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Affiliation(s)
- G Talas
- University College London, Division of Plastic and Reconstructive Surgery, U.K
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Ingram CD, Adams TS, Jiang QB, Terenzi MG, Lambert RC, Wakerley JB, Moos F. Mortyn Jones Memorial Lecture. Limbic regions mediating central actions of oxytocin on the milk-ejection reflex in the rat. J Neuroendocrinol 1995; 7:1-13. [PMID: 7735292 DOI: 10.1111/j.1365-2826.1995.tb00661.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Central oxytocin administration has a profound facilitatory effect on the patterning of the milk-ejection reflex in the lactating rat. Lesion and microinjection studies indicate that this action is, in part, mediated via a population of limbic neurones in the bed nuclei of the stria terminalis and ventrolateral septum, which have been shown to possess oxytocin receptors and to be activated by selective oxytocin-receptor agonists in vitro. In vivo electrophysiological recordings reveal that some of these neurones display cyclical activity which is highly correlated to each milk ejection, and are rapidly activated following i.c.v. administration of oxytocin, coincident with the facilitation of milk ejection activity. A hypothetical model is proposed in which this population of limbic neurones serves to gate the activity of a pacemaker which, in turn, coordinates the bursting of hypothalamic magnocellular neurones. The oxytocin innervation of these neurones and their expression of oxytocin receptors increases in the postpartum period, and the resultant enhanced sensitivity leads to a greater facilitatory response during lactation. Inhibitory opioid and noradrenergic inputs which converge on these oxytocin-sensitive neurones may function to switch off the facilitatory circuit during periods of stress. Thus, this population of limbic neurones participates in the regulation of neuroendocrine activity during lactation by providing an appropriate degree of feedback to alter the patterning of the milk-ejection reflex.
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Affiliation(s)
- C D Ingram
- Department of Anatomy, School of Medical Sciences, University of Bristol, UK
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Nelson DR, Flint HM, Adams TS. The effects of partial or whole-body irradiation of pupal or adult female house-flies on ovarian maturation and retention of pupal fat body. Int J Radiat Biol Relat Stud Phys Chem Med 1970; 18:71-9. [PMID: 5311615 DOI: 10.1080/09553007014550831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Adams TS, Hintz AM. Relationship of age, ovarian development, and the corpus allatum to mating in the house-fly, Musca domestica. J Insect Physiol 1969; 15:201-215. [PMID: 5767699 DOI: 10.1016/0022-1910(69)90269-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Adams TS, Hintz AM, Pomonis JG. Oöstatic hormone production in houseflies, Musca domestica, with developing ovaries. J Insect Physiol 1968; 14:983-993. [PMID: 5761656 DOI: 10.1016/0022-1910(68)90008-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Adams TS, Nelson DR. Bioassay of crude extracts for the factor that prevents second matings in female musca domestica. Ann Entomol Soc Am 1968; 61:112-116. [PMID: 5636727 DOI: 10.1093/aesa/61.1.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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