1
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Li YH, Yang YS, Xue YB, Lei H, Zhang SS, Qian J, Yao Y, Zhou R, Huang L. G protein subunit G γ13-mediated signaling pathway is critical to the inflammation resolution and functional recovery of severely injured lungs. eLife 2024; 12:RP92956. [PMID: 38836551 DOI: 10.7554/elife.92956] [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: 06/06/2024] Open
Abstract
Tuft cells are a group of rare epithelial cells that can detect pathogenic microbes and parasites. Many of these cells express signaling proteins initially found in taste buds. It is, however, not well understood how these taste signaling proteins contribute to the response to the invading pathogens or to the recovery of injured tissues. In this study, we conditionally nullified the signaling G protein subunit Gγ13 and found that the number of ectopic tuft cells in the injured lung was reduced following the infection of the influenza virus H1N1. Furthermore, the infected mutant mice exhibited significantly larger areas of lung injury, increased macrophage infiltration, severer pulmonary epithelial leakage, augmented pyroptosis and cell death, greater bodyweight loss, slower recovery, worsened fibrosis and increased fatality. Our data demonstrate that the Gγ13-mediated signal transduction pathway is critical to tuft cells-mediated inflammation resolution and functional repair of the damaged lungs.To our best knowledge, it is the first report indicating subtype-specific contributions of tuft cells to the resolution and recovery.
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Affiliation(s)
- Yi-Hong Li
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yi-Sen Yang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan-Bo Xue
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Lei
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sai-Sai Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junbin Qian
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Yushi Yao
- Institute of Immunology and Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruhong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Zhejiang University Shanghai Institute for Advanced Study, Shanghai, Shanghai, China
| | - Liquan Huang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Zhejiang University Shanghai Institute for Advanced Study, Shanghai, Shanghai, China
- Monell Chemical Senses Center, Philadelphia, United States
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2
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Turuvekere Vittala Murthy N, Vlasova K, Renner J, Jozic A, Sahay G. A new era of targeting cystic fibrosis with non-viral delivery of genomic medicines. Adv Drug Deliv Rev 2024; 209:115305. [PMID: 38626860 DOI: 10.1016/j.addr.2024.115305] [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: 01/06/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
Cystic fibrosis (CF) is a complex genetic respiratory disorder that necessitates innovative gene delivery strategies to address the mutations in the gene. This review delves into the promises and challenges of non-viral gene delivery for CF therapy and explores strategies to overcome these hurdles. Several emerging technologies and nucleic acid cargos for CF gene therapy are discussed. Novel formulation approaches including lipid and polymeric nanoparticles promise enhanced delivery through the CF mucus barrier, augmenting the potential of non-viral strategies. Additionally, safety considerations and regulatory perspectives play a crucial role in navigating the path toward clinical translation of gene therapy.
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Affiliation(s)
| | - Kseniia Vlasova
- Department of Pharmaceutical Sciences, College of Pharmacy at Oregon State University, Corvallis, OR 97331, USA
| | - Jonas Renner
- Department of Pharmaceutical Sciences, College of Pharmacy at Oregon State University, Corvallis, OR 97331, USA
| | - Antony Jozic
- Department of Pharmaceutical Sciences, College of Pharmacy at Oregon State University, Corvallis, OR 97331, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy at Oregon State University, Corvallis, OR 97331, USA; Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97201, USA; Department of Biomedical Engineering, Robertson Life Sciences Building, Oregon Health & Science University, Portland, OR 97201, USA.
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3
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Loske J, Völler M, Lukassen S, Stahl M, Thürmann L, Seegebarth A, Röhmel J, Wisniewski S, Messingschlager M, Lorenz S, Klages S, Eils R, Lehmann I, Mall MA, Graeber SY, Trump S. Pharmacological Improvement of Cystic Fibrosis Transmembrane Conductance Regulator Function Rescues Airway Epithelial Homeostasis and Host Defense in Children with Cystic Fibrosis. Am J Respir Crit Care Med 2024; 209:1338-1350. [PMID: 38259174 PMCID: PMC11146576 DOI: 10.1164/rccm.202310-1836oc] [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: 10/21/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
Rationale: Pharmacological improvement of cystic fibrosis transmembrane conductance regulator (CFTR) function with elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes in patients with cystic fibrosis (CF). However, ETI effects on impaired mucosal homeostasis and host defense at the molecular and cellular levels in the airways of patients with CF remain unknown. Objectives: To investigate effects of ETI on the transcriptome of nasal epithelial and immune cells from children with CF at the single-cell level. Methods: Nasal swabs from 13 children with CF and at least one F508del allele aged 6 to 11 years were collected at baseline and 3 months after initiation of ETI, subjected to single-cell RNA sequencing, and compared with swabs from 12 age-matched healthy children. Measurements and Main Results: Proportions of CFTR-positive cells were decreased in epithelial basal, club, and goblet cells, but not in ionocytes, from children with CF at baseline and were restored by ETI therapy to nearly healthy levels. Single-cell transcriptomics revealed an impaired IFN signaling and reduced expression of major histocompatibility complex classes I and II encoding genes in epithelial cells of children with CF at baseline, which was partially restored by ETI. In addition, ETI therapy markedly reduced the inflammatory phenotype of immune cells, particularly of neutrophils and macrophages. Conclusions: Pharmacological improvement of CFTR function improves innate mucosal immunity and reduces immune cell inflammatory responses in the upper airways of children with CF at the single-cell level, highlighting the potential to restore epithelial homeostasis and host defense in CF airways by early initiation of ETI therapy.
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Affiliation(s)
- Jennifer Loske
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology and
| | - Mirjam Völler
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sören Lukassen
- Center of Digital Health, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mirjam Stahl
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Loreen Thürmann
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Anke Seegebarth
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Sebastian Wisniewski
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marey Messingschlager
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology and
| | - Stephan Lorenz
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Roland Eils
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Center of Digital Health, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
- Health Data Science Unit, BioQuant, Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Irina Lehmann
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Simon Y. Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Saskia Trump
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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4
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Choksi SP, Byrnes LE, Konjikusic MJ, Tsai BWH, Deleon R, Lu Q, Westlake CJ, Reiter JF. An alternative cell cycle coordinates multiciliated cell differentiation. Nature 2024; 630:214-221. [PMID: 38811726 DOI: 10.1038/s41586-024-07476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
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Affiliation(s)
- Semil P Choksi
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Lauren E Byrnes
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mia J Konjikusic
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict W H Tsai
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Deleon
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Quanlong Lu
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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5
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Coatti GC, Vaghela N, Gillurkar P, Leir SH, Harris A. A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195031. [PMID: 38679287 DOI: 10.1016/j.bbagrm.2024.195031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an anion-selective channel found in epithelial cell membranes. Mutations in CFTR cause cystic fibrosis (CF), an inherited disorder that impairs epithelial function in multiple organs. Most men with CF are infertile due to loss of intact genital ducts. Here we investigated a novel epididymis-selective cis-regulatory element (CRE), located within a peak of open chromatin at -9.5 kb 5' to the CFTR gene promoter. Activation of the -9.5 kb CRE alone by CRISPRa had no impact on CFTR gene expression. However, CRISPRa co-activation of the -9.5 kb CRE and the CFTR gene promoter in epididymis cells significantly augmented CFTR mRNA and protein expression when compared to promoter activation alone. This increase was accompanied by enhanced chromatin accessibility at both sites. Furthermore, the combined CRISPRa strategy activated CFTR expression in other epithelial cells that lack open chromatin at the -9.5 kb site and in which the locus is normally inactive. However, the -9.5 kb CRE does not function as a classical enhancer of the CFTR promoter in transient reporter gene assays. These data provide a novel mechanism for activating/augmenting CFTR expression, which may have therapeutic utility for mutations that perturb CFTR transcription.
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Affiliation(s)
- Giuliana C Coatti
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pulak Gillurkar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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6
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Finlay JB, Ireland AS, Hawgood SB, Reyes T, Ko T, Olsen RR, Abi Hachem R, Jang DW, Bell D, Chan JM, Goldstein BJ, Oliver TG. Olfactory neuroblastoma mimics molecular heterogeneity and lineage trajectories of small-cell lung cancer. Cancer Cell 2024:S1535-6108(24)00164-8. [PMID: 38788720 DOI: 10.1016/j.ccell.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/13/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
The olfactory epithelium undergoes neuronal regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare tumor of unclear origins. Employing alterations in Rb1/Trp53/Myc (RPM), we establish a genetically engineered mouse model of high-grade metastatic ONB exhibiting a NEUROD1+ immature neuronal phenotype. We demonstrate that globose basal cells (GBCs) are a permissive cell of origin for ONB and that ONBs exhibit cell fate heterogeneity that mimics normal GBC developmental trajectories. ASCL1 loss in RPM ONB leads to emergence of non-neuronal histopathologies, including a POU2F3+ microvillar-like state. Similar to small-cell lung cancer (SCLC), mouse and human ONBs exhibit mutually exclusive NEUROD1 and POU2F3-like states, an immune-cold tumor microenvironment, intratumoral cell fate heterogeneity comprising neuronal and non-neuronal lineages, and cell fate plasticity-evidenced by barcode-based lineage tracing and single-cell transcriptomics. Collectively, our findings highlight conserved similarities between ONB and neuroendocrine tumors with significant implications for ONB classification and treatment.
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Affiliation(s)
- John B Finlay
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Abbie S Ireland
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA
| | - Sarah B Hawgood
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA
| | - Tony Reyes
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA; Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA
| | - Tiffany Ko
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Rachelle R Olsen
- Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA
| | - Ralph Abi Hachem
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - David W Jang
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Diana Bell
- Division of Anatomic Pathology, City of Hope Comprehensive Cancer Center, Duarte 91010, CA, USA
| | - Joseph M Chan
- Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York City 10065, NY, USA
| | - Bradley J Goldstein
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA; Department of Neurobiology, Duke University, Durham 27710, NC, USA.
| | - Trudy G Oliver
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA; Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA.
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7
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Rafelski SM, Theriot JA. Establishing a conceptual framework for holistic cell states and state transitions. Cell 2024; 187:2633-2651. [PMID: 38788687 DOI: 10.1016/j.cell.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Cell states were traditionally defined by how they looked, where they were located, and what functions they performed. In this post-genomic era, the field is largely focused on a molecular view of cell state. Moving forward, we anticipate that the observables used to define cell states will evolve again as single-cell imaging and analytics are advancing at a breakneck pace via the collection of large-scale, systematic cell image datasets and the application of quantitative image-based data science methods. This is, therefore, a key moment in the arc of cell biological research to develop approaches that integrate the spatiotemporal observables of the physical structure and organization of the cell with molecular observables toward the concept of a holistic cell state. In this perspective, we propose a conceptual framework for holistic cell states and state transitions that is data-driven, practical, and useful to enable integrative analyses and modeling across many data types.
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Affiliation(s)
- Susanne M Rafelski
- Allen Institute for Cell Science, 615 Westlake Avenue N, Seattle, WA 98125, USA.
| | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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8
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Xie X, Wei Y, Cui Y, Zhang Q, Lu H, Chen L, He J. Transcriptomics reveals age-related changes in ion transport-related factors in yak lungs. Front Vet Sci 2024; 11:1374794. [PMID: 38779034 PMCID: PMC11110679 DOI: 10.3389/fvets.2024.1374794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
Yaks inhabit high-altitude, low-oxygen regions, where ion transport functions play a crucial role in maintaining intracellular and extracellular ionic balance and regulating pulmonary vascular tension. These functions affect pulmonary ventilation and blood flow rate, aiding tissue development and enhancing oxygen transfer efficiency, thus facilitating better adaptation to hypoxic environments. To investigate the regulatory mechanisms of ion transport-related factors on the growth and development of yak lungs, we employed RNA sequencing (RNA-seq)for sequencing the transcriptome in the lung tissues of neonatal (1-day-old), juvenile (1-year-old), and adult (4-year-old) yaks. We also performed differential gene expression and functional analyses. The results yielded 26 genes associated with ion transport, mainly enriched in the salivary and pancreatic secretion pathways. Finally, we used several methods including quantitative polymerase chain reaction (qRT-PCR), and Western blotting (WB), immunohistochemical (IHC) and immunofluorescence (IF) staining to determine the distribution of the expression of the ion transport genes FOXI1, KCNMA1, and SLC12A2 in yak lung tissues. qRT-PCR and WB results indicated that mRNA and protein relative expression levels of FOXI1 and SLC12A2 were significantly higher in neonatal yaks than in juvenile and adult yaks (all p < 0.05), whereas those of KCNMA1 were significantly higher in adult yaks than in neonatal and juvenile yaks (all p < 0.05). IHC and IF results demonstrated that FOXI1, KCNMA1, and SLC12A2 were distributed among the epithelial mucosal layers (including ciliated, goblet, and Clara cells) of the yaks' bronchi and their branches in the lungs across different age groups of yak. Therefore, our results suggested that FOXI1, KCNMA1, and SLC12A2 may be strongly associated with the development and aging processes in yak lungs. These results provide insights into the molecular mechanisms underlying the yak's adaptation to high-altitude environments and valuable references for further research.
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Affiliation(s)
- Xiating Xie
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yating Wei
- Laboratory Animal, Lanzhou Institute of Biological Products, Lanzhou, Gansu, China
| | - Yan Cui
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qian Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Hongqin Lu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Liang Chen
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Junfeng He
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
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9
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Reedy JL, Jensen KN, Crossen AJ, Basham KJ, Ward RA, Reardon CM, Harding HB, Hepworth OW, Simaku P, Kwaku GN, Tone K, Willment JA, Reid DM, Stappers MHT, Brown GD, Rajagopal J, Vyas JM. Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534632. [PMID: 37034634 PMCID: PMC10081279 DOI: 10.1101/2023.03.28.534632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Respiratory infections caused by the human fungal pathogen Aspergillus fumigatus are a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway both in vitro and in vivo . Aspergillus -derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.
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10
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Huang ZQ, Liu J, Sun LY, Ong HH, Ye J, Xu Y, Wang DY. Updated epithelial barrier dysfunction in chronic rhinosinusitis: Targeting pathophysiology and treatment response of tight junctions. Allergy 2024; 79:1146-1165. [PMID: 38372149 DOI: 10.1111/all.16064] [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: 10/30/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
Tight junction (TJ) proteins establish a physical barrier between epithelial cells, playing a crucial role in maintaining tissue homeostasis by safeguarding host tissues against pathogens, allergens, antigens, irritants, etc. Recently, an increasing number of studies have demonstrated that abnormal expression of TJs plays an essential role in the development and progression of inflammatory airway diseases, including chronic obstructive pulmonary disease, asthma, allergic rhinitis, and chronic rhinosinusitis (CRS) with or without nasal polyps. Among them, CRS with nasal polyps is a prevalent chronic inflammatory disease that affects the nasal cavity and paranasal sinuses, leading to a poor prognosis and significantly impacting patients' quality of life. Its pathogenesis primarily involves dysfunction of the nasal epithelial barrier, impaired mucociliary clearance, disordered immune response, and excessive tissue remodeling. Numerous studies have elucidated the pivotal role of TJs in both the pathogenesis and response to traditional therapies in CRS. We therefore to review and discuss potential factors contributing to impair and repair of TJs in the nasal epithelium based on their structure, function, and formation process.
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Affiliation(s)
- Zhi-Qun Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jing Liu
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Li-Ying Sun
- First School of Clinical Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hsiao Hui Ong
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jing Ye
- Department of Otolaryngology-Head and Neck Surgery, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - De-Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
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11
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Emanuel E, Arifuzzaman M, Artis D. Epithelial-neuronal-immune cell interactions: Implications for immunity, inflammation, and tissue homeostasis at mucosal sites. J Allergy Clin Immunol 2024; 153:1169-1180. [PMID: 38369030 PMCID: PMC11070312 DOI: 10.1016/j.jaci.2024.02.004] [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: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
The epithelial lining of the respiratory tract and intestine provides a critical physical barrier to protect host tissues against environmental insults, including dietary antigens, allergens, chemicals, and microorganisms. In addition, specialized epithelial cells communicate directly with hematopoietic and neuronal cells. These epithelial-immune and epithelial-neuronal interactions control host immune responses and have important implications for inflammatory conditions associated with defects in the epithelial barrier, including asthma, allergy, and inflammatory bowel diseases. In this review, we discuss emerging research that identifies the mechanisms and impact of epithelial-immune and epithelial-neuronal cross talk in regulating immunity, inflammation, and tissue homeostasis at mucosal barrier surfaces. Understanding the regulation and impact of these pathways could provide new therapeutic targets for inflammatory diseases at mucosal sites.
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Affiliation(s)
- Elizabeth Emanuel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY; Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Allen Discovery Center for Neuroimmune Interactions, New York, NY; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY.
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12
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Yan B, Lan F, Li J, Wang C, Zhang L. The mucosal concept in chronic rhinosinusitis: Focus on the epithelial barrier. J Allergy Clin Immunol 2024; 153:1206-1214. [PMID: 38295881 DOI: 10.1016/j.jaci.2024.01.015] [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: 12/14/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Chronic rhinosinusitis (CRS) is a common chronic nasal cavity and sinus disease affecting a growing number of individuals worldwide. Recent advances have shifted our understanding of CRS pathophysiology from a physical obstruction model of ventilation and drainage to a mucosal concept that recognizes the complexities of mucosal immunologic variations and cellular aberrations. A growing number of studies have demonstrated the alteration of the epithelial barrier during inflammatory states. Therefore, the current review has focused on the crucial role of epithelial cells within this mucosal framework in CRS, detailing the perturbed epithelial homeostasis, impaired epithelial cell barrier, dysregulated epithelial cell repair processes, and enhanced interactions between epithelial cells and immune cells. Notably, the utilization of novel technologies, such as single-cell transcriptomics, has revealed the novel functions of epithelial barriers, such as inflammatory memory and neuroendocrine functions. Therefore, this review also emphasizes the importance of epithelial inflammatory memory and the necessity of further investigations into neuroendocrine epithelial cells and neurogenic inflammation in CRS. We conclude by contemplating the prospective benefits of epithelial cell-oriented biological treatments, which are currently under investigation in rigorous randomized, double-blind clinical trials in patients with CRS with nasal polyps.
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Affiliation(s)
- Bing Yan
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Lan
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingyun Li
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Chengshuo Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China.
| | - Luo Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China.
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13
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Lin B, Shah VS, Chernoff C, Sun J, Shipkovenska GG, Vinarsky V, Waghray A, Xu J, Leduc AD, Hintschich CA, Surve MV, Xu Y, Capen DE, Villoria J, Dou Z, Hariri LP, Rajagopal J. Airway hillocks are injury-resistant reservoirs of unique plastic stem cells. Nature 2024; 629:869-877. [PMID: 38693267 DOI: 10.1038/s41586-024-07377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Airway hillocks are stratified epithelial structures of unknown function1. Hillocks persist for months and have a unique population of basal stem cells that express genes associated with barrier function and cell adhesion. Hillock basal stem cells continually replenish overlying squamous barrier cells. They exhibit dramatically higher turnover than the abundant, largely quiescent classic pseudostratified airway epithelium. Hillocks resist a remarkably broad spectrum of injuries, including toxins, infection, acid and physical injury because hillock squamous cells shield underlying hillock basal stem cells from injury. Hillock basal stem cells are capable of massive clonal expansion that is sufficient to resurface denuded airway, and eventually regenerate normal airway epithelium with each of its six component cell types. Hillock basal stem cells preferentially stratify and keratinize in the setting of retinoic acid signalling inhibition, a known cause of squamous metaplasia2,3. Here we show that mouse hillock expansion is the cause of vitamin A deficiency-induced squamous metaplasia. Finally, we identify human hillocks whose basal stem cells generate functional squamous barrier structures in culture. The existence of hillocks reframes our understanding of airway epithelial regeneration. Furthermore, we show that hillocks are one origin of 'squamous metaplasia', which is long thought to be a precursor of lung cancer.
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Affiliation(s)
- Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA.
- Department of Developmental, Molecular and Chemical Biology, School of Medicine, Tufts University, Boston, MA, USA.
| | - Viral S Shah
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chaim Chernoff
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Developmental and Regenerative Biology Program, Harvard, Cambridge, MA, USA
| | - Jiawei Sun
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Gergana G Shipkovenska
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Jiajie Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Andrew D Leduc
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Constantin A Hintschich
- Department of Developmental, Molecular and Chemical Biology, School of Medicine, Tufts University, Boston, MA, USA
- Department of Otorhinolaryngology, Regensburg University Hospital, Regensburg, Germany
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Manalee Vishnu Surve
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Diane E Capen
- Program in Membrane Biology and Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Villoria
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Lida P Hariri
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA.
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Developmental and Regenerative Biology Program, Harvard, Cambridge, MA, USA.
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14
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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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15
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Vijaykumar K, Leung HM, Barrios A, Wade J, Hathorne HY, Nichols DP, Tearney GJ, Rowe SM, Solomon GM. Longitudinal improvements in clinical and functional outcomes following initiation of elexacaftor/tezacaftor/ivacaftor in patients with cystic fibrosis. Heliyon 2024; 10:e29188. [PMID: 38681615 PMCID: PMC11052906 DOI: 10.1016/j.heliyon.2024.e29188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Background Use of elexacaftor/tezacaftor/ivacaftor (ETI) for treatment of cystic fibrosis (CF) has resulted in unprecedented clinical improvements necessitating development of outcome measures for monitoring disease course. Intranasal micro-optical coherence tomography (μOCT) has previously helped detect and characterize mucociliary abnormalities in patients with CF. This study was done to determine if μOCT can define the effects of ETI on nasal mucociliary clearance and monitor changes conferred to understand mechanistic effects of CFTR modulators beyond CFTR activation. Methods 26 subjects, with at least 1 F508del mutation were recruited and followed at baseline (visit 1), +1 month (visit 2) and +6 months (visit 4) following initiation of ETI therapy. Clinical outcomes were computed at visits 1, 2 and 4. Intranasal μOCT imaging and functional metrics analysis including mucociliary transport rate (MCT) estimation were done at visits 1 and 2. Results Percent predicted forced expiratory volume in 1 s (ppFEV1) showed a significant increase of +10.9 % at visit 2, which sustained at visit 4 (+10.6 %). Sweat chloride levels significantly decreased by -36.6 mmol/L and -41.3 mmol/L at visits 2 and 4, respectively. μOCT analysis revealed significant improvement in MCT rate (2.8 ± 1.5, visit 1 vs 4.0 ± 1.5 mm/min, visit 2; P = 0.048). Conclusions Treatment with ETI resulted in significant and sustained clinical improvements over 6 months. Functional improvements in MCT rate were evident within a month after initiation of ETI therapy indicating that μOCT imaging is sensitive to the treatment effect of HEMT and suggests improved mucociliary transport as a probable mechanism of action underlying the clinical benefits.
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Affiliation(s)
- Kadambari Vijaykumar
- Department of Medicine, University of Alabama at Birmingham, AL, United States
- Gregory Fleming James CF Research Center, Birmingham, AL, United States
| | - Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States
| | - Amilcar Barrios
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States
| | - Justin Wade
- Gregory Fleming James CF Research Center, Birmingham, AL, United States
| | | | | | - Guillermo J. Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States
| | - Steven M. Rowe
- Department of Medicine, University of Alabama at Birmingham, AL, United States
- Gregory Fleming James CF Research Center, Birmingham, AL, United States
| | - George M. Solomon
- Department of Medicine, University of Alabama at Birmingham, AL, United States
- Gregory Fleming James CF Research Center, Birmingham, AL, United States
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16
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Dodd DO, Mechaussier S, Yeyati PL, McPhie F, Anderson JR, Khoo CJ, Shoemark A, Gupta DK, Attard T, Zariwala MA, Legendre M, Bracht D, Wallmeier J, Gui M, Fassad MR, Parry DA, Tennant PA, Meynert A, Wheway G, Fares-Taie L, Black HA, Mitri-Frangieh R, Faucon C, Kaplan J, Patel M, McKie L, Megaw R, Gatsogiannis C, Mohamed MA, Aitken S, Gautier P, Reinholt FR, Hirst RA, O'Callaghan C, Heimdal K, Bottier M, Escudier E, Crowley S, Descartes M, Jabs EW, Kenia P, Amiel J, Bacci GM, Calogero C, Palazzo V, Tiberi L, Blümlein U, Rogers A, Wambach JA, Wegner DJ, Fulton AB, Kenna M, Rosenfeld M, Holm IA, Quigley A, Hall EA, Murphy LC, Cassidy DM, von Kriegsheim A, Papon JF, Pasquier L, Murris MS, Chalmers JD, Hogg C, Macleod KA, Urquhart DS, Unger S, Aitman TJ, Amselem S, Leigh MW, Knowles MR, Omran H, Mitchison HM, Brown A, Marsh JA, Welburn JPI, Ti SC, Horani A, Rozet JM, Perrault I, Mill P. Ciliopathy patient variants reveal organelle-specific functions for TUBB4B in axonemal microtubules. Science 2024; 384:eadf5489. [PMID: 38662826 DOI: 10.1126/science.adf5489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Tubulin, one of the most abundant cytoskeletal building blocks, has numerous isotypes in metazoans encoded by different conserved genes. Whether these distinct isotypes form cell type- and context-specific microtubule structures is poorly understood. Based on a cohort of 12 patients with primary ciliary dyskinesia as well as mouse mutants, we identified and characterized variants in the TUBB4B isotype that specifically perturbed centriole and cilium biogenesis. Distinct TUBB4B variants differentially affected microtubule dynamics and cilia formation in a dominant-negative manner. Structure-function studies revealed that different TUBB4B variants disrupted distinct tubulin interfaces, thereby enabling stratification of patients into three classes of ciliopathic diseases. These findings show that specific tubulin isotypes have distinct and nonredundant subcellular functions and establish a link between tubulinopathies and ciliopathies.
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Affiliation(s)
- Daniel O Dodd
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sabrina Mechaussier
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris 75015, France
| | - Patricia L Yeyati
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Fraser McPhie
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jacob R Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Chen Jing Khoo
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Amelia Shoemark
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee DD1 9SY, UK
- Respiratory Paediatrics, Royal Brompton Hospital, London SW3 6NP, UK
| | - Deepesh K Gupta
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Thomas Attard
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Maimoona A Zariwala
- Department of Pathology and Laboratory Medicine, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Marie Legendre
- Molecular Genetics Laboratory, Sorbonne Université, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Armand Trousseau, Paris 75012, France
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris 75012, France
| | - Diana Bracht
- Department of General Pediatrics, University Children's Hospital Münster, Münster 48149, Germany
| | - Julia Wallmeier
- Department of General Pediatrics, University Children's Hospital Münster, Münster 48149, Germany
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria 21561, Egypt
| | - David A Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Peter A Tennant
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Lucas Fares-Taie
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris 75015, France
| | - Holly A Black
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- South East of Scotland Genetics Service, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Rana Mitri-Frangieh
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil 94000, France
- Biomechanics and Respiratory Apparatus, IMRB, U955 INSERM - Université Paris Est Créteil, CNRS ERL 7000, Créteil 94000, France
| | - Catherine Faucon
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil 94000, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris 75015, France
| | - Mitali Patel
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
- MRC Prion Unit, Institute of Prion Diseases, University College London, London W1W 7FF, UK
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Roly Megaw
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Princess Alexandra Eye Pavilion, Edinburgh EH3 9HA, UK
| | - Christos Gatsogiannis
- Center for Soft Nanoscience and Institute of Medical Physics and Biophysics, Münster 48149, Germany
| | - Mai A Mohamed
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
- Biochemistry Division, Chemistry Department, Faculty of Science, Zagazig University, Ash Sharqiyah 44519, Egypt
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Finn R Reinholt
- Core Facility for Electron Microscopy, Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Respiratory Sciences, University of Leicester, Leicester LE1 9HN, UK
| | - Chris O'Callaghan
- Centre for PCD Diagnosis and Research, Department of Respiratory Sciences, University of Leicester, Leicester LE1 9HN, UK
| | - Ketil Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo 0407, Norway
| | - Mathieu Bottier
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Estelle Escudier
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris 75012, France
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil 94000, France
| | - Suzanne Crowley
- Paediatric Department of Allergy and Lung Diseases, Oslo University Hospital, Oslo 0407, Norway
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Ethylin W Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029-6504, New York, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, NY 55905, USA
| | - Priti Kenia
- Department of Paediatric Respiratory Medicine, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), Paris 75015, France
- Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Université de Paris, Paris 75015, France
| | - Giacomo Maria Bacci
- Pediatric Ophthalmology Unit, Meyer Children's Hospital IRCCS, Florence 50139, Italy
| | - Claudia Calogero
- Pediatric Pulmonary Unit, Meyer Children's Hospital IRCCS, Florence 50139, Italy
| | - Viviana Palazzo
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence 50139, Italy
| | - Lucia Tiberi
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence 50139, Italy
| | | | - Andrew Rogers
- Respiratory Paediatrics, Royal Brompton Hospital, London SW3 6NP, UK
| | - Jennifer A Wambach
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Anne B Fulton
- Department of Ophthalmology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Margaret Kenna
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, WA 98015, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Alan Quigley
- Department of Paediatric Radiology, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
| | - Emma A Hall
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Diane M Cassidy
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jean-François Papon
- ENT Department, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris-Saclay University, Le Kremlin-Bicêtre 94270, France
| | - Laurent Pasquier
- Medical Genetics Department, CHU Pontchaillou, Rennes 35033, France
| | - Marlène S Murris
- Department of Pulmonology, Transplantation, and Cystic Fibrosis Centre, Larrey Hospital, Toulouse 31400, France
| | - James D Chalmers
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Claire Hogg
- Respiratory Paediatrics, Royal Brompton Hospital, London SW3 6NP, UK
| | - Kenneth A Macleod
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
| | - Don S Urquhart
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
- Department of Child Life and Health, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Stefan Unger
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
- Department of Child Life and Health, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Serge Amselem
- Molecular Genetics Laboratory, Sorbonne Université, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Armand Trousseau, Paris 75012, France
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris 75012, France
| | - Margaret W Leigh
- Department of Pediatrics, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Michael R Knowles
- Department of Medicine, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Münster, Münster 48149, Germany
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Shih-Chieh Ti
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris 75015, France
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris 75015, France
| | - Pleasantine Mill
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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17
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Zhang D, Zhao H, Li P, Wu X, Liang Y. Research Progress on Liposome Pulmonary Delivery of Mycobacterium tuberculosis Nucleic Acid Vaccine and Its Mechanism of Action. J Aerosol Med Pulm Drug Deliv 2024. [PMID: 38669118 DOI: 10.1089/jamp.2023.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024] Open
Abstract
Traditional vaccines have played an important role in the prevention and treatment of infectious diseases, but they still have problems such as low immunogenicity, poor stability, and difficulty in inducing lasting immune responses. In recent years, the nucleic acid vaccine has emerged as a relatively cheap and safe new vaccine. Compared with traditional vaccines, nucleic acid vaccine has some unique advantages, such as easy production and storage, scalability, and consistency between batches. However, the direct administration of naked nucleic acid vaccine is not ideal, and safer and more effective vaccine delivery systems are needed. With the rapid development of nanocarrier technology, the combination of gene therapy and nanodelivery systems has broadened the therapeutic application of molecular biology and the medical application of biological nanomaterials. Nanoparticles can be used as potential drug-delivery vehicles for the treatment of hereditary and infectious diseases. In addition, due to the advantages of lung immunity, such as rapid onset of action, good efficacy, and reduced adverse reactions, pulmonary delivery of nucleic acid vaccine has become a hot spot in the field of research. In recent years, lipid nanocarriers have become safe, efficient, and ideal materials for vaccine delivery due to their unique physical and chemical properties, which can effectively reduce the toxic side effects of drugs and achieve the effect of slow release and controlled release, and there have been a large number of studies using lipid nanocarriers to efficiently deliver target components into the body. Based on the delivery of tuberculosis (TB) nucleic acid vaccine by lipid carrier, this article systematically reviews the advantages and mechanism of liposomes as a nucleic acid vaccine delivery carrier, so as to lay a solid foundation for the faster and more effective development of new anti-TB vaccine delivery systems in the future.
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Affiliation(s)
- Danyang Zhang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
- Postgraduate Department of Heibei North University, Zhangjiakou, China
| | - Haimei Zhao
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
- Postgraduate Department of Heibei North University, Zhangjiakou, China
| | - Ping Li
- Postgraduate Department of Heibei North University, Zhangjiakou, China
| | - Xueqiong Wu
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Yan Liang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
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18
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Vilà-González M, Pinte L, Fradique R, Causa E, Kool H, Rodrat M, Morell CM, Al-Thani M, Porter L, Guo W, Maeshima R, Hart SL, McCaughan F, Granata A, Sheppard DN, Floto RA, Rawlins EL, Cicuta P, Vallier L. In vitro platform to model the function of ionocytes in the human airway epithelium. Respir Res 2024; 25:180. [PMID: 38664797 PMCID: PMC11045446 DOI: 10.1186/s12931-024-02800-7] [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: 09/03/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Pulmonary ionocytes have been identified in the airway epithelium as a small population of ion transporting cells expressing high levels of CFTR (cystic fibrosis transmembrane conductance regulator), the gene mutated in cystic fibrosis. By providing an infinite source of airway epithelial cells (AECs), the use of human induced pluripotent stem cells (hiPSCs) could overcome some challenges of studying ionocytes. However, the production of AEC epithelia containing ionocytes from hiPSCs has proven difficult. Here, we present a platform to produce hiPSC-derived AECs (hiPSC-AECs) including ionocytes and investigate their role in the airway epithelium. METHODS hiPSCs were differentiated into lung progenitors, which were expanded as 3D organoids and matured by air-liquid interface culture as polarised hiPSC-AEC epithelia. Using CRISPR/Cas9 technology, we generated a hiPSCs knockout (KO) for FOXI1, a transcription factor that is essential for ionocyte specification. Differences between FOXI1 KO hiPSC-AECs and their wild-type (WT) isogenic controls were investigated by assessing gene and protein expression, epithelial composition, cilia coverage and motility, pH and transepithelial barrier properties. RESULTS Mature hiPSC-AEC epithelia contained basal cells, secretory cells, ciliated cells with motile cilia, pulmonary neuroendocrine cells (PNECs) and ionocytes. There was no difference between FOXI1 WT and KO hiPSCs in terms of their capacity to differentiate into airway progenitors. However, FOXI1 KO led to mature hiPSC-AEC epithelia without ionocytes with reduced capacity to produce ciliated cells. CONCLUSION Our results suggest that ionocytes could have role beyond transepithelial ion transport by regulating epithelial properties and homeostasis in the airway epithelium.
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Affiliation(s)
- Marta Vilà-González
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Cell Therapy and Tissue Engineering Group, Research Institute of Health Sciences (IUNICS), University of Balearic Islands, Palma, 07122, Spain.
- Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain.
| | - Laetitia Pinte
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ricardo Fradique
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Erika Causa
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Heleen Kool
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mayuree Rodrat
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Center of Research and Development for Biomedical Instrumentation, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Carola Maria Morell
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- IRCCS Humanitas Research Hospital, via Manzoni 56, Rozzano, Milan, 20089, Italy
| | - Maha Al-Thani
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Linsey Porter
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Wenrui Guo
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Ruhina Maeshima
- Genetics and Genome Medicine Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Stephen L Hart
- Genetics and Genome Medicine Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Frank McCaughan
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Alessandra Granata
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, CB2 0QH, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital NHS Foundation Trust, Cambridge, CB2 0AY, UK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité, Augustenburger Platz 1, 13353, Berlin, DE, Germany.
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.
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19
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Wu M, Chen JH. CFTR dysfunction leads to defective bacterial eradication on cystic fibrosis airways. Front Physiol 2024; 15:1385661. [PMID: 38699141 PMCID: PMC11063615 DOI: 10.3389/fphys.2024.1385661] [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: 02/16/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel by genetic mutations causes the inherited disease cystic fibrosis (CF). CF lung disease that involves multiple disorders of epithelial function likely results from loss of CFTR function as an anion channel conducting chloride and bicarbonate ions and its function as a cellular regulator modulating the activity of membrane and cytosol proteins. In the absence of CFTR activity, abundant mucus accumulation, bacterial infection and inflammation characterize CF airways, in which inflammation-associated tissue remodeling and damage gradually destroys the lung. Deciphering the link between CFTR dysfunction and bacterial infection in CF airways may reveal the pathogenesis of CF lung disease and guide the development of new treatments. Research efforts towards this goal, including high salt, low volume, airway surface liquid acidosis and abnormal mucus hypotheses are critically reviewed.
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Affiliation(s)
| | - Jeng-Haur Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
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20
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McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [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: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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21
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Gao F, Lin W, Wang X, Liao M, Zhang M, Qin N, Chen X, Xia L, Chen Q, Sha O. Identification of receptors and factors associated with human coronaviruses in the oral cavity using single-cell RNA sequencing. Heliyon 2024; 10:e28280. [PMID: 38560173 PMCID: PMC10981076 DOI: 10.1016/j.heliyon.2024.e28280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) ravaged the world, and Coronavirus Disease 2019 (COVID-19) exhibited highly prevalent oral symptoms that had significantly impacted the lives of affected patients. However, the involvement of four human coronavirus (HCoVs), namely SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-229E, in oral cavity infections remained poorly understood. We integrated single-cell RNA sequencing (scRNA-seq) data of seven human oral tissues through consistent normalization procedure, including minor salivary gland (MSG), parotid gland (PG), tongue, gingiva, buccal, periodontium and pulp. The Seurat, scDblFinder, Harmony, SingleR, Ucell and scCancer packages were comprehensively used for analysis. We identified specific cell clusters and generated expression profiles of SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) in seven oral regions, providing direction for predicting the tropism of four HCoVs for oral tissues, as well as for dental clinical treatment. Based on our analysis, it appears that various SCARFs, including ACE2, ASGR1, KREMEN1, DPP4, ANPEP, CD209, CLEC4G/M, TMPRSS family proteins (including TMPRSS2, TMPRSS4, and TMPRSS11A), and FURIN, are expressed at low levels in the oral cavity. Conversely, BSG, CTSB, and CTSL exhibit enrichment in oral tissues. Our study also demonstrates widespread expression of restriction factors, particularly IFITM1-3 and LY6E, in oral cells. Additionally, some replication, assembly, and trafficking factors appear to exhibit broad oral tissues expression patterns. Overall, the oral cavity could potentially serve as a high-risk site for SARS-CoV-2 infection, while displaying a comparatively lower degree of susceptibility towards other HCoVs (including SARS-CoV, MERS-CoV and HCoV-229E). Specifically, MSG, tongue, and gingiva represent potential sites of vulnerability for four HCoVs infection, with the MSG exhibiting a particularly high susceptibility. However, the expression patterns of SCARFs in other oral sites demonstrate relatively intricate and may only be specifically associated with SARS-CoV-2 infection. Our study sheds light on the mechanisms of HCoVs infection in the oral cavity as well as gains insight into the characteristics and distribution of possible HCoVs target cells in oral tissues, providing potential therapeutic targets for HCoVs infection in the oral cavity.
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Affiliation(s)
- Feng Gao
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
| | - Weiming Lin
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xia Wang
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- The Chinese University of Hong Kong Shenzhen, School of Medicine, Shenzhen, China
| | - Mingfeng Liao
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Mingxia Zhang
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Nianhong Qin
- Department of Stomatology, Shenzhen People's Hospital, Shenzhen, China
| | - Xianxiong Chen
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Lixin Xia
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Ou Sha
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
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22
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AlBloushi S, Al-Ahmad M. Exploring the immunopathology of type 2 inflammatory airway diseases. Front Immunol 2024; 15:1285598. [PMID: 38680486 PMCID: PMC11045947 DOI: 10.3389/fimmu.2024.1285598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/22/2024] [Indexed: 05/01/2024] Open
Abstract
Significant advancements have been achieved in understanding the roles of different immune cells, as well as cytokines and chemokines, in the pathogenesis of eosinophilic airway conditions. This review examines the pathogenesis of Chronic Rhinosinusitis with Nasal Polyps (CRSwNP), marked by complex immune dysregulation, with major contributions from type 2 inflammation and dysfunctional airway epithelium. The presence of eosinophils and the role of T-cell subsets, particularly an imbalance between Treg and Th17 cells, are crucial to the disease's pathogenesis. The review also investigates the pathogenesis of eosinophilic asthma, a unique asthma subtype. It is characterized by inflammation and high eosinophil levels, with eosinophils playing a pivotal role in triggering type 2 inflammation. The immune response involves Th2 cells, eosinophils, and IgE, among others, all activated by genetic and environmental factors. The intricate interplay among these elements, chemokines, and innate lymphoid cells results in airway inflammation and hyper-responsiveness, contributing to the pathogenesis of eosinophilic asthma. Another scope of this review is the pathogenesis of Eosinophilic Granulomatosis with Polyangiitis (EGPA); a complex inflammatory disease that commonly affects the respiratory tract and small to medium-sized blood vessels. It is characterized by elevated eosinophil levels in blood and tissues. The pathogenesis involves the activation of adaptive immune responses by antigens leading to T and B cell activation and eosinophil stimulation, which causes tissue and vessel damage. On the other hand, Allergic Bronchopulmonary Aspergillosis (ABPA) is a hypersensitive response that occurs when the airways become colonized by aspergillus fungus, with the pathogenesis involving activation of Th2 immune responses, production of IgE antibodies, and eosinophilic action leading to bronchial inflammation and subsequent lung damage. This analysis scrutinizes how an imbalanced immune system contributes to these eosinophilic diseases. The understanding derived from this assessment can steer researchers toward designing new potential therapeutic targets for efficient control of these disorders.
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Affiliation(s)
| | - Mona Al-Ahmad
- Al-Rashed Allergy Center, Ministry of Health, Kuwait City, Kuwait
- Microbiology Department, College of Medicine, Kuwait University, Kuwait City, Kuwait
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23
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Feng DC, Zhu WZ, Wang J, Li DX, Shi X, Xiong Q, You J, Han P, Qiu S, Wei Q, Yang L. The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy. Mil Med Res 2024; 11:21. [PMID: 38605399 PMCID: PMC11007901 DOI: 10.1186/s40779-024-00526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.
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Affiliation(s)
- De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Division of Surgery & Interventional Science, University College London, London, WC1E 6BT, UK.
| | - Wei-Zhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiao Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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24
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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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25
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Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, Zappia L, Palla G, Lewis W, Dimitrov D, Vinyard ME, Magruder DS, Andersson A, Dann E, Qin Q, Otto DJ, Klein M, Botvinnik OB, Deconinck L, Waldrant K, Bloom JM, Pisco AO, Saez-Rodriguez J, Wulsin D, Pinello L, Saeys Y, Theis FJ, Krishnaswamy S. Defining and benchmarking open problems in single-cell analysis. RESEARCH SQUARE 2024:rs.3.rs-4181617. [PMID: 38645152 PMCID: PMC11030530 DOI: 10.21203/rs.3.rs-4181617/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.
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Affiliation(s)
- Malte D Luecken
- Institute of computational Biology, Helmholtz Munich, Neuherberg, Germany
- Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | | | - Robrecht Cannoodt
- Data Intuitive, Lebbeke, Belgium
- Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
| | - Daniel C Strobl
- Institute of computational Biology, Helmholtz Munich, Neuherberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University
| | - Luke Zappia
- Institute of computational Biology, Helmholtz Munich, Neuherberg, Germany
- Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
| | - Giovanni Palla
- Institute of computational Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Wesley Lewis
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Michael E Vinyard
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - D S Magruder
- Department of Computer Science, Yale University, New Haven CT, USA
| | - Alma Andersson
- Genentech Inc
- Royal Institute of Technology (KTH), Gene Technology
- Science for Life Laboratory (SciLifeLab)
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Qian Qin
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dominik J Otto
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | | | - Olga Borisovna Botvinnik
- Data Sciences Platform, Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158
- Bridge Bio Pharma, 3160 Porter Drive, Suite 250, Palo Alto, CA, 94304
| | - Louise Deconinck
- Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
| | | | | | - Angela Oliveira Pisco
- Data Sciences Platform, Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158
- Insitro, South San Francisco
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | | | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
- VIB Center for AI & Computational Biology (VIB.AI), Gent, Belgium
| | - Fabian J Theis
- Institute of computational Biology, Helmholtz Munich, Neuherberg, Germany
- Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
- Cellular Genetics Programme, Wellcome Sanger Institute, Hinxton, UK (associated faculty)
| | - Smita Krishnaswamy
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Department of Computer Science, Yale University, New Haven CT, USA
- Department of Genetics, Yale University, New Haven CT, USA
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26
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Barr J, Xu L, Li R, Verheyden J, Sun X. Airway Microfold Cells Emerge in the Post-Influenza Lung. Am J Respir Cell Mol Biol 2024; 70:322-325. [PMID: 38127584 DOI: 10.1165/rcmb.2023-0351le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Justinn Barr
- University of California, San Diego La Jolla, California
| | - Le Xu
- University of California, San Diego La Jolla, California
| | - Rongbo Li
- University of California, San Diego La Jolla, California
| | | | - Xin Sun
- University of California, San Diego La Jolla, California
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27
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Rinderknecht CH, Ning M, Wu C, Wilson MS, Gampe C. Designing inhaled small molecule drugs for severe respiratory diseases: an overview of the challenges and opportunities. Expert Opin Drug Discov 2024; 19:493-506. [PMID: 38407117 DOI: 10.1080/17460441.2024.2319049] [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: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
INTRODUCTION Inhaled drugs offer advantages for the treatment of respiratory diseases over oral drugs by delivering the drug directly to the lung, thus improving the therapeutic index. There is an unmet medical need for novel therapies for lung diseases, exacerbated by a multitude of challenges for the design of inhaled small molecule drugs. AREAS COVERED The authors review the challenges and opportunities for the design of inhaled drugs for respiratory diseases with a focus on new target discovery, medicinal chemistry, and pharmacokinetic, pharmacodynamic, and toxicological evaluation of drug candidates. EXPERT OPINION Inhaled drug discovery is facing multiple unique challenges. Novel biological targets are scarce, as is the guidance for medicinal chemistry teams to design compounds with inhalation-compatible features. It is exceedingly difficult to establish a PK/PD relationship given the complexity of pulmonary PK and the impact of physical properties of the drug substance on PK. PK, PD and toxicology studies are technically challenging and require large amounts of drug substance. Despite the current challenges, the authors foresee that the design of inhaled drugs will be facilitated in the future by our increasing understanding of pathobiology, emerging medicinal chemistry guidelines, advances in drug formulation, PBPK models, and in vitro toxicology assays.
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Affiliation(s)
| | - Miaoran Ning
- Drug Metabolism and Pharmacokinetics, gRED, Genentech, South San Francisco, CA, USA
| | - Connie Wu
- Development Sciences Safety Assessment, Genentech, South San Francisco, CA, USA
| | - Mark S Wilson
- Discovery Immunology, gRED, Genentech, South San Francisco, CA, USA
| | - Christian Gampe
- Discovery Chemistry, gRED, Genentech, South San Francisco, CA, USA
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28
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Han S. Unveiling an Important New Cell Type in the Lung: Microfold Cells. Am J Respir Cell Mol Biol 2024; 70:235-236. [PMID: 38301262 DOI: 10.1165/rcmb.2024-0002ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024] Open
Affiliation(s)
- SeungHye Han
- Department of Medicine Northwestern University Chicago, Illinois
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29
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Weine E, Carbonetto P, Stephens M. Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586420. [PMID: 38585920 PMCID: PMC10996495 DOI: 10.1101/2024.03.23.586420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Motivated by theoretical and practical issues that arise when applying Principal Components Analysis (PCA) to count data, Townes et al introduced "Poisson GLM-PCA", a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (RNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call "Alternating Poisson Regression" (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient, and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large single-cell RNA-seq data sets. We illustrate the benefits of this approach in two published single-cell RNA-seq data sets. The new algorithms are implemented in an R package, fastglmpca.
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Affiliation(s)
- Eric Weine
- Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Statistics, University of Chicago, Chicago, IL 60637, USA
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30
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Abay T, Stickels RR, Takizawa MT, Nalbant BN, Hsieh YH, Hwang S, Snopkowski C, Yu KKH, Abou-Mrad Z, Tabar V, Ludwig LS, Chaligné R, Satpathy AT, Lareau CA. Transcript-specific enrichment enables profiling rare cell states via scRNA-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587039. [PMID: 38586040 PMCID: PMC10996707 DOI: 10.1101/2024.03.27.587039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing (scRNA-seq) identifies many rare populations of interest that express specific marker transcript combinations, traditional flow sorting limits our ability to enrich these populations for further profiling, including requiring cell surface markers with high-fidelity antibodies. Additionally, many single-cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. To address these limitations, we describe Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay that enables scRNA-seq profiling of subpopulations from complex cellular mixtures defined by the presence or absence of specific RNA transcripts. Across immune populations (n = 141,227 cells) and fresh-frozen and formalin-fixed paraffin-embedded brain tissue (n = 29,522 nuclei), we demonstrate the sorting logic that can be used to enrich for cell populations via RNA-based cytometry followed by high-throughput scRNA-seq. Our approach provides a rational, programmable method for studying rare populations identified by one or more marker transcripts.
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Affiliation(s)
- Tsion Abay
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford CA, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Robert R. Stickels
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford CA, USA
| | - Meril T. Takizawa
- Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benan N. Nalbant
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Hsin Hsieh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Charité Universitätsmedizin Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Sidney Hwang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford CA, USA
| | - Catherine Snopkowski
- Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenny Kwok Hei Yu
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zaki Abou-Mrad
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leif S. Ludwig
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Ronan Chaligné
- Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ansuman T. Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Caleb A. Lareau
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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31
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Sackville MA, Gillis JA, Brauner CJ. The origins of gas exchange and ion regulation in fish gills: evidence from structure and function. J Comp Physiol B 2024:10.1007/s00360-024-01545-5. [PMID: 38530435 DOI: 10.1007/s00360-024-01545-5] [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: 12/18/2023] [Revised: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 03/28/2024]
Abstract
Gill function in gas exchange and ion regulation has played key roles in the evolution of fishes. In this review, we summarize data from the fields of palaeontology, developmental biology and comparative physiology for when and how the gills first acquired these functions. Data from across disciplines strongly supports a stem vertebrate origin for gas exchange structures and function at the gills with the emergence of larger, more active fishes. However, the recent discovery of putative ionocytes in extant cephalochordates and hemichordates suggests that ion regulation at gills might have originated much earlier than gas exchange, perhaps in the ciliated pharyngeal arches in the last common ancestor of deuterostomes. We hypothesize that the ancestral form of ion regulation served a filter-feeding function in the ciliated pharyngeal arches, and was later coopted in vertebrates to regulate extracellular ion and acid-base balance. We propose that future research should explore ionocyte homology and function across extant deuterostomes to test this hypothesis and others in order to determine the ancestral origins of ion regulation in fish gills.
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Affiliation(s)
| | - J Andrew Gillis
- Bay Paul Centre, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Colin J Brauner
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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32
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Strine MS, Fagerberg E, Darcy PW, Barrón GM, Filler RB, Alfajaro MM, D'Angelo-Gavrish N, Wang F, Graziano VR, Menasché BL, Damo M, Wang YT, Howitt MR, Lee S, Joshi NS, Mucida D, Wilen CB. Intestinal tuft cell immune privilege enables norovirus persistence. Sci Immunol 2024; 9:eadi7038. [PMID: 38517952 DOI: 10.1126/sciimmunol.adi7038] [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: 05/12/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
The persistent murine norovirus strain MNVCR6 is a model for human norovirus and enteric viral persistence. MNVCR6 causes chronic infection by directly infecting intestinal tuft cells, rare chemosensory epithelial cells. Although MNVCR6 induces functional MNV-specific CD8+ T cells, these lymphocytes fail to clear infection. To examine how tuft cells promote immune escape, we interrogated tuft cell interactions with CD8+ T cells by adoptively transferring JEDI (just EGFP death inducing) CD8+ T cells into Gfi1b-GFP tuft cell reporter mice. Unexpectedly, some intestinal tuft cells partially resisted JEDI CD8+ T cell-mediated killing-unlike Lgr5+ intestinal stem cells and extraintestinal tuft cells-despite seemingly normal antigen presentation. When targeting intestinal tuft cells, JEDI CD8+ T cells predominantly adopted a T resident memory phenotype with decreased effector and cytotoxic capacity, enabling tuft cell survival. JEDI CD8+ T cells neither cleared nor prevented MNVCR6 infection in the colon, the site of viral persistence, despite targeting a virus-independent antigen. Ultimately, we show that intestinal tuft cells are relatively resistant to CD8+ T cells independent of norovirus infection, representing an immune-privileged niche that can be leveraged by enteric microbes.
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Affiliation(s)
- Madison S Strine
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Fagerberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick W Darcy
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
| | - Gabriel M Barrón
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Fang Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R Graziano
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, USA
| | - Bridget L Menasché
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Martina Damo
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ya-Ting Wang
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Tsinghua University School of Medicine, Beijing, China
| | - Michael R Howitt
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Sanghyun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nikhil S Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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33
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Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O’Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal viral infection rewires the tissue-scale memory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.539887. [PMID: 38562902 PMCID: PMC10983857 DOI: 10.1101/2023.05.11.539887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission. Recent work has started to clarify the independent responses of epithelial, myeloid, and lymphoid cells to viral infection in the nasal mucosa, but their spatiotemporal coordination and relative contributions remain unclear. Furthermore, understanding whether and how primary infection shapes tissue-scale memory responses to secondary challenge is critical for the rational design of nasal-targeting therapeutics and vaccines. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in cell type, subset, and state composition over time. Type I Interferon (IFN)-responsive neutrophils appeared 2 days post infection (dpi) and preceded transient IFN-responsive/cycling epithelial cell responses 5 dpi, which coincided with broader antiviral monocyte and NK cell accumulation. By 8 dpi, monocyte-derived macrophages (MDMs) expressing Cxcl9 and Cxcl16 arose alongside effector cytotoxic CD8 and Ifng-expressing CD4 T cells. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16-CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses upon rechallenge.
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Affiliation(s)
- Samuel W. Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M. Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O’Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H. von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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34
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Martins LR, Sieverling L, Michelhans M, Schiller C, Erkut C, Grünewald TGP, Triana S, Fröhling S, Velten L, Glimm H, Scholl C. Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung. Nat Commun 2024; 15:2246. [PMID: 38472236 DOI: 10.1038/s41467-024-46469-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.
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Affiliation(s)
- Leila R Martins
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| | - Lina Sieverling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
| | - Michelle Michelhans
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Chiara Schiller
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | - Cihan Erkut
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas G P Grünewald
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, DKFZ, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sergio Triana
- Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Broad Institute of Harvard and MIT, Cambridge, USA
- Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
- DKTK, partner site Dresden, Dresden, Germany
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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35
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López-Posadas R, Bagley DC, Pardo-Pastor C, Ortiz-Zapater E. The epithelium takes the stage in asthma and inflammatory bowel diseases. Front Cell Dev Biol 2024; 12:1258859. [PMID: 38529406 PMCID: PMC10961468 DOI: 10.3389/fcell.2024.1258859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
The epithelium is a dynamic barrier and the damage to this epithelial layer governs a variety of complex mechanisms involving not only epithelial cells but all resident tissue constituents, including immune and stroma cells. Traditionally, diseases characterized by a damaged epithelium have been considered "immunological diseases," and research efforts aimed at preventing and treating these diseases have primarily focused on immuno-centric therapeutic strategies, that often fail to halt or reverse the natural progression of the disease. In this review, we intend to focus on specific mechanisms driven by the epithelium that ensure barrier function. We will bring asthma and Inflammatory Bowel Diseases into the spotlight, as we believe that these two diseases serve as pertinent examples of epithelium derived pathologies. Finally, we will argue how targeting the epithelium is emerging as a novel therapeutic strategy that holds promise for addressing these chronic diseases.
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Affiliation(s)
- Rocío López-Posadas
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universtiy Eralngen-Nürnberg, Erlangen, Germany
| | - Dustin C. Bagley
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Carlos Pardo-Pastor
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- Instituto Investigación Hospital Clínico-INCLIVA, Valencia, Spain
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36
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Farinha CM, Santos L, Ferreira JF. Cell type-specific regulation of CFTR trafficking-on the verge of progress. Front Cell Dev Biol 2024; 12:1338892. [PMID: 38505263 PMCID: PMC10949533 DOI: 10.3389/fcell.2024.1338892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein is a complex process that starts with its biosynthesis and folding in the endoplasmic reticulum. Exit from the endoplasmic reticulum (ER) is coupled with the acquisition of a compact structure that can be processed and traffic through the secretory pathway. Once reaching its final destination-the plasma membrane, CFTR stability is regulated through interaction with multiple protein partners that are involved in its post-translation modification, connecting the channel to several signaling pathways. The complexity of the process is further boosted when analyzed in the context of the airway epithelium. Recent advances have characterized in detail the different cell types that compose the surface epithelium and shifted the paradigm on which cells express CFTR and on their individual and combined contribution to the total expression (and function) of this chloride/bicarbonate channel. Here we review CFTR trafficking and its relationship with the knowledge on the different cell types of the airway epithelia. We explore the crosstalk between these two areas and discuss what is still to be clarified and how this can be used to develop more targeted therapies for CF.
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Affiliation(s)
- Carlos M. Farinha
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
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37
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Yao Y, Miethe S, Kattler K, Colakoglu B, Walter J, Schneider-Daum N, Herr C, Garn H, Ritzmann F, Bals R, Beisswenger C. Mutual Regulation of Transcriptomes between Murine Pneumocytes and Fibroblasts Mediates Alveolar Regeneration in Air-Liquid Interface Cultures. Am J Respir Cell Mol Biol 2024; 70:203-214. [PMID: 38051640 DOI: 10.1165/rcmb.2023-0078oc] [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: 03/02/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Alveolar type 2 and club cells are part of the stem cell niche of the lung and their differentiation is required for pulmonary homeostasis and tissue regeneration. A disturbed crosstalk between fibroblasts and epithelial cells contributes to the loss of lung structure in chronic lung diseases. Therefore, it is important to understand how fibroblasts and lung epithelial cells interact during regeneration. Here, we analyzed the interaction of fibroblasts and the alveolar epithelium modeled in air-liquid interface cultures. Single-cell transcriptomics showed that cocultivation with fibroblasts leads to increased expression of type 2 markers in pneumocytes, activation of regulons associated with the maintenance of alveolar type 2 cells (e.g., Etv5), and transdifferentiation of club cells toward pneumocytes. This was accompanied by an intensified transepithelial barrier. Vice versa, the activation of NF-κB pathways and the CEBPB regulon and the expression of IL-6 and other differentiation factors (e.g., fibroblast growth factors) were increased in fibroblasts cocultured with epithelial cells. Recombinant IL-6 enhanced epithelial barrier formation. Therefore, in our coculture model, regulatory loops were identified by which lung epithelial cells mediate regeneration and differentiation of the alveolar epithelium in a cooperative manner with the mesenchymal compartment.
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Affiliation(s)
- Yiwen Yao
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
- Department of Clinical Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sarah Miethe
- Translational Inflammation Research Division and Core Facility for Single Cell Multiomics and
- German Center for Lung Research (DZL), Philipps University of Marburg, Marburg, Germany
- The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Kathrin Kattler
- Department of Genetics and Epigenetics, Saarland University, Homburg, Germany
| | - Betül Colakoglu
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Homburg, Germany
| | - Nicole Schneider-Daum
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
| | - Holger Garn
- Translational Inflammation Research Division and Core Facility for Single Cell Multiomics and
- German Center for Lung Research (DZL), Philipps University of Marburg, Marburg, Germany
- The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Felix Ritzmann
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Christoph Beisswenger
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine and
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Barrera-Lopez JF, Cumplido-Laso G, Olivera-Gomez M, Garrido-Jimenez S, Diaz-Chamorro S, Mateos-Quiros CM, Benitez DA, Centeno F, Mulero-Navarro S, Roman AC, Carvajal-Gonzalez JM. Early Atf4 activity drives airway club and goblet cell differentiation. Life Sci Alliance 2024; 7:e202302284. [PMID: 38176727 PMCID: PMC10766780 DOI: 10.26508/lsa.202302284] [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: 07/19/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
Activating transcription factor 4 (Atf4), which is modulated by the protein kinase RNA-like ER kinase (PERK), is a stress-induced transcription factor responsible for controlling the expression of a wide range of adaptive genes, enabling cells to withstand stressful conditions. However, the impact of the Atf4 signaling pathway on airway regeneration remains poorly understood. In this study, we used mouse airway epithelial cell culture models to investigate the role of PERK/Atf4 in respiratory tract differentiation. Through pharmacological inhibition and silencing of ATF4, we uncovered the crucial involvement of PERK/Atf4 in the differentiation of basal stem cells, leading to a reduction in the number of secretory cells. ChIP-seq analysis revealed direct binding of ATF4 to regulatory elements of genes associated with osteoblast differentiation and secretory cell function. Our findings provide valuable insights into the role of ATF4 in airway epithelial differentiation and its potential involvement in innate immune responses and cellular adaptation to stress.
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Affiliation(s)
- Juan F Barrera-Lopez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Guadalupe Cumplido-Laso
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Marcos Olivera-Gomez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sergio Garrido-Jimenez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Selene Diaz-Chamorro
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Clara M Mateos-Quiros
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Dixan A Benitez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Francisco Centeno
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Angel C Roman
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Jose M Carvajal-Gonzalez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
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Schappe MS, Brinn PA, Joshi NR, Greenberg RS, Min S, Alabi AA, Zhang C, Liberles SD. A vagal reflex evoked by airway closure. Nature 2024; 627:830-838. [PMID: 38448588 PMCID: PMC10972749 DOI: 10.1038/s41586-024-07144-2] [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: 06/21/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Airway integrity must be continuously maintained throughout life. Sensory neurons guard against airway obstruction and, on a moment-by-moment basis, enact vital reflexes to maintain respiratory function1,2. Decreased lung capacity is common and life-threatening across many respiratory diseases, and lung collapse can be acutely evoked by chest wall trauma, pneumothorax or airway compression. Here we characterize a neuronal reflex of the vagus nerve evoked by airway closure that leads to gasping. In vivo vagal ganglion imaging revealed dedicated sensory neurons that detect airway compression but not airway stretch. Vagal neurons expressing PVALB mediate airway closure responses and innervate clusters of lung epithelial cells called neuroepithelial bodies (NEBs). Stimulating NEBs or vagal PVALB neurons evoked gasping in the absence of airway threats, whereas ablating NEBs or vagal PVALB neurons eliminated gasping in response to airway closure. Single-cell RNA sequencing revealed that NEBs uniformly express the mechanoreceptor PIEZO2, and targeted knockout of Piezo2 in NEBs eliminated responses to airway closure. NEBs were dispensable for the Hering-Breuer inspiratory reflex, which indicated that discrete terminal structures detect airway closure and inflation. Similar to the involvement of Merkel cells in touch sensation3,4, NEBs are PIEZO2-expressing epithelial cells and, moreover, are crucial for an aspect of lung mechanosensation. These findings expand our understanding of neuronal diversity in the airways and reveal a dedicated vagal pathway that detects airway closure to help preserve respiratory function.
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Affiliation(s)
- Michael S Schappe
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Philip A Brinn
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Narendra R Joshi
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rachel S Greenberg
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Soohong Min
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - AbdulRasheed A Alabi
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Chuchu Zhang
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen D Liberles
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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Shiratsuchi G, Konishi S, Yano T, Yanagihashi Y, Nakayama S, Katsuno T, Kashihara H, Tanaka H, Tsukita K, Suzuki K, Herawati E, Watanabe H, Hirai T, Yagi T, Kondoh G, Gotoh S, Tamura A, Tsukita S. Dual-color live imaging unveils stepwise organization of multiple basal body arrays by cytoskeletons. EMBO Rep 2024; 25:1176-1207. [PMID: 38316902 PMCID: PMC10933483 DOI: 10.1038/s44319-024-00066-0] [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: 05/03/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 02/07/2024] Open
Abstract
For mucociliary clearance of pathogens, tracheal multiciliated epithelial cells (MCCs) organize coordinated beating of cilia, which originate from basal bodies (BBs) with basal feet (BFs) on one side. To clarify the self-organizing mechanism of coordinated intracellular BB-arrays composed of a well-ordered BB-alignment and unidirectional BB-orientation, determined by the direction of BB to BF, we generated double transgenic mice with GFP-centrin2-labeled BBs and mRuby3-Cep128-labeled BFs for long-term, high-resolution, dual-color live-cell imaging in primary-cultured tracheal MCCs. At early timepoints of MCC differentiation, BB-orientation and BB-local alignment antecedently coordinated in an apical microtubule-dependent manner. Later during MCC differentiation, fluctuations in BB-orientation were restricted, and locally aligned BB-arrays were further coordinated to align across the entire cell (BB-global alignment), mainly in an apical intermediate-sized filament-lattice-dependent manner. Thus, the high coordination of the BB-array was established for efficient mucociliary clearance as the primary defense against pathogen infection, identifying apical cytoskeletons as potential therapeutic targets.
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Affiliation(s)
- Gen Shiratsuchi
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Satoshi Konishi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Tomoki Yano
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | | | - Shogo Nakayama
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Tatsuya Katsuno
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Center for Anatomical Studies, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroo Tanaka
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- School of Medicine, Teikyo University, Tokyo, Japan
| | - Kazuto Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koya Suzuki
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Elisa Herawati
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Surakarta, Central Java, Indonesia
| | - Hitomi Watanabe
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Yagi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Gen Kondoh
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shimpei Gotoh
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Atsushi Tamura
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
- School of Medicine, Teikyo University, Tokyo, Japan.
| | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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41
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024:10.1038/s41592-024-02191-z. [PMID: 38366243 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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42
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Conrad C, Magnen M, Tsui J, Wismer H, Naser M, Venkataramani U, Samad B, Cleary SJ, Qiu L, Tian JJ, De Giovanni M, Mende N, Passegue E, Laurenti E, Combes AJ, Looney MR. Decoding functional hematopoietic progenitor cells in the adult human lung. RESEARCH SQUARE 2024:rs.3.rs-3576483. [PMID: 38077002 PMCID: PMC10705601 DOI: 10.21203/rs.3.rs-3576483/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The bone marrow is the main site of blood cell production in adults, however, rare pools of hematopoietic stem and progenitor cells with self-renewal and differentiation potential have been found in extramedullary organs. The lung is primarily known for its role in gas exchange but has recently been described as a site of blood production in mice. Here, we show that functional hematopoietic precursors reside in the extravascular spaces of the human lung, at a frequency similar to the bone marrow, and are capable of proliferation and engraftment. The organ-specific gene signature of pulmonary and medullary CD34+ hematopoietic progenitors indicates greater baseline activation of immune, megakaryocyte/platelet and erythroid-related pathways in lung progenitors. Spatial transcriptomics mapped blood progenitors in the lung to a vascular-rich alveolar interstitium niche. These results identify the lung as a pool for uniquely programmed blood stem and progenitor cells with the potential to support hematopoiesis in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Nicole Mende
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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Hoki M, Yamada Y, Hiratomo E, Hirata M, Takeuchi Y, Yoshimatsu M, Kikuchi M, Kishimoto Y, Marx A, Haga H. Expression of FOXI1 and POU2F3 varies among different salivary gland neoplasms and is higher in Warthin tumor. Discov Oncol 2024; 15:36. [PMID: 38358561 PMCID: PMC10869675 DOI: 10.1007/s12672-024-00892-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
PURPOSE Salivary gland tumors are histologically diverse. Ionocytes and tuft cells, rare epithelial cells found in normal salivary glands, might be associated with salivary tumors. Here, we explored the expression of FOXI1 and POU2F3, master regulators of ionocytes and tuft cells, respectively, for common salivary neoplasms using immunohistochemistry. METHODS We analyzed normal salivary tissues and nine salivary gland tumors; Warthin tumors (WT), pleomorphic adenomas (PA), basal cell adenomas, and oncocytomas were benign, whereas mucoepidermoid, adenoid cystic, acinic cell, salivary duct carcinomas, and polymorphous adenocarcinomas were malignant. RESULTS Normal salivary glands contained a few FOXI1- and POU2F3-positive cells in the ducts instead of the acini, consistent with ionocytes and tuft cells, respectively. Among the benign tumors, only WTs and PAs consistently expressed FOXI1 (10/10 and 9/10, respectively). The median H-score of WTs was significantly higher than that of PAs (17.5 vs. 4, P = 0.01). While WTs and PAs harbored POU2F3-positive cells (10/10 and 9/10, respectively), the median H-score was higher in WTs than in PAs (10.5 vs 4, respectively). Furthermore, WTs exhibited a unique staining pattern of FOXI1- and POU2F3-positive cells, which were present in luminal and abluminal locations, respectively. Whereas none of the malignant tumors expressed FOXI1, only adenoid cystic carcinoma consistently expressed POU2F3 (5/5), with a median H-score of 4. CONCLUSION The expression patterns of the characteristic transcription factors found in ionocytes and tuft cells vary among salivary gland tumor types and are higher in WT, which might be relevant for understanding and diagnosing salivary gland neoplasms.
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Affiliation(s)
- Masahito Hoki
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yosuke Yamada
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Emi Hiratomo
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yasuhide Takeuchi
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Masayoshi Yoshimatsu
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masahiro Kikuchi
- Department of Otolaryngology-Head & Neck Surgery, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Yo Kishimoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexander Marx
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
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Kudrna K, Staab EB, Eilers E, Thomes P, Maurya S, Brody SL, Wyatt TA, Bailey KL, Dickinson JD. mTOR signaling regulates aberrant epithelial cell proliferative and migratory behaviors characteristic of airway mucous metaplasia in asthma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579905. [PMID: 38405874 PMCID: PMC10888751 DOI: 10.1101/2024.02.12.579905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In asthma, the airway epithelium is hyperplastic, hypertrophied, and lined with numerous large MUC5AC-containing goblet cells (GC). Furthermore, the normal epithelial architecture is disorganized with numerous, what we here describe as, ectopic goblet cells (eGC) deep within the thickened epithelial layer disconnected from the lumenal surface. mTOR is a highly conserved pathway that regulates cell size and proliferation. We hypothesized that the balance between mTOR and autophagy signaling regulates key features of the asthma epithelial layer. Airway histological sections from subjects with asthma had increased frequency of eGC and increased levels of mTOR phosphorylation target-Ribosomal S6. Using human airway epithelial cells (hAECs) with IL-13 stimulation and timed withdrawal to stimulate resolution, we found that multiple key downstream phosphorylation targets downstream from the mTOR complex were increased during early IL-13-mediated mucous metaplasia, and then significantly declined during resolution. The IL-13-mediated changes in mTOR signaling were paralleled by morphologic changes with airway epithelial hypertrophy, hyperplasia, and frequency of eGC. We then examined the relationship between mTOR and autophagy using mice deficient in autophagy protein Atg16L1. Despite having increased cytoplasmic mucins, mouse AECs from Atg16L1 deficient mice had no significant difference in mTOR downstream signaling. mTOR inhibition with rapamycin led to a loss of IL-13-mediated epithelial hypertrophy, hyperplasia, ectopic GC distribution, and reduction in cytoplasmic MUC5AC levels. mTOR inhibition was also associated with a reduction in aberrant IL-13-mediated hAEC proliferation and migration. Our findings demonstrate that mTOR signaling is associated with mucous metaplasia and is crucial to the disorganized airway epithelial structure and function characteristic of muco-obstructive airway diseases such as asthma. Graphical Abstract Key Concepts The airway epithelium in asthma is disorganized and characterized by cellular proliferation, aberrant migration, and goblet cell mucous metaplasia.mTOR signaling is a dynamic process during IL-13-mediated mucous metaplasia, increasing with IL-13 stimulation and declining during resolution.mTOR signaling is strongly increased in the asthmatic airway epithelium.mTOR signaling is associated with the development of key features of the metaplastic airway epithelium including cell proliferation and ectopic distribution of goblet cells and aberrant cellular migration.Inhibition of mTOR leads to decreased epithelial hypertrophy, reduced ectopic goblet cells, and cellular migration.
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45
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Silverman JB, Vega PN, Tyska MJ, Lau KS. Intestinal Tuft Cells: Morphology, Function, and Implications for Human Health. Annu Rev Physiol 2024; 86:479-504. [PMID: 37863104 DOI: 10.1146/annurev-physiol-042022-030310] [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: 10/22/2023]
Abstract
Tuft cells are a rare and morphologically distinct chemosensory cell type found throughout many organs, including the gastrointestinal tract. These cells were identified by their unique morphologies distinguished by large apical protrusions. Ultrastructural data have begun to describe the molecular underpinnings of their cytoskeletal features, and tuft cell-enriched cytoskeletal proteins have been identified, although the connection of tuft cell morphology to tuft cell functionality has not yet been established. Furthermore, tuft cells display variations in function and identity between and within tissues, leading to the delineation of distinct tuft cell populations. As a chemosensory cell type, they display receptors that are responsive to ligands specific for their environment. While many studies have demonstrated the tuft cell response to protists and helminths in the intestine, recent research has highlighted other roles of tuft cells as well as implicated tuft cells in other disease processes including inflammation, cancer, and viral infections. Here, we review the literature on the cytoskeletal structure of tuft cells. Additionally, we focus on new research discussing tuft cell lineage, ligand-receptor interactions, tuft cell tropism, and the role of tuft cells in intestinal disease. Finally, we discuss the implication of tuft cell-targeted therapies in human health and how the morphology of tuft cells may contribute to their functionality.
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Affiliation(s)
- Jennifer B Silverman
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Paige N Vega
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Matthew J Tyska
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
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46
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Gardner EE, Earlie EM, Li K, Thomas J, Hubisz MJ, Stein BD, Zhang C, Cantley LC, Laughney AM, Varmus H. Lineage-specific intolerance to oncogenic drivers restricts histological transformation. Science 2024; 383:eadj1415. [PMID: 38330136 PMCID: PMC11155264 DOI: 10.1126/science.adj1415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
Lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC) are thought to originate from different epithelial cell types in the lung. Intriguingly, LUAD can histologically transform into SCLC after treatment with targeted therapies. In this study, we designed models to follow the conversion of LUAD to SCLC and found that the barrier to histological transformation converges on tolerance to Myc, which we implicate as a lineage-specific driver of the pulmonary neuroendocrine cell. Histological transformations are frequently accompanied by activation of the Akt pathway. Manipulating this pathway permitted tolerance to Myc as an oncogenic driver, producing rare, stem-like cells that transcriptionally resemble the pulmonary basal lineage. These findings suggest that histological transformation may require the plasticity inherent to the basal stem cell, enabling tolerance to previously incompatible oncogenic driver programs.
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Affiliation(s)
| | - Ethan M. Earlie
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Kate Li
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Jerin Thomas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Melissa J. Hubisz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY
| | - Benjamin D. Stein
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Chen Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Ashley M. Laughney
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Harold Varmus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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47
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Abrami M, Biasin A, Tescione F, Tierno D, Dapas B, Carbone A, Grassi G, Conese M, Di Gioia S, Larobina D, Grassi M. Mucus Structure, Viscoelastic Properties, and Composition in Chronic Respiratory Diseases. Int J Mol Sci 2024; 25:1933. [PMID: 38339210 PMCID: PMC10856136 DOI: 10.3390/ijms25031933] [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: 12/31/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The respiratory mucus, a viscoelastic gel, effectuates a primary line of the airway defense when operated by the mucociliary clearance. In chronic respiratory diseases (CRDs), such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF), the mucus is overproduced and its solid content augments, changing its structure and viscoelastic properties and determining a derangement of essential defense mechanisms against opportunistic microbial (virus and bacteria) pathogens. This ensues in damaging of the airways, leading to a vicious cycle of obstruction and infection responsible for the harsh clinical evolution of these CRDs. Here, we review the essential features of normal and pathological mucus (i.e., sputum in CF, COPD, and asthma), i.e., mucin content, structure (mesh size), micro/macro-rheology, pH, and osmotic pressure, ending with the awareness that sputum biomarkers (mucins, inflammatory proteins and peptides, and metabolites) might serve to indicate acute exacerbation and response to therapies. There are some indications that old and novel treatments may change the structure, viscoelastic properties, and biomarker content of sputum; however, a wealth of work is still needed to embrace these measures as correlates of disease severity in association with (or even as substitutes of) pulmonary functional tests.
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Affiliation(s)
- Michela Abrami
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
| | - Alice Biasin
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
| | - Fabiana Tescione
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, P.le E. Fermi 1, I-80055 Portici, Italy; (F.T.); (D.L.)
| | - Domenico Tierno
- Clinical Department of Medical, Surgical and Health Sciences, Cattinara University Hospital, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.)
| | - Barbara Dapas
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy;
| | - Annalucia Carbone
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Gabriele Grassi
- Clinical Department of Medical, Surgical and Health Sciences, Cattinara University Hospital, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.)
| | - Massimo Conese
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Sante Di Gioia
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Domenico Larobina
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, P.le E. Fermi 1, I-80055 Portici, Italy; (F.T.); (D.L.)
| | - Mario Grassi
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
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48
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Ualiyeva S, Lemire E, Wong C, Perniss A, Boyd A, Avilés EC, Minichetti DG, Maxfield A, Roditi R, Matsumoto I, Wang X, Deng W, Barrett NA, Buchheit KM, Laidlaw TM, Boyce JA, Bankova LG, Haber AL. A nasal cell atlas reveals heterogeneity of tuft cells and their role in directing olfactory stem cell proliferation. Sci Immunol 2024; 9:eabq4341. [PMID: 38306414 PMCID: PMC11127180 DOI: 10.1126/sciimmunol.abq4341] [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: 04/07/2022] [Accepted: 12/08/2023] [Indexed: 02/04/2024]
Abstract
The olfactory neuroepithelium serves as a sensory organ for odors and forms part of the nasal mucosal barrier. Olfactory sensory neurons are surrounded and supported by epithelial cells. Among them, microvillous cells (MVCs) are strategically positioned at the apical surface, but their specific functions are enigmatic, and their relationship to the other specialized epithelial cells is unclear. Here, we establish that the family of MVCs comprises tuft cells and ionocytes in both mice and humans. Integrating analysis of the respiratory and olfactory epithelia, we define the distinct receptor expression of TRPM5+ tuft-MVCs compared with Gɑ-gustducinhigh respiratory tuft cells and characterize a previously undescribed population of glandular DCLK1+ tuft cells. To establish how allergen sensing by tuft-MVCs might direct olfactory mucosal responses, we used an integrated single-cell transcriptional and protein analysis. Inhalation of Alternaria induced mucosal epithelial effector molecules including Chil4 and a distinct pathway leading to proliferation of the quiescent olfactory horizontal basal stem cell (HBC) pool, both triggered in the absence of olfactory apoptosis. Alternaria- and ATP-elicited HBC proliferation was dependent on TRPM5+ tuft-MVCs, identifying these specialized epithelial cells as regulators of olfactory stem cell responses. Together, our data provide high-resolution characterization of nasal tuft cell heterogeneity and identify a function of TRPM5+ tuft-MVCs in directing the olfactory mucosal response to allergens.
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Affiliation(s)
- Saltanat Ualiyeva
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Evan Lemire
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Caitlin Wong
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Alexander Perniss
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Amelia Boyd
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Evelyn C. Avilés
- Department of Neurobiology, Harvard Medical School, Boston, MA; currently at Faculty of Biological Sciences, Pontificia Universidad Católica de Chile
| | - Dante G. Minichetti
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Alice Maxfield
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women’s Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA
| | - Rachel Roditi
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women’s Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA
| | | | - Xin Wang
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Wenjiang Deng
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Nora A. Barrett
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Kathleen M. Buchheit
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Tanya M. Laidlaw
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Joshua A. Boyce
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Lora G. Bankova
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Adam L. Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
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49
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Tchoukalova YD, Phung TN, Kennedy MM, Miranda-Grandjean D, Becquer E, Chen L, Zhang N, Dinu V, Wilson MA, Lott DG. Idiopathic Subglottic Stenosis Is Associated With More Frequent and Abnormal Squamous Metaplasia. Ann Otol Rhinol Laryngol 2024; 133:214-223. [PMID: 37740367 DOI: 10.1177/00034894231201016] [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] [Indexed: 09/24/2023]
Abstract
OBJECTIVES Gain insights into the pathophysiology of idiopathic subglottic stenosis (iSGS) by investigating differences in transcriptome of subglottic mucosal tissue between patients with iSGS and controls, and between tracheal and subglottic tissue within patients. METHODS RNA sequencing was conducted on biopsied mucosal samples collected from subglottic and tracheal (in-patient control) regions in iSGS patients, and from subglottis in controls. The gene expression differences were validated on a protein level by (1) staining the tissue samples obtained from a second cohort of patients and controls; and (2) in vitro functional assays using primary subglottic epithelial cells from both iSGS patients and healthy donors. RESULTS We found 7 upregulated genes in the subglottic region of iSGS patients relative to both the tracheal mucosa and subglottic region of controls. A gene ontology enrichment analysis found that the epithelial cell differentiation and cornification pathways are significant, involving specifically 3 of the genes: involucrin (IVL), small proline rich protein 1B (SPRR1B), and keratin 16 (KRT16). Involvement of these pathways suggests squamous metaplasia of the epithelium. Histological analyses of epithelium in subglottic mucosal biopsies revealed squamous metaplasia in 41% of the samples from iSGS patients and in 25% from controls. Immunohistochemical evaluation of the samples presented with squamous epithelium revealed increased expression of the protein encoded by SPRR1B, hyperproliferative basal cells, shedding of apical layers, and accompanying lesions in iSGS compared to CTRL. Cultured primary subglottic epithelial cells from iSGS patients had higher proliferation rates compared to healthy donors and squamous metaplastic differentiation formed thinner epithelia with increased expression proteins encoded by INV, SPRR1B, and KRT16, suggesting intrinsic dysfunction of basal cells in iSGS. CONCLUSIONS Abnormal squamous differentiation of epithelial cells may contribute to the pathogenesis of iSGS. Patients having metaplastic epithelial phenotype may be sensitive to drugs that reverse it to a normal phenotype.
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Affiliation(s)
- Yourka D Tchoukalova
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Tanya N Phung
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Faculty of Science, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maeve M Kennedy
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Baylor College of Medicine, Houston, TX, USA
| | | | - Emanuel Becquer
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Contexture, Phoenix, AZ, USA
| | - Longwen Chen
- Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Nan Zhang
- Department of Quantitative Health Sciences, Mayo, AZ Clinic, Scottsdale, AZ, USA
| | - Valentin Dinu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Basic Medical Sciences, Arizona State University, Phoenix, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - David G Lott
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Otolaryngology-Head and Neck Surgery, Division of Laryngology, Mayo Clinic Arizona, Phoenix, AZ, USA
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50
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Kucinski I, Campos J, Barile M, Severi F, Bohin N, Moreira PN, Allen L, Lawson H, Haltalli MLR, Kinston SJ, O'Carroll D, Kranc KR, Göttgens B. A time- and single-cell-resolved model of murine bone marrow hematopoiesis. Cell Stem Cell 2024; 31:244-259.e10. [PMID: 38183977 PMCID: PMC7615671 DOI: 10.1016/j.stem.2023.12.001] [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: 09/07/2023] [Revised: 09/25/2023] [Accepted: 12/04/2023] [Indexed: 01/08/2024]
Abstract
The paradigmatic hematopoietic tree model is increasingly recognized to be limited, as it is based on heterogeneous populations largely defined by non-homeostatic assays testing cell fate potentials. Here, we combine persistent labeling with time-series single-cell RNA sequencing to build a real-time, quantitative model of in vivo tissue dynamics for murine bone marrow hematopoiesis. We couple cascading single-cell expression patterns with dynamic changes in differentiation and growth speeds. The resulting explicit linkage between molecular states and cellular behavior reveals widely varying self-renewal and differentiation properties across distinct lineages. Transplanted stem cells show strong acceleration of differentiation at specific stages of erythroid and neutrophil production, illustrating how the model can quantify the impact of perturbations. Our reconstruction of dynamic behavior from snapshot measurements is akin to how a kinetoscope allows sequential images to merge into a movie. We posit that this approach is generally applicable to understanding tissue-scale dynamics at high resolution.
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Affiliation(s)
- Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Joana Campos
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; Institute of Cancer Research, London SM2 5NG, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Francesco Severi
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Natacha Bohin
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Pedro N Moreira
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Lewis Allen
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; Institute of Cancer Research, London SM2 5NG, UK
| | - Hannah Lawson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; Institute of Cancer Research, London SM2 5NG, UK
| | - Myriam L R Haltalli
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sarah J Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Dónal O'Carroll
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Kamil R Kranc
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; Institute of Cancer Research, London SM2 5NG, UK.
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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