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Acosta-Plasencia M, Castellano JJ, Díaz T, He Y, Marrades RM, Navarro A. Discovering genes and microRNAs involved in human lung development unveils IGFBP3/miR-34a dynamics and their relevance for alveolar differentiation. Stem Cell Res Ther 2024; 15:263. [PMID: 39183355 DOI: 10.1186/s13287-024-03883-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/10/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND During pseudoglandular stage of the human lung development the primitive bronchial buds are initially conformed by simple tubules lined by endoderm-derived epithelium surrounded by mesenchyme, which will progressively branch into airways and start to form distal epithelial saculles. For first time alveolar type II (AT2) pneumocytes appears. This study aims to characterize the genes and microRNAs involved in this differentiation process and decipher its role in the starting alveolar differentiation. METHODS Gene and microRNA profiling was performed in human embryonic lungs from 7 to 12 post conception weeks (pcw). Protein expression location of candidate genes were analyzed by immunofluorescense in embryonic lung tissue sections. mRNA/miRNA target pairs were identified using computational approaches and their expression was studied in purified epithelial/mesenchymal cell populations and in isolated tips and stalks from the bronchial tree. Additionally, silencing experiments in human embryonic lung mesenchymal cells and in human embryonic tip-derived lung organoids were performed, as well as organoid differentiation studies. AT2 cell markers were studied by qRT-PCR and by immunofluorescence. The TGFB-β phosphorylated pathways was analyzed with membrane protein arrays. Lung explants were cultured in air/liquid interface with/without peptides. RESULTS We identified 88 differentially expressed genes, including IGFBP3. Although IGFBP3 mRNA was detected in both epithelial and mesenchymal populations, the protein was restricted to the epithelium, indicating post-transcriptional regulation preventing IGFBP3 protein expression in the mesenchyme. MicroRNA profiling identified miR-34a as an IGFBP3 regulator. miR-34a was up-regulated in mesenchymal cells, and its silencing in human embryonic lung mesenchymal cells increased IGFBP3 levels. Additionally, IGFBP3 expression showed a marked downregulation from 7 to 12 pcw, suggesting its involvement in the differentiation process. The differentiation of human tip-derived lung embryonic organoids showed a drastic reduction in IGFBP3, supported by the scRNAseq data. IGFBP3 silencing in organoids activated an alveolar-like differentiation process characterized by stem cell markers downregulation and upregulation of AT2 markers. This process was mediated by TGFβ signalling inhibition and BMP pathway activation. CONCLUSIONS The IGFBP3/miR-34a axis restricts IGFBP3 expression in the embryonic undifferentiated lung epithelium, and the progressive downregulation of IGFBP3 during the pseudoglandular stage is required for alveolar differentiation.
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Affiliation(s)
- Melissa Acosta-Plasencia
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, Department of Surgery and Medical Specializations, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036, Barcelona, Spain
| | - Joan J Castellano
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, Department of Surgery and Medical Specializations, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036, Barcelona, Spain
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Tania Díaz
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, Department of Surgery and Medical Specializations, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036, Barcelona, Spain
| | - Yangyi He
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, Department of Surgery and Medical Specializations, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036, Barcelona, Spain
- School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Ramón M Marrades
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036, Barcelona, Spain
- Department of Pneumology, Institut Clínic Respiratori (ICR), Hospital Clínic de Barcelona, University of Barcelona, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, Department of Surgery and Medical Specializations, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036, Barcelona, Spain.
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036, Barcelona, Spain.
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2
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Lim K, Rawlins EL. Protocol for the derivation and alveolar type 2 differentiation of late-stage lung tip progenitors from the developing human lungs. STAR Protoc 2024; 5:103201. [PMID: 39028617 DOI: 10.1016/j.xpro.2024.103201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/21/2024] Open
Abstract
Molecular and cellular mechanisms of human lung alveolar development are poorly understood due to a lack of in vitro model systems. This protocol details the isolation, derivation, and genetic modification of lung tip epithelial progenitors from human fetal lungs. It includes steps for isolating distal lung epithelial cells, expanding tip progenitor organoids, culturing tip organoids in vitro, and differentiating them into alveolar type 2 cells. This will aid in understanding alveolar differentiation mechanisms and neonatal diseases. For complete details on the use and execution of this protocol, please refer to Lim et al.1.
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Affiliation(s)
- Kyungtae Lim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea.
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust/MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK.
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3
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Quach H, Farrell S, Wu MJM, Kanagarajah K, Leung JWH, Xu X, Kallurkar P, Turinsky AL, Bear CE, Ratjen F, Kalish B, Goyal S, Moraes TJ, Wong AP. Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity. Nat Commun 2024; 15:5898. [PMID: 39003323 PMCID: PMC11246468 DOI: 10.1038/s41467-024-50281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
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Affiliation(s)
- Henry Quach
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer Farrell
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Jia Michael Wu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kayshani Kanagarajah
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Wai-Hin Leung
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoqiao Xu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prajkta Kallurkar
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine E Bear
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Felix Ratjen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Kalish
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy P Wong
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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4
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Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Chingpan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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5
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Yang X, Chen Y, Yang Y, Li S, Mi P, Jing N. The molecular and cellular choreography of early mammalian lung development. MEDICAL REVIEW (2021) 2024; 4:192-206. [PMID: 38919401 PMCID: PMC11195428 DOI: 10.1515/mr-2023-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/08/2024] [Indexed: 06/27/2024]
Abstract
Mammalian lung development starts from a specific cluster of endodermal cells situated within the ventral foregut region. With the orchestrating of delicate choreography of transcription factors, signaling pathways, and cell-cell communications, the endodermal diverticulum extends into the surrounding mesenchyme, and builds the cellular and structural basis of the complex respiratory system. This review provides a comprehensive overview of the current molecular insights of mammalian lung development, with a particular focus on the early stage of lung cell fate differentiation and spatial patterning. Furthermore, we explore the implications of several congenital respiratory diseases and the relevance to early organogenesis. Finally, we summarize the unprecedented knowledge concerning lung cell compositions, regulatory networks as well as the promising prospect for gaining an unbiased understanding of lung development and lung malformations through state-of-the-art single-cell omics.
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Affiliation(s)
- Xianfa Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yingying Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yun Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Shiting Li
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan Province, China
| | - Panpan Mi
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Naihe Jing
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
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6
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Chang L, Chen Q, Wang B, Liu J, Zhang M, Zhu W, Jiang J. Single cell RNA analysis uncovers the cell differentiation and functionalization for air breathing of frog lung. Commun Biol 2024; 7:665. [PMID: 38816547 PMCID: PMC11139932 DOI: 10.1038/s42003-024-06369-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
The evolution and development of vertebrate lungs have been widely studied due to their significance in terrestrial adaptation. Amphibians possess the most primitive lungs among tetrapods, underscoring their evolutionary importance in bridging the transition from aquatic to terrestrial life. However, the intricate process of cell differentiation during amphibian lung development remains poorly understood. Using single-cell RNA sequencing, we identify 13 cell types in the developing lungs of a land-dwelling frog (Microhyla fissipes). We elucidate the differentiation trajectories and mechanisms of mesenchymal cells, identifying five cell fates and their respective driver genes. Using temporal dynamics analyses, we reveal the gene expression switches of epithelial cells, which facilitate air breathing during metamorphosis. Furthermore, by integrating the published data from another amphibian and two terrestrial mammals, we illuminate both conserved and divergent cellular repertoires during the evolution of tetrapod lungs. These findings uncover the frog lung cell differentiation trajectories and functionalization for breathing in air and provide valuable insights into the cell-type evolution of vertebrate lungs.
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Affiliation(s)
- Liming Chang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiheng Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Meihua Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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De Zuani M, Xue H, Park JS, Dentro SC, Seferbekova Z, Tessier J, Curras-Alonso S, Hadjipanayis A, Athanasiadis EI, Gerstung M, Bayraktar O, Cvejic A. Single-cell and spatial transcriptomics analysis of non-small cell lung cancer. Nat Commun 2024; 15:4388. [PMID: 38782901 PMCID: PMC11116453 DOI: 10.1038/s41467-024-48700-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer and the leading cause of cancer-related mortality worldwide. Tumour ecosystems feature diverse immune cell types. Myeloid cells, in particular, are prevalent and have a well-established role in promoting the disease. In our study, we profile approximately 900,000 cells from 25 treatment-naive patients with adenocarcinoma and squamous-cell carcinoma by single-cell and spatial transcriptomics. We note an inverse relationship between anti-inflammatory macrophages and NK cells/T cells, and with reduced NK cell cytotoxicity within the tumour. While we observe a similar cell type composition in both adenocarcinoma and squamous-cell carcinoma, we detect significant differences in the co-expression of various immune checkpoint inhibitors. Moreover, we reveal evidence of a transcriptional "reprogramming" of macrophages in tumours, shifting them towards cholesterol export and adopting a foetal-like transcriptional signature which promotes iron efflux. Our multi-omic resource offers a high-resolution molecular map of tumour-associated macrophages, enhancing our understanding of their role within the tumour microenvironment.
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Affiliation(s)
- Marco De Zuani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Haoliang Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Jun Sung Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Stefan C Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Zaira Seferbekova
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Julien Tessier
- Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, USA
| | | | | | - Emmanouil I Athanasiadis
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Moritz Gerstung
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
| | - Ana Cvejic
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- OpenTargets, Wellcome Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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8
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Burgess CL, Huang J, Bawa PS, Alysandratos KD, Minakin K, Ayers LJ, Morley MP, Babu A, Villacorta-Martin C, Yampolskaya M, Hinds A, Thapa BR, Wang F, Matschulat A, Mehta P, Morrisey EE, Varelas X, Kotton DN. Generation of human alveolar epithelial type I cells from pluripotent stem cells. Cell Stem Cell 2024; 31:657-675.e8. [PMID: 38642558 PMCID: PMC11147407 DOI: 10.1016/j.stem.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/31/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Alveolar epithelial type I cells (AT1s) line the gas exchange barrier of the distal lung and have been historically challenging to isolate or maintain in cell culture. Here, we engineer a human in vitro AT1 model system via directed differentiation of induced pluripotent stem cells (iPSCs). We use primary adult AT1 global transcriptomes to suggest benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, enriched in these cells. Next, we generate iPSC-derived alveolar epithelial type II cells (AT2s) and find that nuclear YAP signaling is sufficient to promote a broad transcriptomic shift from AT2 to AT1 gene programs. The resulting cells express a molecular, morphologic, and functional phenotype reminiscent of human AT1 cells, including the capacity to form a flat epithelial barrier producing characteristic extracellular matrix molecules and secreted ligands. Our results provide an in vitro model of human alveolar epithelial differentiation and a potential source of human AT1s.
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Affiliation(s)
- Claire L Burgess
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pushpinder S Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Kasey Minakin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lauren J Ayers
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apoorva Babu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Adeline Matschulat
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xaralabos Varelas
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
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9
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Candeli N, Dayton T. Investigating pulmonary neuroendocrine cells in human respiratory diseases with airway models. Dis Model Mech 2024; 17:dmm050620. [PMID: 38813849 DOI: 10.1242/dmm.050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
Despite accounting for only ∼0.5% of the lung epithelium, pulmonary neuroendocrine cells (PNECs) appear to play an outsized role in respiratory health and disease. Increased PNEC numbers have been reported in a variety of respiratory diseases, including chronic obstructive pulmonary disease and asthma. Moreover, PNECs are the primary cell of origin for lung neuroendocrine cancers, which account for 25% of aggressive lung cancers. Recent research has highlighted the crucial roles of PNECs in lung physiology, including in chemosensing, regeneration and immune regulation. Yet, little is known about the direct impact of PNECs on respiratory diseases. In this Review, we summarise the current associations of PNECs with lung pathologies, focusing on how new experimental disease models, such as organoids derived from human pluripotent stem cells or tissue stem cells, can help us to better understand the contribution of PNECs to respiratory diseases.
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Affiliation(s)
- Noah Candeli
- European Molecular Biology Laboratory (EMBL) Barcelona, Tissue Biology and Disease Modelling, 08003, Barcelona, Spain
| | - Talya Dayton
- European Molecular Biology Laboratory (EMBL) Barcelona, Tissue Biology and Disease Modelling, 08003, Barcelona, Spain
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10
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Werder RB, Zhou X, Cho MH, Wilson AA. Breathing new life into the study of COPD with genes identified from genome-wide association studies. Eur Respir Rev 2024; 33:240019. [PMID: 38811034 PMCID: PMC11134200 DOI: 10.1183/16000617.0019-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 05/31/2024] Open
Abstract
COPD is a major cause of morbidity and mortality globally. While the significance of environmental exposures in disease pathogenesis is well established, the functional contribution of genetic factors has only in recent years drawn attention. Notably, many genes associated with COPD risk are also linked with lung function. Because reduced lung function precedes COPD onset, this association is consistent with the possibility that derangements leading to COPD could arise during lung development. In this review, we summarise the role of leading genes (HHIP, FAM13A, DSP, AGER and TGFB2) identified by genome-wide association studies in lung development and COPD. Because many COPD genome-wide association study genes are enriched in lung epithelial cells, we focus on the role of these genes in the lung epithelium in development, homeostasis and injury.
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Affiliation(s)
- Rhiannon B Werder
- Murdoch Children's Research Institute, Melbourne, Australia
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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11
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Chen K, Han Y, Wang Y, Zhou D, Wu F, Cai W, Zheng S, Xiao Q, Zhang H, Li W. scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. iScience 2024; 27:109567. [PMID: 38617561 PMCID: PMC11015448 DOI: 10.1016/j.isci.2024.109567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/26/2023] [Accepted: 03/22/2024] [Indexed: 04/16/2024] Open
Abstract
The human respiratory system is a complex and important system that can suffer a variety of diseases. Single-cell sequencing technologies, applied in many respiratory disease studies, have enhanced our ability in characterizing molecular and phenotypic features at a single-cell resolution. The exponentially increasing data from these studies have consequently led to difficulties in data sharing and analysis. Here, we present scMoresDB, a single-cell multi-omics database platform with extensive omics types tailored for human respiratory diseases. scMoresDB re-analyzes single-cell multi-omics datasets, providing a user-friendly interface with cross-omics search capabilities, interactive visualizations, and analytical tools for comprehensive data sharing and integrative analysis. Our example applications highlight the potential significance of BSG receptor in SARS-CoV-2 infection as well as the involvement of HHIP and TGFB2 in the development and progression of chronic obstructive pulmonary disease. scMoresDB significantly increases accessibility and utility of single-cell data relevant to human respiratory system and associated diseases.
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Affiliation(s)
- Kang Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yutong Han
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yanni Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Dingli Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Fanjie Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Wenhao Cai
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Shikang Zheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Qinyuan Xiao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
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12
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Veland N, Gleneadie HJ, Brown KE, Sardini A, Pombo J, Dimond A, Burns V, Sarkisyan K, Schiering C, Webster Z, Merkenschlager M, Fisher AG. Bioluminescence imaging of Cyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung. Commun Biol 2024; 7:442. [PMID: 38600349 PMCID: PMC11006662 DOI: 10.1038/s42003-024-06089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
Aryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such as Cyp1a1. To dynamically visualise AHR activity in vivo, we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenous Cyp1a1 locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal and Cyp1a1 expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustained Cyp1a1 expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespoke Cyp1a1-Fluc reporters to longitudinally monitor AHR activity in vivo.
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Affiliation(s)
- Nicolas Veland
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Hannah J Gleneadie
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen E Brown
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC Laboratory of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Joaquim Pombo
- Senescence Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vanessa Burns
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen Sarkisyan
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Chris Schiering
- Inflammation and Obesity Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Zoe Webster
- Transgenics & Embryonic Stem Cell Facility, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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13
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Masui A, Hashimoto R, Matsumura Y, Yamamoto T, Nagao M, Noda T, Takayama K, Gotoh S. Micro-patterned culture of iPSC-derived alveolar and airway cells distinguishes SARS-CoV-2 variants. Stem Cell Reports 2024; 19:545-561. [PMID: 38552631 PMCID: PMC11096626 DOI: 10.1016/j.stemcr.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
The emergence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants necessitated a rapid evaluation system for their pathogenesis. Lung epithelial cells are their entry points; however, in addition to their limited source, the culture of human alveolar epithelial cells is especially complicated. Induced pluripotent stem cells (iPSCs) are an alternative source of human primary stem cells. Here, we report a model for distinguishing SARS-CoV-2 variants at high resolution, using separately induced iPSC-derived alveolar and airway cells in micro-patterned culture plates. The position-specific signals induced the apical-out alveolar type 2 and multiciliated airway cells at the periphery and center of the colonies, respectively. The infection studies in each lineage enabled profiling of the pathogenesis of SARS-CoV-2 variants: infection efficiency, tropism to alveolar and airway lineages, and their responses. These results indicate that this culture system is suitable for predicting the pathogenesis of emergent SARS-CoV-2 variants.
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Affiliation(s)
- Atsushi Masui
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Rina Hashimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Shimpei Gotoh
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
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14
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Jia H, Chang Y, Chen Y, Chen X, Zhang H, Hua X, Xu M, Sheng Y, Zhang N, Cui H, Han L, Zhang J, Fu X, Song J. A single-cell atlas of lung homeostasis reveals dynamic changes during development and aging. Commun Biol 2024; 7:427. [PMID: 38589700 PMCID: PMC11001898 DOI: 10.1038/s42003-024-06111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Aging is a global challenge, marked in the lungs by function decline and structural disorders, which affects the health of the elderly population. To explore anti-aging strategies, we develop a dynamic atlas covering 45 cell types in human lungs, spanning from embryonic development to aging. We aim to apply the discoveries of lung's development to address aging-related issues. We observe that both epithelial and immune cells undergo a process of acquisition and loss of essential function as they transition from development to aging. During aging, we identify cellular phenotypic alternations that result in reduced pulmonary compliance and compromised immune homeostasis. Furthermore, we find a distinctive expression pattern of the ferritin light chain (FTL) gene, which increases during development but decreases in various types of lung cells during the aging process.
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Affiliation(s)
- Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yulin Chen
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Traditional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xiao Chen
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hang Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiumeng Hua
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengda Xu
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yixuan Sheng
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ningning Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Han
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Yanan Hospital, Kunming Medical University, Kunming, China
| | - Jian Zhang
- Thoracic Surgery Department, the third affiliated hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China.
| | - Xiaodong Fu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Basil MC, Alysandratos KD, Kotton DN, Morrisey EE. Lung repair and regeneration: Advanced models and insights into human disease. Cell Stem Cell 2024; 31:439-454. [PMID: 38492572 PMCID: PMC11070171 DOI: 10.1016/j.stem.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The respiratory system acts as both the primary site of gas exchange and an important sensor and barrier to the external environment. The increase in incidences of respiratory disease over the past decades has highlighted the importance of developing improved therapeutic approaches. This review will summarize recent research on the cellular complexity of the mammalian respiratory system with a focus on gas exchange and immunological defense functions of the lung. Different models of repair and regeneration will be discussed to help interpret human and animal data and spur the investigation of models and assays for future drug development.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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16
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Li Y, Prakash YS, Tan Q, Tschumperlin D. Defining signals that promote human alveolar type I differentiation. Am J Physiol Lung Cell Mol Physiol 2024; 326:L409-L418. [PMID: 38349124 PMCID: PMC11281788 DOI: 10.1152/ajplung.00191.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/29/2024] Open
Abstract
Alveolar type I (ATI) cells cover >95% of the lung's distal surface and facilitate gas exchange through their exceptionally thin shape. ATI cells in vivo are replenished by alveolar type II cell division and differentiation, but a detailed understanding of ATI biology has been hampered by the challenges in direct isolation of these cells due to their fragility and incomplete understanding of the signaling interactions that promote differentiation of ATII to ATI cells. Here, we explored the signals that maintain ATII versus promote ATI fates in three-dimensional (3-D) organoid cultures and developed a human alveolar type I differentiation medium (hATIDM) suitable for generating ATI cells from either mixed distal human lung cells or purified ATII cells. This media adds bone morphogenetic protein 4 (BMP4) and removes epidermal growth factor (EGF), Wnt agonist CHIR99021, and transforming growth factor-beta (TGF-β) inhibitor SB431542 from previously developed alveolar organoid culture media. We demonstrate that BMP4 promotes expression of the ATI marker gene AGER and HOPX, whereas CHIR99021 and SB431542 maintain expression of the ATII marker gene SFTPC. The human ATI spheroids generated with hATIDM express multiple molecular and morphological features reminiscent of human ATI cells. Our results demonstrate that signaling interactions among BMP, TGF-β, and Wnt signaling pathways in alveolar spheroids and distal lung organoids including IPF-organoids coordinate human ATII to ATI differentiation.NEW & NOTEWORTHY Alveolar type I (ATI) epithelial cells perform essential roles in maintaining lung function but have been challenging to study. We explored the signals that promote ATI fate in 3-D organoid cultures generated from either mixed distal human lung cells or purified alveolar type II (ATII) cells. This work fills an important void in our experimental repertoire for studying alveolar epithelial cells and identifies signals that promote human ATII to ATI cell differentiation.
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Affiliation(s)
- Yong Li
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States
| | - Y S Prakash
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Qi Tan
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States
| | - Daniel Tschumperlin
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States
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17
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Yaremenko AV, Pechnikova NA, Porpodis K, Damdoumis S, Aggeli A, Theodora P, Domvri K. Association of Fetal Lung Development Disorders with Adult Diseases: A Comprehensive Review. J Pers Med 2024; 14:368. [PMID: 38672994 PMCID: PMC11051200 DOI: 10.3390/jpm14040368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal lung development is a crucial and complex process that lays the groundwork for postnatal respiratory health. However, disruptions in this delicate developmental journey can lead to fetal lung development disorders, impacting neonatal outcomes and potentially influencing health outcomes well into adulthood. Recent research has shed light on the intriguing association between fetal lung development disorders and the development of adult diseases. Understanding these links can provide valuable insights into the developmental origins of health and disease, paving the way for targeted preventive measures and clinical interventions. This review article aims to comprehensively explore the association of fetal lung development disorders with adult diseases. We delve into the stages of fetal lung development, examining key factors influencing fetal lung maturation. Subsequently, we investigate specific fetal lung development disorders, such as respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), congenital diaphragmatic hernia (CDH), and other abnormalities. Furthermore, we explore the potential mechanisms underlying these associations, considering the role of epigenetic modifications, transgenerational effects, and intrauterine environmental factors. Additionally, we examine the epidemiological evidence and clinical findings linking fetal lung development disorders to adult respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), and other respiratory ailments. This review provides valuable insights for healthcare professionals and researchers, guiding future investigations and shaping strategies for preventive interventions and long-term care.
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Affiliation(s)
- Alexey V. Yaremenko
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Nadezhda A. Pechnikova
- Laboratory of Chemical Engineering A’, School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (N.A.P.); (A.A.)
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Konstantinos Porpodis
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Savvas Damdoumis
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Amalia Aggeli
- Laboratory of Chemical Engineering A’, School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (N.A.P.); (A.A.)
| | - Papamitsou Theodora
- Laboratory of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Kalliopi Domvri
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
- Laboratory of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
- Pathology Department, George Papanikolaou Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
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18
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Gerli MFM, Calà G, Beesley MA, Sina B, Tullie L, Sun KY, Panariello F, Michielin F, Davidson JR, Russo FM, Jones BC, Lee DDH, Savvidis S, Xenakis T, Simcock IC, Straatman-Iwanowska AA, Hirst RA, David AL, O'Callaghan C, Olivo A, Eaton S, Loukogeorgakis SP, Cacchiarelli D, Deprest J, Li VSW, Giobbe GG, De Coppi P. Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids. Nat Med 2024; 30:875-887. [PMID: 38438734 PMCID: PMC10957479 DOI: 10.1038/s41591-024-02807-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/05/2024] [Indexed: 03/06/2024]
Abstract
Isolation of tissue-specific fetal stem cells and derivation of primary organoids is limited to samples obtained from termination of pregnancies, hampering prenatal investigation of fetal development and congenital diseases. Therefore, new patient-specific in vitro models are needed. To this aim, isolation and expansion of fetal stem cells during pregnancy, without the need for tissue samples or reprogramming, would be advantageous. Amniotic fluid (AF) is a source of cells from multiple developing organs. Using single-cell analysis, we characterized the cellular identities present in human AF. We identified and isolated viable epithelial stem/progenitor cells of fetal gastrointestinal, renal and pulmonary origin. Upon culture, these cells formed clonal epithelial organoids, manifesting small intestine, kidney tubule and lung identity. AF organoids exhibit transcriptomic, protein expression and functional features of their tissue of origin. With relevance for prenatal disease modeling, we derived lung organoids from AF and tracheal fluid cells of congenital diaphragmatic hernia fetuses, recapitulating some features of the disease. AF organoids are derived in a timeline compatible with prenatal intervention, potentially allowing investigation of therapeutic tools and regenerative medicine strategies personalized to the fetus at clinically relevant developmental stages.
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Affiliation(s)
- Mattia Francesco Maria Gerli
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK.
- Great Ormond Street Institute of Child Health, University College London, London, UK.
| | - Giuseppe Calà
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Max Arran Beesley
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Beatrice Sina
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Politecnico di Milano, Milan, Italy
| | - Lucinda Tullie
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | - Kylin Yunyan Sun
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Francesco Panariello
- Armenise/Harvard Laboratory of Integrative Genomics, Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Federica Michielin
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Joseph R Davidson
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Francesca Maria Russo
- Department of Development and Regeneration, Woman and Child and UZ Leuven Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | - Brendan C Jones
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dani Do Hyang Lee
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Savvas Savvidis
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Theodoros Xenakis
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ian C Simcock
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | | | - Robert A Hirst
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Anna L David
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
- Department of Development and Regeneration, Woman and Child and UZ Leuven Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | | | - Alessandro Olivo
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Simon Eaton
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Stavros P Loukogeorgakis
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Specialist Neonatal and Paediatric Surgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Davide Cacchiarelli
- Armenise/Harvard Laboratory of Integrative Genomics, Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
- Genomics and Experimental Medicine Program, Scuola Superiore Meridionale, Naples, Italy
| | - Jan Deprest
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
- Department of Development and Regeneration, Woman and Child and UZ Leuven Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Paolo De Coppi
- Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Development and Regeneration, Woman and Child and UZ Leuven Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium.
- Specialist Neonatal and Paediatric Surgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
- Medical and Surgical Department of the Fetus, Newborn and Infant, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK.
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19
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Kelly A, Lavender P. Epigenetic Approaches to Identifying Asthma Endotypes. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2024; 16:130-141. [PMID: 38528381 DOI: 10.4168/aair.2024.16.2.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/03/2024] [Accepted: 02/13/2024] [Indexed: 03/27/2024]
Abstract
The prevalence of asthma escalated rapidly in the late 20th century. In 2019, the World Health Organization estimated the global number of people affected by the condition to be approximately 260 million, causing 450,000 deaths during that year. While there have been advances in therapeutics with the emergence of biologics targeting T2-high asthma, there is still little clarity on the mechanisms underlying the origins of both the condition and all of its endotypes. Several biomarkers for particular asthma phenotypes have been documented. These are generally identified from transcriptomics and proteomics protocols and tend to be biased to T2-high phenotypes. In this review, we summarize some suggestions that analysis of epigenomes may provide alternative datasets that inform of broader asthma endotypes and might highlight pathways amenable for therapeutic intervention.
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Affiliation(s)
- Audrey Kelly
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Science, King's College London, London, United Kingdom
| | - Paul Lavender
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Science, King's College London, London, United Kingdom.
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20
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Yang X, Wu X, Wang Y, Li W, Wu X, Yuan L, Yu T, Li N, Zhang S, Hua J. Induction of lung progenitor cell-like organoids by porcine pluripotent stem cells. FASEB J 2024; 38:e23481. [PMID: 38334430 DOI: 10.1096/fj.202302402r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Organoids are in vitro 3D models that are generated using stem cells to study organ development and regeneration. Despite the extensive research on lung organoids, there is limited information on pig lung cell generation or development. Here, we identified five epithelial cell types along with their characteristic markers using scRNA-seq. Additionally, we found that NKX2.1 and FOXA2 acted as the crucial core transcription factors in porcine lung development. The presence of SOX9/SOX2 double-positive cells was identified as a key marker for lung progenitor cells. The Monocle algorithm was used to create a pseudo-temporal differentiation trajectory of epithelial cells, leading to the identification of signaling pathways related to porcine lung development. Moreover, we established the differentiation method from porcine pluripotent stem cells (pPSCs) to SOX17+ FOXA2+ definitive endoderm (DE) and NKX2.1+ FOXA2+ CDX2- anterior foregut endoderm (AFE). The AFE is further differentiated into lung organoids while closely monitoring the differentiation process. We showed that NKX2.1 overexpression facilitated the induction of lung organoids and supported subsequent lung differentiation and maturation. This model offers valuable insights into studying the interaction patterns between cells and the signaling pathways during the development of the porcine lung.
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Affiliation(s)
- Xinchun Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolong Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuqi Wang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenhao Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojie Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Liming Yuan
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Taiyong Yu
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
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21
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Miao Y, Tan C, Pek NM, Yu Z, Iwasawa K, Kechele DO, Sundaram N, Pastrana-Gomez V, Kishimoto K, Yang MC, Jiang C, Tchieu J, Whitsett JA, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M. Deciphering Endothelial and Mesenchymal Organ Specification in Vascularized Lung and Intestinal Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.577460. [PMID: 38370768 PMCID: PMC10871227 DOI: 10.1101/2024.02.06.577460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To investigate the co-development of vasculature, mesenchyme, and epithelium crucial for organogenesis and the acquisition of organ-specific characteristics, we constructed a human pluripotent stem cell-derived organoid system comprising lung or intestinal epithelium surrounded by organotypic mesenchyme and vasculature. We demonstrated the pivotal role of co-differentiating mesoderm and endoderm via precise BMP regulation in generating multilineage organoids and gut tube patterning. Single-cell RNA-seq analysis revealed organ specificity in endothelium and mesenchyme, and uncovered key ligands driving endothelial specification in the lung (e.g., WNT2B and Semaphorins) or intestine (e.g., GDF15). Upon transplantation under the kidney capsule in mice, these organoids further matured and developed perfusable human-specific sub-epithelial capillaries. Additionally, our model recapitulated the abnormal endothelial-epithelial crosstalk in patients with FOXF1 deletion or mutations. Multilineage organoids provide a unique platform to study developmental cues guiding endothelial and mesenchymal cell fate determination, and investigate intricate cell-cell communications in human organogenesis and disease. Highlights BMP signaling fine-tunes the co-differentiation of mesoderm and endoderm.The cellular composition in multilineage organoids resembles that of human fetal organs.Mesenchyme and endothelium co-developed within the organoids adopt organ-specific characteristics.Multilineage organoids recapitulate abnormal endothelial-epithelial crosstalk in FOXF1-associated disorders.
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22
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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23
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Zhang K, Aung T, Yao E, Chuang PT. Lung patterning: Is a distal-to-proximal gradient of cell allocation and fate decision a general paradigm?: A gradient of distal-to-proximal distribution and differentiation of tip progenitors produces distinct compartments in the lung. Bioessays 2024; 46:e2300083. [PMID: 38010492 DOI: 10.1002/bies.202300083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023]
Abstract
Recent studies support a model in which the progeny of SOX9+ epithelial progenitors at the distal tip of lung branches undergo cell allocation and differentiation sequentially along the distal-to-proximal axis. Concomitant with the elongation and ramification of lung branches, the descendants of the distal SOX9+ progenitors are distributed proximally, express SOX2, and differentiate into cell types in the conducting airways. Amid subsequent sacculation, the distal SOX9+ progenitors generate alveolar epithelial cells to form alveoli. Sequential cell allocation and differentiation are integrated with the branching process to generate a functional branching organ. This review focuses on the roles of SOX9+ cells as precursors for new branches, as the source of various cell types in the conducting airways, and as progenitors of the alveolar epithelium. All of these processes are controlled by multiple signaling pathways. Many mouse mutants with defective lung branching contain underlying defects in one or more steps of cell allocation and differentiation of SOX9+ progenitors. This model provides a framework to understand the molecular basis of lung phenotypes and to elucidate the molecular mechanisms of lung patterning. It builds a foundation on which comparing and contrasting the mechanisms employed by different branching organs in diverse species can be made.
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Affiliation(s)
- Kuan Zhang
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Thin Aung
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Erica Yao
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Pao-Tien Chuang
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
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24
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Joo H, Min S, Cho SW. Advanced lung organoids for respiratory system and pulmonary disease modeling. J Tissue Eng 2024; 15:20417314241232502. [PMID: 38406820 PMCID: PMC10894554 DOI: 10.1177/20417314241232502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Amidst the recent coronavirus disease 2019 (COVID-19) pandemic, respiratory system research has made remarkable progress, particularly focusing on infectious diseases. Lung organoid, a miniaturized structure recapitulating lung tissue, has gained global attention because of its advantages over other conventional models such as two-dimensional (2D) cell models and animal models. Nevertheless, lung organoids still face limitations concerning heterogeneity, complexity, and maturity compared to the native lung tissue. To address these limitations, researchers have employed co-culture methods with various cell types including endothelial cells, mesenchymal cells, and immune cells, and incorporated bioengineering platforms such as air-liquid interfaces, microfluidic chips, and functional hydrogels. These advancements have facilitated applications of lung organoids to studies of pulmonary diseases, providing insights into disease mechanisms and potential treatments. This review introduces recent progress in the production methods of lung organoids, strategies for improving maturity, functionality, and complexity of organoids, and their application in disease modeling, including respiratory infection and pulmonary fibrosis.
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Affiliation(s)
- Hyebin Joo
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sungjin Min
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
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25
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Blain R, Couly G, Shotar E, Blévinal J, Toupin M, Favre A, Abjaghou A, Inoue M, Hernández-Garzón E, Clarençon F, Chalmel F, Mazaud-Guittot S, Giacobini P, Gitton Y, Chédotal A. A tridimensional atlas of the developing human head. Cell 2023; 186:5910-5924.e17. [PMID: 38070509 PMCID: PMC10783631 DOI: 10.1016/j.cell.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/01/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023]
Abstract
The evolution and development of the head have long captivated researchers due to the crucial role of the head as the gateway for sensory stimuli and the intricate structural complexity of the head. Although significant progress has been made in understanding head development in various vertebrate species, our knowledge of early human head ontogeny remains limited. Here, we used advanced whole-mount immunostaining and 3D imaging techniques to generate a comprehensive 3D cellular atlas of human head embryogenesis. We present detailed developmental series of diverse head tissues and cell types, including muscles, vasculature, cartilage, peripheral nerves, and exocrine glands. These datasets, accessible through a dedicated web interface, provide insights into human embryogenesis. We offer perspectives on the branching morphogenesis of human exocrine glands and unknown features of the development of neurovascular and skeletomuscular structures. These insights into human embryology have important implications for understanding craniofacial defects and neurological disorders and advancing diagnostic and therapeutic strategies.
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Affiliation(s)
- Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Gérard Couly
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eimad Shotar
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | | | - Maryne Toupin
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Anais Favre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ali Abjaghou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Frédéric Clarençon
- Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Frédéric Chalmel
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Séverine Mazaud-Guittot
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Paolo Giacobini
- University of Lille, INSERM, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, 59000 Lille, France
| | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Institut de pathologie, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France; University Claude Bernard Lyon 1, MeLiS, CNRS UMR 5284, INSERM U1314, 69008 Lyon, France.
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26
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Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell 2023; 186:5876-5891.e20. [PMID: 38134877 DOI: 10.1016/j.cell.2023.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/24/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023]
Abstract
Harmonizing cell types across the single-cell community and assembling them into a common framework is central to building a standardized Human Cell Atlas. Here, we present CellHint, a predictive clustering tree-based tool to resolve cell-type differences in annotation resolution and technical biases across datasets. CellHint accurately quantifies cell-cell transcriptomic similarities and places cell types into a relationship graph that hierarchically defines shared and unique cell subtypes. Application to multiple immune datasets recapitulates expert-curated annotations. CellHint also reveals underexplored relationships between healthy and diseased lung cell states in eight diseases. Furthermore, we present a workflow for fast cross-dataset integration guided by harmonized cell types and cell hierarchy, which uncovers underappreciated cell types in adult human hippocampus. Finally, we apply CellHint to 12 tissues from 38 datasets, providing a deeply curated cross-tissue database with ∼3.7 million cells and various machine learning models for automatic cell annotation across human tissues.
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Affiliation(s)
- Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simone Webb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Laura Jardine
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Benjamin J Stewart
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
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27
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Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, Suo C, Pett JP, Wilbrey-Clark A, Dann E, Mamanova L, Richardson L, Polanski K, Pennycuick A, Allen-Hyttinen J, Herczeg IT, Arzili R, Hynds RE, Teixeira VH, Haniffa M, Lim K, Sun D, Rawlins EL, Oliver AJ, Lyons PA, Marioni JC, Ruhrberg C, Tuong ZK, Clatworthy MR, Reading JL, Janes SM, Teichmann SA, Meyer KB, Nikolić MZ. Early human lung immune cell development and its role in epithelial cell fate. Sci Immunol 2023; 8:eadf9988. [PMID: 38100545 PMCID: PMC7615868 DOI: 10.1126/sciimmunol.adf9988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 11/03/2023] [Indexed: 12/17/2023]
Abstract
Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.
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Affiliation(s)
- Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
- Division of Respiratory Diseases, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Adam Pennycuick
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Iván T Herczeg
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Romina Arzili
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James L Reading
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
- Tumour Immunodynamics and Interception Laboratory, Cancer Institute, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
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28
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Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA. A human embryonic limb cell atlas resolved in space and time. Nature 2023:10.1038/s41586-023-06806-x. [PMID: 38057666 DOI: 10.1038/s41586-023-06806-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months1. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common2. Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species.
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Affiliation(s)
- Bao Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Peng He
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Trauma and Orthopaedics, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Shuaiyu Wang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Genomics England, London, UK
| | | | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nadav Yayon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yixi Fu
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hao Yang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Liang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Alain Chedotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Institut de pathologie, groupe hospitalier Est, hospices civils de Lyon, Lyon, France
- University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, Lyon, France
| | | | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Dean
- Department of Clinical Neurosciences, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Mekayla A Storer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hongbo Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, the First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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29
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Gu Y, Zhang W, Wu X, Zhang Y, Xu K, Su J. Organoid assessment technologies. Clin Transl Med 2023; 13:e1499. [PMID: 38115706 PMCID: PMC10731122 DOI: 10.1002/ctm2.1499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
Despite enormous advances in the generation of organoids, robust and stable protocols of organoids are still a major challenge to researchers. Research for assessing structures of organoids and the evaluations of their functions on in vitro or in vivo is often limited by precision strategies. A growing interest in assessing organoids has arisen, aimed at standardizing the process of obtaining organoids to accurately resemble human-derived tissue. The complex microenvironment of organoids, intricate cellular crosstalk, organ-specific architectures and further complicate functions urgently quest for high-through schemes. By utilizing multi-omics analysis and single-cell analysis, cell-cell interaction mechanisms can be deciphered, and their structures can be investigated in a detailed view by histological analysis. In this review, we will conclude the novel approaches to study the molecular mechanism and cell heterogeneity of organoids and discuss the histological and morphological similarity of organoids in comparison to the human body. Future perspectives on functional analysis will be developed and the organoids will become mature models.
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Affiliation(s)
- Yuyuan Gu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- School of MedicineShanghai UniversityShanghaiChina
| | - Wencai Zhang
- Department of OrthopedicsFirst Affiliated HospitalJinan UniversityGuangzhouChina
| | - Xianmin Wu
- Department of OrthopedicsShanghai Zhongye HospitalShanghaiChina
| | - Yuanwei Zhang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Department of OrthopaedicsXinhua Hospital Affiliated to Shanghai JiaoTong University School of MedicineShanghaiChina
| | - Ke Xu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Wenzhou Institute of Shanghai UniversityWenzhouChina
| | - Jiacan Su
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Department of OrthopaedicsXinhua Hospital Affiliated to Shanghai JiaoTong University School of MedicineShanghaiChina
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30
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Yang Y, McCullough CG, Seninge L, Guo L, Kwon WJ, Zhang Y, Li NY, Gaddam S, Pan C, Zhen H, Torkelson J, Glass IA, Charville G, Que J, Stuart J, Ding H, Oro A. A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563664. [PMID: 37961271 PMCID: PMC10634774 DOI: 10.1101/2023.10.24.563664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Human pluripotent stem cell-derived tissue engineering offers great promise in designer cell-based personalized therapeutics. To harness such potential, a broader approach requires a deeper understanding of tissue-level interactions. We previously developed a manufacturing system for the ectoderm-derived skin epithelium for cell replacement therapy. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium, despite both possessing similar stratified structure. Here we employ single cell and spatial technologies to generate a spatiotemporal multi-omics cell atlas for human esophageal development. We illuminate the cellular diversity, dynamics and signal communications for the developing esophageal epithelium and stroma. Using the machine-learning based Manatee, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of the Manatee predictions leads to a clinically-compatible system for manufacturing human esophageal mucosa. Our approach creates a versatile platform to accelerate human tissue manufacturing for future cell replacement therapies to treat human genetic defects and wounds.
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31
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Frum T, Hsu PP, Hein RFC, Conchola AS, Zhang CJ, Utter OR, Anand A, Zhang Y, Clark SG, Glass I, Sexton JZ, Spence JR. Opposing roles for TGFβ- and BMP-signaling during nascent alveolar differentiation in the developing human lung. NPJ Regen Med 2023; 8:48. [PMID: 37689780 PMCID: PMC10492838 DOI: 10.1038/s41536-023-00325-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 08/31/2023] [Indexed: 09/11/2023] Open
Abstract
Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in repair after injury. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development. Using lung explant and organoid models, we identified opposing effects of TGFβ- and BMP-signaling, where inhibition of TGFβ- and activation of BMP-signaling in the context of high WNT- and FGF-signaling efficiently differentiated early lung progenitors into AT2-like cells in vitro. AT2-like cells differentiated in this manner exhibit surfactant processing and secretion capabilities, and long-term commitment to a mature AT2 phenotype when expanded in media optimized for primary AT2 culture. Comparing AT2-like cells differentiated with TGFβ-inhibition and BMP-activation to alternative differentiation approaches revealed improved specificity to the AT2 lineage and reduced off-target cell types. These findings reveal opposing roles for TGFβ- and BMP-signaling in AT2 differentiation and provide a new strategy to generate a therapeutically relevant cell type in vitro.
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Affiliation(s)
- Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Peggy P Hsu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Renee F C Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ansley S Conchola
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olivia R Utter
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abhinav Anand
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yi Zhang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sydney G Clark
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Drug Repurposing, University of Michigan, Ann Arbor, MI, 48109, USA
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, 48109, USA.
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32
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Lim K, Rutherford EN, Sun D, Van den Boomen DJH, Edgar JR, Bang JH, Matesic LE, Lee JH, Lehner PJ, Marciniak SJ, Rawlins EL, Dickens JA. A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555522. [PMID: 37693487 PMCID: PMC10491189 DOI: 10.1101/2023.08.30.555522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Alveolar type 2 (AT2) cells maintain lung health by acting as stem cells and producing pulmonary surfactant1-3. AT2 dysfunction underlies many lung diseases including interstitial lung disease (ILD), in which some inherited forms result from mislocalisation of surfactant protein C (SFTPC) variants4,5. Disease modelling and dissection of mechanisms remains challenging due to complexities in deriving and maintaining AT2 cells ex vivo. Here, we describe the development of expandable adult AT2-like organoids derived from human fetal lung which are phenotypically stable, can differentiate into AT1-like cells and are genetically manipulable. We use these organoids to test key effectors of SFTPC maturation identified in a forward genetic screen including the E3 ligase ITCH, demonstrating that their depletion phenocopies the pathological SFTPC redistribution seen for the SFTPC-I73T variant. In summary, we demonstrate the development of a novel alveolar organoid model and use it to identify effectors of SFTPC maturation necessary for AT2 health.
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Affiliation(s)
- Kyungtae Lim
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | | | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
- Current address: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Dick J H Van den Boomen
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Harvard Medical School, Department of Cell Biology, Harvard University, LHRRB building, 45 Shattuck Street, Boston MA 02115, USA
| | - James R Edgar
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Jae Hak Bang
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lydia E Matesic
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC 29208, USA
| | - Joo-Hyeon Lee
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
- Royal Papworth Hospital, Papworth Road, Trumpington, CB2 0AY
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Jennifer A Dickens
- Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
- Royal Papworth Hospital, Papworth Road, Trumpington, CB2 0AY
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33
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Blutt SE, Coarfa C, Neu J, Pammi M. Multiomic Investigations into Lung Health and Disease. Microorganisms 2023; 11:2116. [PMID: 37630676 PMCID: PMC10459661 DOI: 10.3390/microorganisms11082116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions.
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Affiliation(s)
- Sarah E. Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josef Neu
- Department of Pediatrics, Section of Neonatology, University of Florida, Gainesville, FL 32611, USA;
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
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34
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Lee W, Lee S, Yoon JK, Lee D, Kim Y, Han YB, Kim R, Moon S, Park YJ, Park K, Cha B, Choi J, Kim J, Ha NY, Kim K, Cho S, Cho NH, Desai TJ, Chung JH, Lee JH, Kim JI. A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung. Exp Mol Med 2023; 55:1831-1842. [PMID: 37582976 PMCID: PMC10474282 DOI: 10.1038/s12276-023-01076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/14/2023] [Accepted: 04/26/2023] [Indexed: 08/17/2023] Open
Abstract
We present an in-depth single-cell atlas of in vitro multiculture systems on human primary airway epithelium derived from normal and diseased lungs of 27 individual donors. Our large-scale single-cell profiling identified new cell states and differentiation trajectories of rare airway epithelial cell types in human distal lungs. By integrating single-cell datasets of human lung tissues, we discovered immune-primed subsets enriched in lungs and organoids derived from patients with chronic respiratory disease. To demonstrate the full potential of our platform, we further illustrate transcriptomic responses to various respiratory virus infections in vitro airway models. Our work constitutes a single-cell roadmap for the cellular and molecular characteristics of human primary lung cells in vitro and their relevance to human tissues in vivo.
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Affiliation(s)
- Woochan Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Seyoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jung-Ki Yoon
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dakyung Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Yuri Kim
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
| | - Yeon Bi Han
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Rokhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, College of Medicine, Seoul National University, Seoul, Korea
| | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Bukyoung Cha
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Na-Young Ha
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
| | - Kwhanmien Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Nam-Hyuk Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Korea
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jin-Haeng Chung
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
- Interdisciplinary Program in Cancer Biology, College of Medicine, Seoul National University, Seoul, Korea.
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
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35
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El Agha E, Thannickal VJ. The lung mesenchyme in development, regeneration, and fibrosis. J Clin Invest 2023; 133:e170498. [PMID: 37463440 DOI: 10.1172/jci170498] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Mesenchymal cells are uniquely located at the interface between the epithelial lining and the stroma, allowing them to act as a signaling hub among diverse cellular compartments of the lung. During embryonic and postnatal lung development, mesenchyme-derived signals instruct epithelial budding, branching morphogenesis, and subsequent structural and functional maturation. Later during adult life, the mesenchyme plays divergent roles wherein its balanced activation promotes epithelial repair after injury while its aberrant activation can lead to pathological remodeling and fibrosis that are associated with multiple chronic pulmonary diseases, including bronchopulmonary dysplasia, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. In this Review, we discuss the involvement of the lung mesenchyme in various morphogenic, neomorphogenic, and dysmorphogenic aspects of lung biology and health, with special emphasis on lung fibroblast subsets and smooth muscle cells, intercellular communication, and intrinsic mesenchymal mechanisms that drive such physiological and pathophysiological events throughout development, homeostasis, injury repair, regeneration, and aging.
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Affiliation(s)
- Elie El Agha
- Department of Medicine V, Internal Medicine, Infectious Diseases and Infection Control, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Cardio-Pulmonary Institute (CPI), Giessen, Germany
- Institute for Lung Health (ILH), Giessen, Germany
| | - Victor J Thannickal
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA
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36
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Conchola AS, Frum T, Xiao Z, Hsu PP, Kaur K, Downey MS, Hein RFC, Miller AJ, Tsai YH, Wu A, Holloway EM, Anand A, Murthy PKL, Glass I, Tata PR, Spence JR. Regionally distinct progenitor cells in the lower airway give rise to neuroendocrine and multiciliated cells in the developing human lung. Proc Natl Acad Sci U S A 2023; 120:e2210113120. [PMID: 37279279 PMCID: PMC10268599 DOI: 10.1073/pnas.2210113120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 04/27/2023] [Indexed: 06/08/2023] Open
Abstract
Using scRNA-seq and microscopy, we describe a cell that is enriched in the lower airways of the developing human lung and identified by the unique coexpression of SCGB3A2/SFTPB/CFTR. To functionally interrogate these cells, we apply a single-cell barcode-based lineage tracing method, called CellTagging, to track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro. Lineage tracing reveals that these cells have a distinct differentiation potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. Lineage tracing results are supported by studies using organoids and isolated cells from the lower noncartilaginous airway. We conclude that SCGB3A2/SFTPB/CFTR cells are enriched in the lower airways of the developing human lung and contribute to the epithelial diversity and heterogeneity in this region.
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Affiliation(s)
- Ansley S. Conchola
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Tristan Frum
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Zhiwei Xiao
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Peggy P. Hsu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
| | - Kamika Kaur
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Michael S. Downey
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
| | - Renee F. C. Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Alyssa J. Miller
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Angeline Wu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Abhinav Anand
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | | | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA98195
| | | | - Jason R. Spence
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
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37
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Liu S, Sun D, Butler R, Rawlins EL. RTK signalling promotes epithelial columnar cell shape and apical junction maintenance in human lung progenitor cells. Development 2023; 150:dev201284. [PMID: 37260147 PMCID: PMC10281517 DOI: 10.1242/dev.201284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Multipotent epithelial progenitor cells can be expanded from human embryonic lungs as organoids and maintained in a self-renewing state using a defined medium. The organoid cells are columnar, resembling the cell morphology of the developing lung tip epithelium in vivo. Cell shape dynamics and fate are tightly coordinated during development. We therefore used the organoid system to identify signalling pathways that maintain the columnar shape of human lung tip progenitors. We found that EGF, FGF7 and FGF10 have distinct functions in lung tip progenitors. FGF7 activates MAPK/ERK and PI3K/AKT signalling, and is sufficient to promote columnar cell shape in primary tip progenitors. Inhibitor experiments show that MAPK/ERK and PI3K/AKT signalling are key downstream pathways, regulating cell proliferation, columnar cell shape and cell junctions. We identified integrin signalling as a key pathway downstream of MAPK/ERK in the tip progenitors; disrupting integrin alters polarity, cell adhesion and tight junction assembly. By contrast, stimulation with FGF10 or EGF alone is not sufficient to maintain organoid columnar cell shape. This study employs organoids to provide insight into the cellular mechanisms regulating human lung development.
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Affiliation(s)
- Shuyu Liu
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Richard Butler
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Emma L. Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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38
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Frum T, Hsu PP, Hein RFC, Conchola AS, Zhang CJ, Utter OR, Anand A, Zhang Y, Clark SG, Glass I, Sexton JZ, Spence JR. Opposing roles for TGFβ- and BMP-signaling during nascent alveolar differentiation in the developing human lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539573. [PMID: 37205521 PMCID: PMC10187311 DOI: 10.1101/2023.05.05.539573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in repair after injury. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development. Using lung explant and organoid models, we identified opposing effects of TGFβ- and BMP-signaling, where inhibition of TGFβ- and activation of BMP-signaling in the context of high WNT- and FGF-signaling efficiently differentiated early lung progenitors into AT2-like cells in vitro . AT2-like cells differentiated in this manner exhibit surfactant processing and secretion capabilities, and long-term commitment to a mature AT2 phenotype when expanded in media optimized for primary AT2 culture. Comparing AT2-like cells differentiated with TGFβ-inhibition and BMP-activation to alternative differentiation approaches revealed improved specificity to the AT2 lineage and reduced off-target cell types. These findings reveal opposing roles for TGFβ- and BMP-signaling in AT2 differentiation and provide a new strategy to generate a therapeutically relevant cell type in vitro .
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39
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Bao H, Cao J, Chen M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chhetri JK, Ding Y, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Lv J, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wang Y, Wu R, Xia K, Xiao FH, Xu L, Xu Y, Yan H, Yang L, Yang R, Yang Y, Ying Y, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhou R, Zhu Q, Zhu Z, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Ci W, Ding BS, Ding Q, Gao F, Han JDJ, Huang K, Ju Z, Kong QP, Li J, Li J, Li X, Liu B, Liu F, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren J, Ren R, Song M, Songyang Z, Sun YE, Sun Y, Tian M, Wang S, Wang S, Wang X, Wang X, Wang YJ, Wang Y, Wong CCL, Xiang AP, Xiao Y, Xie Z, Xu D, Ye J, Yue R, Zhang C, Zhang H, Zhang L, Zhang W, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhu D, Zou W, Pei G, Liu GH. Biomarkers of aging. SCIENCE CHINA. LIFE SCIENCES 2023; 66:893-1066. [PMID: 37076725 PMCID: PMC10115486 DOI: 10.1007/s11427-023-2305-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/21/2023]
Abstract
Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.
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Affiliation(s)
- Hainan Bao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengting Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Min Chen
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Chen
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yutian Chen
- The Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlin Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuting He
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Yujuan Jia
- Department of Neurology, First Affiliated Hospital, Shanxi Medical University, Taiyuan, 030001, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Jing
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyi Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Qinhao Liang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Liang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zuojun Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jianwei Lv
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jingyi Ma
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Jiawei Nie
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wang
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xuan Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuhan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Rimo Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Kai Xia
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fu-Hui Xiao
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yingying Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Haoteng Yan
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Liang Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Ruici Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yilin Ying
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China
| | - Le Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weiwei Zhang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China
| | - Wenwan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Qingchen Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Cao
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China.
| | - Zhongwei Cao
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, 510000, China.
| | - Hou-Zao Chen
- Department of Biochemistryand Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Bi-Sen Ding
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Feng Gao
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China.
| | - Qing-Peng Kong
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Baohua Liu
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China.
| | - Feng Liu
- Metabolic Syndrome Research Center, The Second Xiangya Hospital, Central South Unversity, Changsha, 410011, China.
| | - Lin Liu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300000, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China.
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Tianjin Institute of Immunology, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Yong Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China.
| | - Shuai Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Jing Nie
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Center for Aging and Cancer, Hainan Medical University, Haikou, 571199, China.
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, 98195, USA.
| | - Mei Tian
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Shusen Wang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China.
| | - Si Wang
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaoning Wang
- Institute of Geriatrics, The second Medical Center, Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Yunfang Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Andy Peng Xiang
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China.
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, 100101, China.
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Jing Ye
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Cuntai Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China.
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dahai Zhu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Pei
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Biomedicine, The Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China.
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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40
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Cao S, Feng H, Yi H, Pan M, Lin L, Zhang YS, Feng Z, Liang W, Cai B, Li Q, Xiong Z, Shen Q, Ke M, Zhao X, Chen H, He Q, Min M, Cai Q, Liu H, Wang J, Pei D, Chen J, Ma Y. Single-cell RNA sequencing reveals the developmental program underlying proximal-distal patterning of the human lung at the embryonic stage. Cell Res 2023:10.1038/s41422-023-00802-6. [PMID: 37085732 PMCID: PMC10119843 DOI: 10.1038/s41422-023-00802-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/21/2023] [Indexed: 04/23/2023] Open
Abstract
The lung is the primary respiratory organ in human, in which the proximal airway and the distal alveoli are responsible for air conduction and gas exchange, respectively. However, the regulation of proximal-distal patterning at the embryonic stage of human lung development is largely unknown. Here we investigated the early lung development of human embryos at weeks 4-8 post fertilization (Carnegie stages 12-21) using single-cell RNA sequencing, and obtained a transcriptomic atlas of 169,686 cells. We observed discernible gene expression patterns of proximal and distal epithelia at week 4, upon the initiation of lung organogenesis. Moreover, we identified novel transcriptional regulators of the patterning of proximal (e.g., THRB and EGR3) and distal (e.g., ETV1 and SOX6) epithelia. Further dissection revealed various stromal cell populations, including an early-embryonic BDNF+ population, providing a proximal-distal patterning niche with spatial specificity. In addition, we elucidated the cell fate bifurcation and maturation of airway and vascular smooth muscle progenitor cells at the early stage of lung development. Together, our study expands the scope of human lung developmental biology at early embryonic stages. The discovery of intrinsic transcriptional regulators and novel niche providers deepens the understanding of epithelial proximal-distal patterning in human lung development, opening up new avenues for regenerative medicine.
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Affiliation(s)
- Shangtao Cao
- Guangzhou Laboratory, Guangzhou, Guangdong, China.
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Huijian Feng
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Mengjie Pan
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Lihui Lin
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yao Santo Zhang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
| | - Ziyu Feng
- Guangzhou Laboratory, Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Weifang Liang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
| | - Baomei Cai
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Qi Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Zhi Xiong
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qingmei Shen
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Minjing Ke
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xing Zhao
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Huilin Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qina He
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Mingwei Min
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Quanyou Cai
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jie Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China.
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China.
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China.
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41
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Mižíková I, Thébaud B. Perinatal origins of bronchopulmonary dysplasia-deciphering normal and impaired lung development cell by cell. Mol Cell Pediatr 2023; 10:4. [PMID: 37072570 PMCID: PMC10113423 DOI: 10.1186/s40348-023-00158-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/26/2023] [Indexed: 04/20/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a multifactorial disease occurring as a consequence of premature birth, as well as antenatal and postnatal injury to the developing lung. BPD morbidity and severity depend on a complex interplay between prenatal and postnatal inflammation, mechanical ventilation, and oxygen therapy as well as associated prematurity-related complications. These initial hits result in ill-explored aberrant immune and reparative response, activation of pro-fibrotic and anti-angiogenic factors, which further perpetuate the injury. Histologically, the disease presents primarily by impaired lung development and an arrest in lung microvascular maturation. Consequently, BPD leads to respiratory complications beyond the neonatal period and may result in premature aging of the lung. While the numerous prenatal and postnatal stimuli contributing to BPD pathogenesis are relatively well known, the specific cell populations driving the injury, as well as underlying mechanisms are still not well understood. Recently, an effort to gain a more detailed insight into the cellular composition of the developing lung and its progenitor populations has unfold. Here, we provide an overview of the current knowledge regarding perinatal origin of BPD and discuss underlying mechanisms, as well as novel approaches to study the perturbed lung development.
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Affiliation(s)
- I Mižíková
- Experimental Pulmonology, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - B Thébaud
- Sinclair Centre for Regenerative Medicine, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
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42
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Bhattacharya S, Cherry C, Deutsch G, Glass IA, Mariani TJ, Alam DA, Danopoulos S. A Trisomy 21 Lung Cell Atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534839. [PMID: 37066313 PMCID: PMC10103948 DOI: 10.1101/2023.03.30.534839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.
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43
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Ward T, Jha A, Daynes E, Ackland J, Chalmers JD. Review of the British Thoracic Society Winter Meeting 23 November 2022 23-25 November 2022. Thorax 2023; 78:e1. [PMID: 36717241 DOI: 10.1136/thorax-2022-219941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023]
Abstract
The British Thoracic Society Winter Meeting at the QEII Centre in London provided the first opportunity for the respiratory community to meet and disseminate research findings face to face since the start of the COVID-19 pandemic. World-leading researchers from the UK and abroad presented their latest findings across a range of respiratory diseases. This article aims to represent the range of the conference and as such is written from the perspective of a basic scientist, a physiotherapist and two doctors. The authors reviewed showcase sessions plus a selection of symposia based on their personal highlights. Content ranged from exciting new developments in basic science to new and unpublished results from clinical trials, delivered by leading scientists from their fields including former deputy chief medical officer Professor Sir Jonathan Van-Tam and former WHO chief scientist Dr Soumya Swaminathan.
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Affiliation(s)
- Tom Ward
- Department Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, UK
| | - Akhilesh Jha
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Enya Daynes
- Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Jodie Ackland
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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44
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Empowering human lung development. Cell Stem Cell 2023; 30:5-6. [PMID: 36608678 DOI: 10.1016/j.stem.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
By generating a multiomic cell atlas of embryonic human lungs and establishing a human tip progenitor cell organoid culture system, two recent studies demonstrated the exciting research advances in human lung development.
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45
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Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL. Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. Cell Stem Cell 2023; 30:20-37.e9. [PMID: 36493780 DOI: 10.1016/j.stem.2022.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 10/02/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]
Abstract
Variation in lung alveolar development is strongly linked to disease susceptibility. However, underlying cellular and molecular mechanisms are difficult to study in humans. We have identified an alveolar-fated epithelial progenitor in human fetal lungs, which we grow as self-organizing organoids that model key aspects of cell lineage commitment. Using this system, we have functionally validated cell-cell interactions in the developing human alveolar niche, showing that Wnt signaling from differentiating fibroblasts promotes alveolar-type-2 cell identity, whereas myofibroblasts secrete the Wnt inhibitor, NOTUM, providing spatial patterning. We identify a Wnt-NKX2.1 axis controlling alveolar differentiation. Moreover, we show that differential binding of NKX2.1 coordinates alveolar maturation, allowing us to model the effects of human genetic variation in NKX2.1 on alveolar differentiation. Our organoid system recapitulates key aspects of human fetal lung stem cell biology allowing mechanistic experiments to determine the cellular and molecular regulation of human development and disease.
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Affiliation(s)
- Kyungtae Lim
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Alex P A Donovan
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Walfred Tang
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Dawei Sun
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Peng He
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - John C Marioni
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | | | - Andrea H Brand
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Emma L Rawlins
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK.
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