1
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Kavanagh EW, Tzeng SY, Sharma N, Cutting GR, Green JJ. Ligand-free biodegradable poly(beta-amino ester) nanoparticles for targeted systemic delivery of mRNA to the lungs. Biomaterials 2025; 313:122753. [PMID: 39217793 DOI: 10.1016/j.biomaterials.2024.122753] [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: 03/26/2024] [Revised: 07/19/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Non-viral nanoparticles (NPs) have seen heightened interest as a delivery method for a variety of clinically relevant nucleic acid cargoes in recent years. While much of the focus has been on lipid NPs, non-lipid NPs, including polymeric NPs, have the possibility of improved efficacy, safety, and targeting, especially to non-liver organs following systemic administration. A safe and effective systemic approach for intracellular delivery to the lungs could overcome limitations to intratracheal/intranasal delivery of NPs and improve clinical benefit for a range of diseases including cystic fibrosis. Here, engineered biodegradable poly (beta-amino ester) (PBAE) NPs are shown to facilitate efficient delivery of mRNA to primary human airway epithelial cells from both healthy donors and individuals with cystic fibrosis. Optimized NP formulations made with differentially endcapped PBAEs and systemically administered in vivo lead to high expression of mRNA within the lungs in BALB/c and C57 B/L mice without requiring a complex targeting ligand. High levels of mRNA-based gene editing were achieved in an Ai9 mouse model across bronchial, epithelial, and endothelial cell populations. No toxicity was observed either acutely or over time, including after multiple systemic administrations of the NPs. The non-lipid biodegradable PBAE NPs demonstrate high levels of transfection in both primary human airway epithelial cells and in vivo editing of lung cell types that are targets for numerous life-limiting diseases particularly single gene disorders such as cystic fibrosis and surfactant deficiencies.
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Affiliation(s)
- Erin W Kavanagh
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephany Y Tzeng
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neeraj Sharma
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jordan J Green
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Departments of Chemical & Biomolecular Engineering, Materials Science & Engineering, Neurosurgery, Oncology, and Ophthalmology, Johns Hopkins University, Baltimore, MD, USA.
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2
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Feng X, Flüchter P, De Tenorio JC, Schneider C. Tuft cells in the intestine, immunity and beyond. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00978-1. [PMID: 39327439 DOI: 10.1038/s41575-024-00978-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/02/2024] [Indexed: 09/28/2024]
Abstract
Tuft cells have gained substantial attention over the past 10 years due to numerous reports linking them with type 2 immunity and microorganism-sensing capacity in many mucosal tissues. This heightened interest is fuelled by their unique ability to produce an array of biological effector molecules, including IL-25, allergy-related eicosanoids, and the neurotransmitter acetylcholine, enabling downstream responses in diverse cell types. Operating through G protein-coupled receptor-mediated signalling pathways reminiscent of type II taste cells in oral taste buds, tuft cells emerge as chemosensory sentinels that integrate luminal conditions, eliciting appropriate responses in immune, epithelial and neuronal populations. How tuft cells promote tissue alterations and adaptation to the variety of stimuli at mucosal surfaces has been explored in multiple studies in the past few years. Since the initial recognition of the role of tuft cells, the discovery of diverse tuft cell effector functions and associated feedback loops have also revealed the complexity of tuft cell biology. Although earlier work largely focused on extraintestinal tissues, novel genetic tools and recent mechanistic studies on intestinal tuft cells established fundamental concepts of tuft cell activation and functions. This Review is an overview of intestinal tuft cells, providing insights into their development, signalling and interaction modules in immunity and other states.
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Affiliation(s)
- Xiaogang Feng
- Department of Physiology, University of Zurich, Zurich, Switzerland
| | - Pascal Flüchter
- Department of Physiology, University of Zurich, Zurich, Switzerland
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3
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Kulhankova K, Cheng AX, Traore S, Auger M, Pelletier M, Hervault M, Wells KD, Green JA, Byrne A, Nelson B, Sponchiado M, Boosani C, Heffner CS, Snow KJ, Murray SA, Villacreses RA, Rector MV, Gansemer ND, Stoltz DA, Allamargot C, Couture F, Hemez C, Hallée S, Barbeau X, Harvey M, Lauvaux C, Gaillet B, Newby GA, Liu DR, McCray PB, Guay D. Amphiphilic shuttle peptide delivers base editor ribonucleoprotein to correct the CFTR R553X mutation in well-differentiated airway epithelial cells. Nucleic Acids Res 2024:gkae819. [PMID: 39315713 DOI: 10.1093/nar/gkae819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/03/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Base editing could correct nonsense mutations that cause cystic fibrosis (CF), but clinical development is limited by the lack of delivery methods that efficiently breach the barriers presented by airway epithelia. Here, we present a novel amphiphilic shuttle peptide based on the previously reported S10 peptide that substantially improved base editor ribonucleoprotein (RNP) delivery. Studies of the S10 secondary structure revealed that the alpha-helix formed by the endosomal leakage domain (ELD), but not the cell penetrating peptide (CPP), was functionally important for delivery. By isolating and extending the ELD, we created a novel shuttle peptide, termed S237. While S237 achieved lower delivery of green fluorescent protein, it outperformed S10 at Cas9 RNP delivery to cultured human airway epithelial cells and to pig airway epithelia in vivo, possibly due to its lower net charge. In well-differentiated primary human airway epithelial cell cultures, S237 achieved a 4.6-fold increase in base editor RNP delivery, correcting up to 9.4% of the cystic fibrosis transmembrane conductance regulator (CFTR) R553X allele and restoring CFTR channel function close to non-CF levels. These findings deepen the understanding of peptide-mediated delivery and offer a translational approach for base editor RNP delivery for CF airway disease.
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Affiliation(s)
| | | | - Soumba Traore
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Maud Auger
- Feldan Therapeutics, Quebec, Qc, Canada
- Department of Chemical Engineering, Laval University, Quebec, Qc, Canada
| | - Mia Pelletier
- Feldan Therapeutics, Quebec, Qc, Canada
- Department of Chemical Engineering, Laval University, Quebec, Qc, Canada
| | | | - Kevin D Wells
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Jonathan A Green
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Addison Byrne
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Benjamin Nelson
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Mariana Sponchiado
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Chandra Boosani
- Division of Animal Sciences, Swine Somatic Cell Genome Editing Center, University of Missouri, Columbia, MO, USA
| | - Caleb S Heffner
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME, USA
| | - Kathy J Snow
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME, USA
| | - Stephen A Murray
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME, USA
| | - Raul A Villacreses
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael V Rector
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, USA
| | - Nicholas D Gansemer
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, USA
| | - David A Stoltz
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Chantal Allamargot
- Central Microscopy Research Facility (CMRF), and Office for the Vice President of Research (OVPR), University of Iowa, Iowa City, IA, USA
| | | | - Colin Hemez
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | | | | | | | | | - Bruno Gaillet
- Department of Chemical Engineering, Laval University, Quebec, Qc, Canada
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - David Guay
- Feldan Therapeutics, Quebec, Qc, Canada
- Department of Chemical Engineering, Laval University, Quebec, Qc, Canada
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Chatterjee P, Moss CT, Omar S, Dhillon E, Hernandez Borges CD, Tang AC, Stevens DA, Hsu JL. Allergic Bronchopulmonary Aspergillosis (ABPA) in the Era of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Modulators. J Fungi (Basel) 2024; 10:656. [PMID: 39330416 PMCID: PMC11433030 DOI: 10.3390/jof10090656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/11/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Allergic bronchopulmonary aspergillosis (ABPA) is a hypersensitivity disease caused by Aspergillus fumigatus (Af), prevalent in persons with cystic fibrosis (CF) or asthma. In ABPA, Af proteases drive a T-helper cell-2 (Th2)-mediated allergic immune response leading to inflammation that contributes to permanent lung damage. Corticosteroids and antifungals are the mainstays of therapies for ABPA. However, their long-term use has negative sequelae. The treatment of patients with CF (pwCF) has been revolutionized by the efficacy of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy. Pharmacological improvement in CFTR function with highly effective elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes of pwCF. The mechanism behind the improvement in patient outcomes is a continued topic of investigation as our understanding of the role of CFTR function evolves. As ETI therapy gains traction in CF management, understanding its potential impact on ABPA, especially on the allergic immune response pathways and Af infection becomes increasingly crucial for optimizing patient outcomes. This literature review aims to examine the extent of these findings and expand our understanding of the already published research focusing on the intersection between ABPA therapeutic approaches in CF and the rapid impact of the evolving CFTR modulator landscape. While our literature search yielded limited reports specifically focusing on the role of CFTR modulator therapy on CF-ABPA, findings from epidemiologic and retrospective studies suggest the potential for CFTR modulator therapies to positively influence pulmonary outcomes by addressing the underlying pathophysiology of CF-ABPA, especially by decreasing inflammatory response and Af colonization. Thus, this review highlights the promising scope of CFTR modulator therapy in decreasing the overall prevalence and incidence of CF-ABPA.
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Affiliation(s)
- Paulami Chatterjee
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | - Carson Tyler Moss
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sarah Omar
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | - Ekroop Dhillon
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | | | - Alan C. Tang
- Department of Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA;
| | - David A. Stevens
- Division of Infectious Diseases and Geographic Medicine, Stanford University Medical School, Stanford, CA 94305, USA;
| | - Joe L. Hsu
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
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5
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Luan X, Henao Romero N, Campanucci VA, Le Y, Mustofa J, Tam JS, Ianowski JP. Pulmonary Ionocytes Regulate Airway Surface Liquid pH in Primary Human Bronchial Epithelial Cells. Am J Respir Crit Care Med 2024; 210:788-800. [PMID: 38573173 PMCID: PMC11418883 DOI: 10.1164/rccm.202309-1565oc] [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: 09/08/2023] [Accepted: 04/04/2024] [Indexed: 04/05/2024] Open
Abstract
Rationale: Pulmonary ionocytes are a newly discovered airway epithelial cell type proposed to be a major contributor to cystic fibrosis (CF) lung disease based on observations they express the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel at a higher level than any other cell type in the airway epithelia. Moreover, genetically manipulated experimental models that lack ionocytes develop NaCl transport abnormalities and airway surface liquid (ASL) dehydration consistent with CF. However, no direct evidence indicates ionocytes engage in NaCl transport or contribute to ASL formation, questioning the relevance of ionocytes to CF lung disease. Objectives: To determine the ion transport properties of pulmonary ionocytes and club cells in genetically intact healthy and CF airway epithelia. Methods: We measured ion transport at the single-cell level using a self-referencing ion-selective microelectrode technique in primary human bronchial epithelial cell culture. Measurements and Main Results: cAMP-stimulated non-CF ionocytes do not secrete Na+ or Cl- into the ASL, but rather modulate its pH by secreting bicarbonate via CFTR-linked Cl-/bicarbonate exchange. Non-CF club cells secrete Na+ and Cl- to the lumen side after cAMP stimulation. CF ionocytes and club cells do not transport ions in response to cAMP stimulation, but incubation with CFTR modulators elexacaftor/tezacaftor/ivacaftor restores transport properties. Conclusions: We conclude that ionocytes do not contribute to ASL formation but regulate ASL pH. Club cells secrete the bulk of airway fluid. In CF, abnormal ionocyte and club cell function results in acidic and dehydrated ASL, causing reduced antimicrobial properties and mucociliary clearance.
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Affiliation(s)
- Xiaojie Luan
- Department of Anatomy, Physiology, and Pharmacology
- Respiratory Research Centre, and
| | - Nicolas Henao Romero
- Department of Anatomy, Physiology, and Pharmacology
- Respiratory Research Centre, and
| | | | - Yen Le
- Department of Anatomy, Physiology, and Pharmacology
- Respiratory Research Centre, and
| | - Jannatul Mustofa
- Department of Anatomy, Physiology, and Pharmacology
- Respiratory Research Centre, and
| | - Julian S Tam
- Respiratory Research Centre, and
- Division of Respirology, Critical Care, and Sleep Medicine, Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Juan P Ianowski
- Department of Anatomy, Physiology, and Pharmacology
- Respiratory Research Centre, and
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6
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Okuda K, Gentzsch M. Pulmonary Ionocytes: What Are They Transporting and Which Way? Am J Respir Crit Care Med 2024; 210:705-707. [PMID: 38701428 PMCID: PMC11418888 DOI: 10.1164/rccm.202404-0727ed] [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: 04/10/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024] Open
Affiliation(s)
- Kenichi Okuda
- Marsico Lung Institute/Cystic Fibrosis Research Center
- Department of Medicine The University of North Carolina at Chapel Hill Chapel Hill, North Carolina
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center
- Department of Pediatrics The University of North Carolina at Chapel Hill Chapel Hill, North Carolina
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7
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Roe K. The epithelial cell types and their multi-phased defenses against fungi and other pathogens. Clin Chim Acta 2024; 563:119889. [PMID: 39117034 DOI: 10.1016/j.cca.2024.119889] [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: 07/02/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
Abstract
Mucus and its movements are essential to epithelial tissue immune defenses against pathogens, including fungal pathogens, which can infect respiratory, gastrointestinal or the genito-urinary tracts. Several epithelial cell types contribute to their immune defense. This review focuses on the respiratory tract because of its paramount importance, but the observations will apply to epithelial cell defenses of other mucosal tissue, including the gastrointestinal and genito-urinary tracts. Mucus and its movements can enhance or degrade the immune defenses of the respiratory tract, particularly the lungs. The enhancements include inhaled pathogen entrapments, including fungal pathogens, pollutants and particulates, for their removal. The detriments include smaller lung airway obstructions by mucus, impairing the physical removal of pathogens and impairing vital transfers of oxygen and carbon dioxide between the alveolar circulatory system and the pulmonary air. Inflammation, edema and/or alveolar cellular damage can also reduce vital transfers of oxygen and carbon dioxide between the lung alveolar circulatory system and the pulmonary air. Furthermore, respiratory tract defenses are affected by several fatty acid mediators which activate cellular receptors to manipulate neutrophils, macrophages, dendritic cells, various innate lymphoid cells including the natural killer cells, T cells, γδ T cells, mucosal-associated invariant T cells, NKT cells and mast cells. These mediators include the inflammatory and frequently immunosuppressive prostaglandins and leukotrienes, and the special pro-resolving mediators, which normally resolve inflammation and immunosuppression. The total effects on the various epithelial cell and immune cell types, after exposures to pathogens, pollutants or particulates, will determine respiratory tract health or disease.
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Affiliation(s)
- Kevin Roe
- Retired United States Patent and Trademark Office, San Jose, CA, United States.
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Liu X, Wang C, Huang Y, Lv Q, Yu C, Ying J, Duan L, Guo Y, Huang G, Shen W, Jiang M, Mao W, Zuo Z, Zhao A. Abnormal Cellular Populations Shape Thymic Epithelial Tumor Heterogeneity and Anti-Tumor by Blocking Metabolic Interactions in Organoids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2406653. [PMID: 39258580 DOI: 10.1002/advs.202406653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/08/2024] [Indexed: 09/12/2024]
Abstract
A variety of abnormal epithelial cells and immature and mature immune cells in thymic epithelial tumors (TETs) affect histopathological features, the degree of malignancy, and the response to treatment. Here, gene expression, trajectory inference, and T cell antigen receptor (TCR)-based lineage tracking are profiled in TETs at single-cell resolution. An original subpopulation of KRT14+ progenitor cells with a spindle cell phenotype is shown. An abnormal infiltration of immature T cells with a TCR hyper-rearrangement state is revealed, due to the lack of CCL21+ medullary epithelial cells. For thymic carcinoma, the novel biomarkers of MSLN, CCL20, and SLC1A5 are identified and observed an elevated expression of LAG3 and HAVCR2 in malignant tumorn-infiltrating mature T cells. These common features based on the single-cell populations may inform pathological reclassification of TETs. Meanwhile, it is found that macrophages (MACs) attract thymic tumor cells through the LGALS9-SLC1A5 axis, providing them with glutamine to elicit metabolic reprogramming. This MAC-based metabolic pattern can promote malignancy progression. Additionally, an interactive immune environment in TETs is identified that correlates with the infiltration of abnormal FOXI1+ CFTR- ionocytes. Collectively, the data broaden the knowledge of TET cellular ecosystems, providing a basis for tackling histopathological diagnosis and related treatment.
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Affiliation(s)
- Xuefei Liu
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Changchun Wang
- Department of Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Yueyu Huang
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Qiaoli Lv
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
| | - Chang Yu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Jianghua Ying
- Department of Ultrasound, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Lianhui Duan
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yangzhong Guo
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
| | - Guanyin Huang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenhui Shen
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Ming Jiang
- Center for Genetic Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310011, China
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, 310011, China
| | - Weimin Mao
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
- Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Thoracic Cancer, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510308, China
| | - An Zhao
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
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9
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Dora D, Szőcs E, Soós Á, Halasy V, Somodi C, Mihucz A, Rostás M, Mógor F, Lohinai Z, Nagy N. From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy. Front Immunol 2024; 15:1434804. [PMID: 39301033 PMCID: PMC11410641 DOI: 10.3389/fimmu.2024.1434804] [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: 05/18/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024] Open
Abstract
This comprehensive review undertakes a multidisciplinary exploration of the gut-lung axis, from the foundational aspects of anatomy, embryology, and histology, through the functional dynamics of pathophysiology, to implications for clinical science. The gut-lung axis, a bidirectional communication pathway, is central to understanding the interconnectedness of the gastrointestinal- and respiratory systems, both of which share embryological origins and engage in a continuous immunological crosstalk to maintain homeostasis and defend against external noxa. An essential component of this axis is the mucosa-associated lymphoid tissue system (MALT), which orchestrates immune responses across these distant sites. The review delves into the role of the gut microbiome in modulating these interactions, highlighting how microbial dysbiosis and increased gut permeability ("leaky gut") can precipitate systemic inflammation and exacerbate respiratory conditions. Moreover, we thoroughly present the implication of the axis in oncological practice, particularly in lung cancer development and response to cancer immunotherapies. Our work seeks not only to synthesize current knowledge across the spectrum of science related to the gut-lung axis but also to inspire future interdisciplinary research that bridges gaps between basic science and clinical application. Our ultimate goal was to underscore the importance of a holistic understanding of the gut-lung axis, advocating for an integrated approach to unravel its complexities in human health and disease.
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Affiliation(s)
- David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Emőke Szőcs
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Ádám Soós
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Viktória Halasy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csenge Somodi
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Anna Mihucz
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Melinda Rostás
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Mógor
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Zoltan Lohinai
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Nándor Nagy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
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10
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Karmaus PWF. Application of Single Cell Methods in Immunometabolism and Immunotoxicology. CURRENT OPINION IN TOXICOLOGY 2024; 39:100488. [PMID: 39091379 PMCID: PMC11290472 DOI: 10.1016/j.cotox.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Recent developments of novel single-cell analysis techniques have rapidly advanced the fields of immunotoxicology and immunometabolism. Single-cell analyses enable the characterization of immune cells, unraveling heterogeneity, and population dynamics in response to cellular perturbations, including toxicant insults and changes in cellular metabolism. This review provides an overview of current technologies and recent discoveries, illustrating an emerging role of single-cell analyses in the field of immunotoxicology and immunometabolism. Various single-cell techniques, including flow cytometry, mass cytometry, multiplexed imaging, and sequencing, together with their applications to studying immunotoxicology and immunometabolism are discussed. This review emphasizes the potential for single-cell analyses to revolutionize our understanding of immune cell heterogeneity, uncover novel cellular therapeutic targets, and pave the way for novel mechanistic insights.
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Affiliation(s)
- Peer W F Karmaus
- National Institute of Environmental Health Sciences, US
- Institute for Integrative Toxicology, Michigan State University, US
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11
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Dance A. What is a cell type, really? The quest to categorize life's myriad forms. Nature 2024; 633:754-756. [PMID: 39317746 DOI: 10.1038/d41586-024-03073-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
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12
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Xu Y, Wang S, Feng Q, Xia J, Li Y, Li HD, Wang J. scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data. Nat Commun 2024; 15:7561. [PMID: 39215003 PMCID: PMC11364754 DOI: 10.1038/s41467-024-51891-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate rare cell types and achieve accurate identification. We benchmark scCAD on 25 real-world scRNA-seq datasets, demonstrating its superior performance compared to 10 state-of-the-art methods. In-depth case studies across diverse datasets, including mouse airway, brain, intestine, human pancreas, immunology data, and clear cell renal cell carcinoma, showcase scCAD's efficiency in identifying rare cell types in complex biological scenarios. Furthermore, scCAD can correct the annotation of rare cell types and identify immune cell subtypes associated with disease, thereby offering valuable insights into disease progression.
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Affiliation(s)
- Yunpei Xu
- School of Computer Science and Engineering, Central South University, Changsha, China
- Xiangjiang Laboratory, Changsha, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, China
| | - Shaokai Wang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| | - Qilong Feng
- School of Computer Science and Engineering, Central South University, Changsha, China
- Xiangjiang Laboratory, Changsha, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, China
| | - Jiazhi Xia
- School of Computer Science and Engineering, Central South University, Changsha, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, China
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, China.
- Xiangjiang Laboratory, Changsha, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, China.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, China.
- Xiangjiang Laboratory, Changsha, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, China.
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13
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Sun L, Walls SA, Dang H, Quinney NL, Sears PR, Sadritabrizi T, Hasegawa K, Okuda K, Asakura T, Chang X, Zheng M, Mikami Y, Dizmond FU, Danilova D, Zhou L, Deshmukh A, Cholon DM, Radicioni G, Rogers TD, Kissner WJ, Markovetz MR, Guhr Lee TN, Gutay MI, Esther CR, Chua M, Grubb BR, Ehre C, Kesimer M, Hill DB, Ostrowski LE, Button B, Gentzsch M, Robinson C, Olivier KN, Freeman AF, Randell SH, O'Neal WK, Boucher RC, Chen G. Dysregulated Airway Host Defense in Hyper IgE Syndrome due to STAT3 Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607930. [PMID: 39211176 PMCID: PMC11361074 DOI: 10.1101/2024.08.14.607930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Rationale Hyper IgE syndrome (STAT3-HIES), also known as Job's syndrome, is a rare immunodeficiency disease typically caused by dominant-negative STAT3 mutations. STAT3-HIES syndrome is characterized by chronic pulmonary infection and inflammation, suggesting impairment of pulmonary innate host defense. Objectives To identify airway epithelial host defense defects consequent to STAT3 mutations that, in addition to reported mutant STAT3 immunologic abnormalities, produce pulmonary infection. Methods STAT3-HIES sputum was evaluated for biochemical/biophysical properties. STAT3-HIES excised lungs were harvested for histology; bronchial brush samples were collected for RNA sequencing and in vitro culture. A STAT3-HIES-specific mutation (R382W), expressed by lentiviruses, and a STAT3 knockout, generated by CRISPR/Cas9, were maintained in normal human bronchial epithelia under basal or inflammatory (IL1β) conditions. Effects of STAT3 deficiency on transcriptomics, and epithelial ion channel, secretory, antimicrobial, and ciliary functions were assessed. Measurements and Main Results Mucus concentrations and viscoelasticity were increased in STAT3-HIES sputum. STAT3-HIES excised lungs exhibited mucus obstruction and elevated IL1β expression. STAT3 deficiency impaired CFTR-dependent fluid and mucin secretion, inhibited expression of antimicrobial peptides, cytokines, and chemokines, and acidified airway surface liquid at baseline and post-IL1β exposure in vitro. Notably, mutant STAT3 suppressed IL1R1 expression. STAT3 mutations also inhibited ciliogenesis in vivo and impaired mucociliary transport in vitro, a process mediated via HES6 suppression. Administration of a γ-secretase inhibitor increased HES6 expression and improved ciliogenesis in STAT3 R382W mutant cells. Conclusions STAT3 dysfunction leads to multi-component defects in airway epithelial innate defense, which, in conjunction with STAT3-HIES immune deficiency, contributes to chronic pulmonary infection.
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Shankar NR, Garnica L, Stahlschmidt E, Byers D, Kulkarni H. Characteristics of human donor lungs utilized for research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.10.607431. [PMID: 39185158 PMCID: PMC11343100 DOI: 10.1101/2024.08.10.607431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Introduction Many fundamental discoveries have occurred using primary cells from deceased donor lungs. These cells respond differently to injury when there are underlying co-morbidities like diabetes mellitus, hypertension, aging and exposures to cigarette smoke, cocaine and chronic alcohol use. However, the prevalence of these characteristics in donor lungs utilized for research is currently unknown. Methods This retrospective cohort study procured data of lung transplant donors from Mid-America Transplant from January 2017 until July 2023. The donors were characterized based on lung utilization into three groups - lungs used for research, lungs used for transplant, and lungs not recovered from donors for either research or transplantation. Results The mean age of donors whose lungs were utilized for research was 41±18 years. 25% of them were expanded criteria donors (ECD) while 10% of the donors in the transplant cohort were ECD. 14% of the donors whose lungs were utilized for research had history of diabetes compared to 8% of donors whose lungs were transplanted. A quarter of the research donor population had positive history of cigarette use within the preceding 20 years. At least 40% of donors had a positive history of non-intravenous drug use, of whom a majority had a history of continued non-intravenous drug use. Conclusions No strict selection criteria or protocols exist when human donor lungs are obtained for ex-vivo research. There is a high prevalence of diabetes mellitus, history of smoking and non-intravenous drug use along with older age distribution in donors whose lungs used are for research.
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Affiliation(s)
- Nishanth R Shankar
- Kasturba Medical College, Mangalore, India 575001
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Lorena Garnica
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Derek Byers
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Hrishikesh Kulkarni
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63110
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15
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Stack JT, Rayner RE, Nouri R, Suarez CJ, Kim SH, Kanke KL, Vetter TA, Cormet-Boyaka E, Vaidyanathan S. DNA-PKcs Inhibition Improves Sequential Gene Insertion of the Full-Length CFTR cDNA in Airway Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607571. [PMID: 39185207 PMCID: PMC11343149 DOI: 10.1101/2024.08.12.607571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although many people with CF (pwCF) are treated using CFTR modulators, some are non-responsive due to their genotype or other uncharacterized reasons. Autologous airway stem cell therapies, in which the CFTR cDNA has been replaced, may enable a durable therapy for all pwCF. Previously, CRISPR-Cas9 with two AAVs was used to sequentially insert two halves of the CFTR cDNA and an enrichment cassette into the CFTR locus. However, the editing efficiency was <10% and required enrichment to restore CFTR function. Further improvement in gene insertion may enhance cell therapy production. To improve CFTR cDNA insertion in human airway basal stem cells (ABCs), we evaluated the use of the small molecules AZD7648 and ART558 which inhibit non-homologous end joining (NHEJ) and micro-homology mediated end joining (MMEJ). Adding AZD7648 alone improved gene insertion by 2-3-fold. Adding both ART558 and AZD7648 improved gene insertion but induced toxicity. ABCs edited in the presence of AZD7648 produced differentiated airway epithelial sheets with restored CFTR function after enrichment. Adding AZD7648 did not increase off-target editing. Further studies are necessary to validate if AZD7648 treatment enriches cells with oncogenic mutations.
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Affiliation(s)
- Jacob T. Stack
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Rachael E. Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Reza Nouri
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Carlos J. Suarez
- Department of Pathology, Stanford University, Palo Alto, CA 94305
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Karen L. Kanke
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Tatyana A. Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | | | - Sriram Vaidyanathan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210
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16
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Mall MA, Burgel PR, Castellani C, Davies JC, Salathe M, Taylor-Cousar JL. Cystic fibrosis. Nat Rev Dis Primers 2024; 10:53. [PMID: 39117676 DOI: 10.1038/s41572-024-00538-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/09/2024] [Indexed: 08/10/2024]
Abstract
Cystic fibrosis is a rare genetic disease caused by mutations in CFTR, the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR). The discovery of CFTR in 1989 has enabled the unravelling of disease mechanisms and, more recently, the development of CFTR-directed therapeutics that target the underlying molecular defect. The CFTR protein functions as an ion channel that is crucial for correct ion and fluid transport across epithelial cells lining the airways and other organs. Consequently, CFTR dysfunction causes a complex multi-organ disease but, to date, most of the morbidity and mortality in people with cystic fibrosis is due to muco-obstructive lung disease. Cystic fibrosis care has long been limited to treating symptoms using nutritional support, airway clearance techniques and antibiotics to suppress airway infection. The widespread implementation of newborn screening for cystic fibrosis and the introduction of a highly effective triple combination CFTR modulator therapy that has unprecedented clinical benefits in up to 90% of genetically eligible people with cystic fibrosis has fundamentally changed the therapeutic landscape and improved prognosis. However, people with cystic fibrosis who are not eligible based on their CFTR genotype or who live in countries where they do not have access to this breakthrough therapy remain with a high unmet medical need.
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Affiliation(s)
- Marcus A Mall
- Department of Paediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany.
- German Centre for Lung Research (DZL), Associated Partner Site Berlin, Berlin, Germany.
- German Center for Child and Adolescent Health (DZKJ), Partner Site Berlin, Berlin, Germany.
| | - Pierre-Régis Burgel
- Université Paris Cité and Institut Cochin, Inserm U1016, Paris, France
- Department of Respiratory Medicine and National Reference Center for Cystic Fibrosis, Cochin Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Carlo Castellani
- IRCCS Istituto Giannina Gaslini, Cystic Fibrosis Center, Genoa, Italy
| | - Jane C Davies
- National Heart & Lung Institute, Imperial College London, London, UK
- St Thomas' NHS Trust, London, UK
- Royal Brompton Hospital, Part of Guy's & St Thomas' Trust, London, UK
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Jennifer L Taylor-Cousar
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
- Division of Paediatric Pulmonary Medicine, National Jewish Health, Denver, CO, USA
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17
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Wils T, Backaert W, Jacobs I, Ruysseveldt E, Cremer J, Dilissen E, Bullens DM, Talavera K, Steelant B, Van Gerven L, Martens K, Hellings PW. Rare presence and function of neuroendocrine cells in the nasal mucosa. Front Immunol 2024; 15:1394539. [PMID: 39176088 PMCID: PMC11339793 DOI: 10.3389/fimmu.2024.1394539] [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: 03/01/2024] [Accepted: 07/24/2024] [Indexed: 08/24/2024] Open
Abstract
There is growing evidence that neurogenic inflammation contributes to the pathophysiology of upper airway diseases, with nasal hyperreactivity (NHR) being a key symptom. The rare neuroendocrine cells (NECs) in the epithelium have been linked to the pathophysiology of bronchial and intestinal hyperreactivity, however their presence in the nasal mucosa and their potential role in NHR remains unclear. Therefore, we studied the presence of NECs in the nasal epithelium of controls, allergic rhinitis patients and chronic rhinosinusitis with nasal polyps patients, and their link to NHR. The expression of typical NECs markers, CHGA, ASCL1 and CGRP, were evaluated on gene and protein level in human samples using real-time quantitative PCR (RT-qPCR), western blot, immunohistochemistry fluorescence staining, RNA scope assay, flow cytometry and single cell RNA-sequencing. Furthermore, the change in peak nasal inspiratory flow after cold dry air provocation and visual analogue scale scores were used to evaluate NHR or disease severity, respectively. Limited gene expression of the NECs markers CHGA and ASCL1 was measured in patients with upper airway diseases and controls. Gene expression of these markers did not correlate with NHR severity nor disease severity. In vitro, CHGA and ASCL1 expression was also evaluated in primary nasal epithelial cell cultures from patients with upper airway disease and controls using RT-qPCR and western blot. Both on gene and protein level only limited CHGA and ASCL1 expression was found. Additionally, NECs were studied in nasal biopsies of patients with upper airway diseases and controls using immunohistochemistry fluorescence staining, RNA scope and flow cytometry. Unlike in ileum samples, CHGA could not be detected in nasal biopsies of patients with upper airway diseases and control subjects. Lastly, single cell RNA-sequencing of upper airway tissue could not identify a NEC cluster. In summary, in contrast to the bronchi and gut, there is only limited evidence for the presence of NECs in the nasal mucosa, and without correlation with NHR, thereby questioning the relevance of NECs in upper airway pathology.
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Affiliation(s)
- Tine Wils
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Wout Backaert
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Clinical Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Inge Jacobs
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- KU Leuven Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Diseases, KU Leuven, Leuven, Belgium
| | - Emma Ruysseveldt
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Ellen Dilissen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Dominique M. Bullens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Karel Talavera
- KU Leuven Department of Cellular and Molecular Medicine, Laboratory of Ion Channel Research Division of Physiology, KU Leuven, Leuven, Belgium
| | - Brecht Steelant
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Laura Van Gerven
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Clinical Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
- KU Leuven Department of Neurosciences, Experimental Otorhinolaryngology Rhinology Research, KU Leuven, Leuven, Belgium
| | - Katleen Martens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- University of Antwerp (UAntwerp) Department of Bioscience Engineering, Lab of Applied Microbiology and Biotechnology, University of Antwerp (UAntwerp), Antwerp, Belgium
| | - Peter W. Hellings
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Clinical Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
- University of Ghent (UGhent) Department of Head and Skin, Upper Airways Research Laboratory, University of Ghent (UGhent), Ghent, Belgium
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18
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Roach SN, Shepherd FK, Mickelson CK, Fiege JK, Thielen BK, Pross LM, Sanders AE, Mitchell JS, Robertson M, Fife BT, Langlois RA. Tropism for ciliated cells is the dominant driver of influenza viral burst size in the human airway. Proc Natl Acad Sci U S A 2024; 121:e2320303121. [PMID: 39008691 PMCID: PMC11295045 DOI: 10.1073/pnas.2320303121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/26/2024] [Indexed: 07/17/2024] Open
Abstract
Influenza viruses pose a significant burden on global human health. Influenza has a broad cellular tropism in the airway, but how infection of different epithelial cell types impacts replication kinetics and burden in the airways is not fully understood. Using primary human airway cultures, which recapitulate the diverse epithelial cell landscape of the human airways, we investigated the impact of cell type composition on virus tropism and replication kinetics. Cultures were highly diverse across multiple donors and 30 independent differentiation conditions and supported a range of influenza replication. Although many cell types were susceptible to influenza, ciliated and secretory cells were predominantly infected. Despite the strong tropism preference for secretory and ciliated cells, which consistently make up 75% or more of infected cells, only ciliated cells were associated with increased virus production. Surprisingly, infected secretory cells were associated with overall reduced virus output. The disparate response and contribution to influenza virus production could be due to different pro- and antiviral interferon-stimulated gene signatures between ciliated and secretory populations, which were interrogated with single-cell RNA sequencing. These data highlight the heterogeneous outcomes of influenza virus infections in the complex cellular environment of the human airway and the disparate impacts of infected cell identity on multiround burst size, even among preferentially infected cell types.
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Affiliation(s)
- Shanley N. Roach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Clayton K. Mickelson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Jessica K. Fiege
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Beth K. Thielen
- Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, University of Minnesota, Minneapolis, MN55455
| | - Lauren M. Pross
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Autumn E. Sanders
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Jason S. Mitchell
- Center for Immunology, University of Minnesota, Minneapolis, MN55455
| | - Mason Robertson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Brian T. Fife
- Center for Immunology, University of Minnesota, Minneapolis, MN55455
- Department of Medicine, University of Minnesota, Minneapolis, MN55455
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
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19
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Alsaggaf I, Buchan D, Wan C. Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning. Brief Funct Genomics 2024; 23:441-451. [PMID: 38242863 DOI: 10.1093/bfgp/elad059] [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: 07/01/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
Cell type identification is an important task for single-cell RNA-sequencing (scRNA-seq) data analysis. Many prediction methods have recently been proposed, but the predictive accuracy of difficult cell type identification tasks is still low. In this work, we proposed a novel Gaussian noise augmentation-based scRNA-seq contrastive learning method (GsRCL) to learn a type of discriminative feature representations for cell type identification tasks. A large-scale computational evaluation suggests that GsRCL successfully outperformed other state-of-the-art predictive methods on difficult cell type identification tasks, while the conventional random genes masking augmentation-based contrastive learning method also improved the accuracy of easy cell type identification tasks in general.
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Affiliation(s)
- Ibrahim Alsaggaf
- School of Computing and Mathematical Sciences, Birkbeck, University of London, Malet Street, WC1E 7HX, London, United Kingdom
| | - Daniel Buchan
- Department of Computer Science, University College London, Gower Street, WC1E 6BT, London, United Kingdom
| | - Cen Wan
- School of Computing and Mathematical Sciences, Birkbeck, University of London, Malet Street, WC1E 7HX, London, United Kingdom
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20
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Zagoren E, Dias N, Smith ZD, Ameen NA, Sumigray K. A second wave of Notch signaling diversifies the intestinal secretory lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603542. [PMID: 39071399 PMCID: PMC11275776 DOI: 10.1101/2024.07.15.603542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The small intestine is well known for the function of its nutrient-absorbing enterocytes; yet equally critical for the maintenance of homeostasis is a diverse set of secretory cells, all of which are presumed to differentiate from the same intestinal stem cell. Despite major roles in intestinal function and health, understanding how the full spectrum of secretory cell types arises remains a longstanding challenge, largely due to their comparative rarity. Here, we investigate the fate specification of a rare and distinct population of small intestinal epithelial cells found in rats and humans but not mice: C FTR Hi gh E xpressers (CHEs). We use pseudotime trajectory analysis of single-cell RNA-seq data from rat intestinal jejunum to provide evidence that CHEs are specified along the secretory lineage and appear to employ a second wave of Notch-based signal transduction to distinguish these cells from other secretory cell types. We further validate the general order of transcription factors that direct these cells from unspecified progenitors within the crypt and experimentally demonstrate that Notch signaling is necessary to induce CHE fate both in vivo and in vitro . Our results suggest a model in which Notch is reactivated along the secretory lineage to specify the CHE population: a rare secretory cell type with putative functions in localized coordination of luminal pH and direct relevance to cystic fibrosis pathophysiology.
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21
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Turner DL, Amoozadeh S, Baric H, Stanley E, Werder RB. Building a human lung from pluripotent stem cells to model respiratory viral infections. Respir Res 2024; 25:277. [PMID: 39010108 PMCID: PMC11251358 DOI: 10.1186/s12931-024-02912-0] [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: 04/25/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024] Open
Abstract
To protect against the constant threat of inhaled pathogens, the lung is equipped with cellular defenders. In coordination with resident and recruited immune cells, this defence is initiated by the airway and alveolar epithelium following their infection with respiratory viruses. Further support for viral clearance and infection resolution is provided by adjacent endothelial and stromal cells. However, even with these defence mechanisms, respiratory viral infections are a significant global health concern, causing substantial morbidity, socioeconomic losses, and mortality, underlining the need to develop effective vaccines and antiviral medications. In turn, the identification of new treatment options for respiratory infections is critically dependent on the availability of tractable in vitro experimental models that faithfully recapitulate key aspects of lung physiology. For such models to be informative, it is important these models incorporate human-derived, physiologically relevant versions of all cell types that normally form part of the lungs anti-viral response. This review proposes a guideline using human induced pluripotent stem cells (iPSCs) to create all the disease-relevant cell types. iPSCs can be differentiated into lung epithelium, innate immune cells, endothelial cells, and fibroblasts at a large scale, recapitulating in vivo functions and providing genetic tractability. We advocate for building comprehensive iPSC-derived in vitro models of both proximal and distal lung regions to better understand and model respiratory infections, including interactions with chronic lung diseases.
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Affiliation(s)
- Declan L Turner
- Murdoch Children's Research Institute, Melbourne, 3056, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, 3056, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW Melbourne, Melbourne, 3056, Australia
| | - Sahel Amoozadeh
- Murdoch Children's Research Institute, Melbourne, 3056, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, 3056, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW Melbourne, Melbourne, 3056, Australia
| | - Hannah Baric
- Murdoch Children's Research Institute, Melbourne, 3056, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, 3056, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW Melbourne, Melbourne, 3056, Australia
| | - Ed Stanley
- Murdoch Children's Research Institute, Melbourne, 3056, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, 3056, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW Melbourne, Melbourne, 3056, Australia
| | - Rhiannon B Werder
- Murdoch Children's Research Institute, Melbourne, 3056, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, 3056, Australia.
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW Melbourne, Melbourne, 3056, Australia.
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22
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Quach H, Farrell S, Wu MJM, Kanagarajah K, Leung JWH, Xu X, Kallurkar P, Turinsky AL, Bear CE, Ratjen F, Kalish B, Goyal S, Moraes TJ, Wong AP. Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity. Nat Commun 2024; 15:5898. [PMID: 39003323 PMCID: PMC11246468 DOI: 10.1038/s41467-024-50281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
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Affiliation(s)
- Henry Quach
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer Farrell
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Jia Michael Wu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kayshani Kanagarajah
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Wai-Hin Leung
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoqiao Xu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prajkta Kallurkar
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine E Bear
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Felix Ratjen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Kalish
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy P Wong
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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23
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Lee JH, LeCher JC, Parigoris E, Shinagawa N, Sentosa J, Manfredi C, Goh SL, De R, Tao S, Zandi K, Amblard F, Sorscher EJ, Spence JR, Tirouvanziam R, Schinazi RF, Takayama S. Development of robust antiviral assays using relevant apical-out human airway organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573939. [PMID: 38260306 PMCID: PMC10802305 DOI: 10.1101/2024.01.02.573939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
While breakthroughs with organoids have emerged as next-generation in vitro tools, standardization for drug discovery remains a challenge. This work introduces human airway organoids with reversed biopolarity (AORBs), cultured and analyzed in a high-throughput, single-organoid-per-well format, enabling milestones towards standardization. AORBs exhibit a spatio-temporally stable apical-out morphology, facilitating high-yield direct intact-organoid virus infection. Single-cell RNA sequencing and immunohistochemistry confirm the physiologically relevant recapitulation of differentiated human airway epithelia. The cellular tropism of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains along with host response differences between Delta, Washington, and Omicron variants, as observed in transcriptomic profiles, also suggest clinical relevance. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds (remdesivir, bemnifosbuvir, and nirmatrelvir) demonstrates that AORBs efficiently predict human efficacy, comparable to gold-standard air-liquid interface cultures, but with higher throughput (~10-fold) and fewer cells (~100-fold). This combination of throughput and relevance allows AORBs to robustly detect false negative results in efficacy, preventing irretrievable loss of promising lead compounds. While this work leverages the SARS-CoV-2 study as a proof-of-concept application, the standardization capacity of AORB holds broader implications in line with regulatory efforts to push alternatives to animal studies.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Julia C. LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Noriyuki Shinagawa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
| | - Jason Sentosa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
| | - Candela Manfredi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Rabindra Tirouvanziam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Center for Cystic Fibrosis & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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24
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Laitman BM, Charytonowicz D, Zhu AJ, Lynch K, Varelas EA, Burton M, Andreou C, Kore P, Kirke DN, Chen YW, Beaumont KG, Sebra R, Genden EM, Courey MS. High-Resolution Profiling of Human Vocal Fold Cellular Landscapes With Single-Nuclei RNA Sequencing. Laryngoscope 2024; 134:3193-3200. [PMID: 38415934 DOI: 10.1002/lary.31334] [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: 05/17/2023] [Revised: 12/28/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024]
Abstract
INTRODUCTION The function of the vocal folds (VFs) is determined by the phenotype, abundance, and distribution of differentiated cells within specific microenvironments. Identifying this histologic framework is crucial in understanding laryngeal disease. A paucity of studies investigating VF cellular heterogeneity has been undertaken. Here, we examined the cellular landscape of human VFs by utilizing single-nuclei RNA-sequencing. METHODS Normal true VF tissue was excised from five patients undergoing pitch elevation surgery. Tissue was snap frozen in liquid nitrogen and subjected to cellular digestion and nuclear extraction. Nuclei were processed for single-nucleus sequencing using the 10X Genomics Chromium platform. Sequencing reads were assembled using cellranger and analyzed with the scanpy package in python. RESULTS RNA sequencing revealed 18 global cell clusters. While many were of epithelial origin, expected cell types, such as fibroblasts, immune cells, muscle cells, and endothelial cells were present. Subcluster analysis defined unique epithelial, immune, and fibroblast subpopulations. CONCLUSION This study evaluated the cellular heterogeneity of normal human VFs by utilizing single-nuclei RNA-sequencing. With further confirmation through additional spatial sequencing and microscopic imaging, a novel cellular map of the VFs may provide insight into new cellular targets for VF disease. LEVEL OF EVIDENCE NA Laryngoscope, 134:3193-3200, 2024.
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Affiliation(s)
- Benjamin M Laitman
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | | | - Ashley J Zhu
- Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Katie Lynch
- Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Eleni A Varelas
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Madeline Burton
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Christina Andreou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Pragati Kore
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Diana N Kirke
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Ya-Wen Chen
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Eric M Genden
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
| | - Mark S Courey
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, U.S.A
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25
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Korkmaz FT, Quinton LJ. Extra-pulmonary control of respiratory defense. Cell Immunol 2024; 401-402:104841. [PMID: 38878619 DOI: 10.1016/j.cellimm.2024.104841] [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: 03/03/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024]
Abstract
Pneumonia persists as a public health crisis, representing the leading cause of death due to infection. Whether respiratory tract infections progress to pneumonia and its sequelae such as acute respiratory distress syndrome and sepsis depends on numerous underlying conditions related to both the causative agent and host. Regarding the former, pneumonia burden remains staggeringly high, despite the effectiveness of pathogen-targeting strategies such as vaccines and antibiotics. This demands a greater understanding of host features that collaborate to promote immune resistance and tissue resilience in the infected lung. Such features inside the pulmonary compartment have drawn much attention, where major advances have been made related to resident and recruited immune activity. By comparison, extra-pulmonary processes guiding pneumonia susceptibility are relatively elusive, constituting the focus of this review. Here we will highlight examples of when, how, and why tissues outside of the lungs dispatch signals that modulate local immunity in the airspaces. Topics include the liver, gut, bone marrow, brain and more, all of which contribute in direct and indirect ways to pneumonia outcome. When tuned appropriately, it has become clear that these responses can serve protective roles, and this will be considered distinctly from what would otherwise be aberrant responses characteristic of pneumonia-induced organ injury and sepsis. Further advances in this area may reveal novel targetable areas for clinical intervention that are not confined to the intra-pulmonary space.
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Affiliation(s)
- Filiz T Korkmaz
- Department of Medicine, Division of Immunology and Infectious Disease, UMass Chan Medical School, Worcester, MA 01602, United States.
| | - Lee J Quinton
- Department of Medicine, Division of Immunology and Infectious Disease, UMass Chan Medical School, Worcester, MA 01602, United States
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26
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Sin DD. What Single Cell RNA Sequencing Has Taught Us about Chronic Obstructive Pulmonary Disease. Tuberc Respir Dis (Seoul) 2024; 87:252-260. [PMID: 38369875 PMCID: PMC11222093 DOI: 10.4046/trd.2024.0001] [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: 01/03/2024] [Accepted: 02/17/2024] [Indexed: 02/20/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) affects close to 400 million people worldwide and is the 3rd leading cause of mortality. It is a heterogeneous disorder with multiple endophenotypes, each driven by specific molecular networks and processes. Therapeutic discovery in COPD has lagged behind other disease areas owing to a lack of understanding of its pathobiology and scarcity of biomarkers to guide therapies. Single cell RNA sequencing (scRNA-seq) is a powerful new tool to identify important cellular and molecular networks that play a crucial role in disease pathogenesis. This paper provides an overview of the scRNA-seq technology and its application in COPD and the lessons learned to date from scRNA-seq experiments in COPD.
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Affiliation(s)
- Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital and Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
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27
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Kooistra T, Saez B, Roche M, Egea-Zorrilla A, Li D, Anketell D, Nguyen N, Villoria J, Gillis J, Petri E, Vera L, Blasco-Iturri Z, Smith NP, Alladina J, Zhang Y, Vinarsky V, Shivaraju M, Sheng SL, Gonzalez-Celeiro M, Mou H, Waghray A, Lin B, Paksa A, Yanger K, Tata PR, Zhao R, Causton B, Zulueta JJ, Prosper F, Cho JL, Villani AC, Haber A, Rajagopal J, Medoff BD, Pardo-Saganta A. Airway basal stem cells are necessary for the maintenance of functional intraepithelial airway macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600501. [PMID: 38979172 PMCID: PMC11230263 DOI: 10.1101/2024.06.25.600501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Adult stem cells play a crucial role in tissue homeostasis and repair through multiple mechanisms. In addition to being able to replace aged or damaged cells, stem cells provide signals that contribute to the maintenance and function of neighboring cells. In the lung, airway basal stem cells also produce cytokines and chemokines in response to inhaled irritants, allergens, and pathogens, which affect specific immune cell populations and shape the nature of the immune response. However, direct cell-to-cell signaling through contact between airway basal stem cells and immune cells has not been demonstrated. Recently, a unique population of intraepithelial airway macrophages (IAMs) has been identified in the murine trachea. Here, we demonstrate that IAMs require Notch signaling from airway basal stem cells for maintenance of their differentiated state and function. Furthermore, we demonstrate that Notch signaling between airway basal stem cells and IAMs is required for antigen-induced allergic inflammation only in the trachea where the basal stem cells are located whereas allergic responses in distal lung tissues are preserved consistent with a local circuit linking stem cells to proximate immune cells. Finally, we demonstrate that IAM-like cells are present in human conducting airways and that these cells display Notch activation, mirroring their murine counterparts. Since diverse lung stem cells have recently been identified and localized to specific anatomic niches along the proximodistal axis of the respiratory tree, we hypothesize that the direct functional coupling of local stem cell-mediated regeneration and immune responses permits a compartmentalized inflammatory response.
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28
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Rehman T, Pezzulo AA, Thurman AL, Zemans RL, Welsh MJ. Epithelial responses to CFTR modulators are improved by inflammatory cytokines and impaired by antiinflammatory drugs. JCI Insight 2024; 9:e181836. [PMID: 38888974 PMCID: PMC11383177 DOI: 10.1172/jci.insight.181836] [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: 04/08/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Cystic fibrosis (CF) is a genetic disorder that disrupts CF transmembrane conductance regulator (CFTR) anion channels and impairs airway host defenses. Airway inflammation is ubiquitous in CF, and suppressing it has generally been considered to improve outcomes. However, the role of inflammation in people taking CFTR modulators, small-molecule drugs that restore CFTR function, is not well understood. We previously showed that inflammation enhances the efficacy of CFTR modulators. To further elucidate this relationship, we treated human ΔF508-CF epithelia with TNF-α and IL-17, two inflammatory cytokines that are elevated in CF airways. TNF-α+IL-17 enhanced CFTR modulator-evoked anion secretion through mechanisms that raise intracellular Cl- (Na+/K+/2Cl- cotransport) and HCO3- (carbonic anhydrases and Na+/HCO3- cotransport). This enhancement required p38 MAPK signaling. Importantly, CFTR modulators did not affect CF airway surface liquid viscosity under control conditions but prevented the rise in viscosity in epithelia treated with TNF-α+IL-17. Finally, antiinflammatory drugs limited CFTR modulator responses in TNF-α+IL-17-treated epithelia. These results provide critical insights into mechanisms by which inflammation increases responses to CFTR modulators. They also suggest an equipoise between potential benefits and limitations of suppressing inflammation in people taking modulators, call into question current treatment approaches, and highlight a need for additional studies.
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Affiliation(s)
- Tayyab Rehman
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa, USA
| | - Alejandro A Pezzulo
- Department of Internal Medicine, Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa, USA
| | - Andrew L Thurman
- Department of Internal Medicine, Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa, USA
| | - Rachel L Zemans
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J Welsh
- Department of Internal Medicine, Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa, USA
- Howard Hughes Medical Institute, University of Iowa, Iowa City, Iowa, USA
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29
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Liu MY, Chen B, Borji M, Garcia de Alba Rivas C, Dost AFM, Moye AL, Movval Abdulla N, Paschini M, Rollins SD, Wang R, Schnapp LM, Khalil HA, Wu CJ, Sharma NS, Kim CF. Human Airway and Alveolar Organoids from BAL Fluid. Am J Respir Crit Care Med 2024; 209:1501-1504. [PMID: 38652140 PMCID: PMC11208964 DOI: 10.1164/rccm.202310-1831le] [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: 11/01/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Affiliation(s)
- Monica Yun Liu
- Stem Cell Program, Division of Hematology/Oncology, and
- Division of Pulmonary and Critical Care Medicine and
- Department of Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin
| | - Belinda Chen
- Stem Cell Program, Division of Hematology/Oncology, and
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Antonella F. M. Dost
- Stem Cell Program, Division of Hematology/Oncology, and
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Aaron L. Moye
- Stem Cell Program, Division of Hematology/Oncology, and
| | | | | | - Stuart D. Rollins
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Department of Medicine and
| | - Ruobing Wang
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Department of Medicine and
| | - Lynn M. Schnapp
- Department of Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin
| | - Hassan A. Khalil
- Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine and
| | - Nirmal S. Sharma
- Division of Pulmonary and Critical Care Medicine and
- Division of Pulmonary and Critical Care, Veterans Affairs Medical Center, West Roxbury, Boston, Massachusetts; and
| | - Carla F. Kim
- Stem Cell Program, Division of Hematology/Oncology, and
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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30
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Sun Y, Chatterjee S, Lian X, Traylor Z, Sattiraju SR, Xiao Y, Dilliard SA, Sung YC, Kim M, Lee SM, Moore S, Wang X, Zhang D, Wu S, Basak P, Wang J, Liu J, Mann RJ, LePage DF, Jiang W, Abid S, Hennig M, Martinez A, Wustman BA, Lockhart DJ, Jain R, Conlon RA, Drumm ML, Hodges CA, Siegwart DJ. In vivo editing of lung stem cells for durable gene correction in mice. Science 2024; 384:1196-1202. [PMID: 38870301 DOI: 10.1126/science.adk9428] [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: 09/20/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024]
Abstract
In vivo genome correction holds promise for generating durable disease cures; yet, effective stem cell editing remains challenging. In this work, we demonstrate that optimized lung-targeting lipid nanoparticles (LNPs) enable high levels of genome editing in stem cells, yielding durable responses. Intravenously administered gene-editing LNPs in activatable tdTomato mice achieved >70% lung stem cell editing, sustaining tdTomato expression in >80% of lung epithelial cells for 660 days. Addressing cystic fibrosis (CF), NG-ABE8e messenger RNA (mRNA)-sgR553X LNPs mediated >95% cystic fibrosis transmembrane conductance regulator (CFTR) DNA correction, restored CFTR function in primary patient-derived bronchial epithelial cells equivalent to Trikafta for F508del, corrected intestinal organoids and corrected R553X nonsense mutations in 50% of lung stem cells in CF mice. These findings introduce LNP-enabled tissue stem cell editing for disease-modifying genome correction.
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Affiliation(s)
- Yehui Sun
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sumanta Chatterjee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xizhen Lian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachary Traylor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | | - Yufen Xiao
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sean A Dilliard
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun-Chieh Sung
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minjeong Kim
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sang M Lee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephen Moore
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xu Wang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Di Zhang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiying Wu
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pratima Basak
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialu Wang
- ReCode Therapeutics, Menlo Park, CA 94025, USA
| | - Jing Liu
- ReCode Therapeutics, Menlo Park, CA 94025, USA
| | - Rachel J Mann
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - David F LePage
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Weihong Jiang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shadaan Abid
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | | | - Raksha Jain
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ronald A Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mitchell L Drumm
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Craig A Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Daniel J Siegwart
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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31
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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; 42:1086-1105.e13. [PMID: 38788720 PMCID: PMC11186085 DOI: 10.1016/j.ccell.2024.05.003] [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: 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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32
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Sipos F, Műzes G. Colonic Tuft Cells: The Less-Recognized Therapeutic Targets in Inflammatory Bowel Disease and Colorectal Cancer. Int J Mol Sci 2024; 25:6209. [PMID: 38892399 PMCID: PMC11172904 DOI: 10.3390/ijms25116209] [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: 04/28/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Tuft cells are more than guardian chemosensory elements of the digestive tract. They produce a variety of immunological effector molecules in response to stimulation; moreover, they are essential for defense against protozoa and nematodes. Beyond the description of their characteristics, this review aims to elucidate the potential pathogenic and therapeutic roles of colonic tuft cells in inflammatory bowel disease and colorectal cancer, focusing on their primarily immunomodulatory action. Regarding inflammatory bowel disease, tuft cells are implicated in both maintaining the integrity of the intestinal epithelial barrier and in tissue repair and regeneration processes. In addition to maintaining intestinal homeostasis, they display complex immune-regulatory functions. During the development of colorectal cancer, tuft cells can promote the epithelial-to-mesenchymal transition, alter the gastrointestinal microenvironment, and modulate both the anti-tumor immune response and the tumor microenvironment. A wide variety of their biological functions can be targeted for anti-inflammatory or anti-tumor therapies; however, the adverse side effects of immunomodulatory actions must be strictly considered.
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Affiliation(s)
- Ferenc Sipos
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
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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] [Grants] [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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34
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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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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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36
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Laitman BM, Cruz-Encarnacion P, Gordon RE, Genden EM. Case Report: Human Tracheal Transplantation Undergoes Progressive Reepithelialization Over Time. Laryngoscope 2024; 134:2664-2671. [PMID: 37975487 DOI: 10.1002/lary.31170] [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: 05/17/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVES Tracheal transplantation is an ideal option for the reconstruction of long-segment circumferential tracheal defects. Our group performed the first successful vascularized single-staged tracheal transplantation in January 2021. Although a rigid biocompatible structure is necessary for a functioning tracheal replacement, the importance of ciliated epithelium, which allows for critical mucociliary clearance, is now being appreciated. Here, we examined the histological changes of the first single-staged human tracheal transplant from serial endoscopic biopsies. METHODS Biopsies of the tracheal mucosa were serially obtained since the time of the tracheal transplantation. Samples were examined via hematoxylin and eosin, electron microscopy, and immunohistochemistry. RESULTS One week after transplantation, there is loss of ciliated epithelium and seromucinous cells, with only a basal layer of epithelium remaining. By 2 weeks, however, the epithelium begins to recover, albeit differently depending on the location of the biopsy. Near the site of tracheal anastomosis, there is epithelial proliferation, with the appearance of early ciliated cells. However, in the midgraft, there appears to be evidence of squamous metaplasia. Over time, however, normal ciliated epithelium and mucous cells appear without signs of chronic inflammation. CONCLUSIONS Critically, the tracheal allograft regained normal appearing respiratory epithelium after initial ischemic injury. The histologic differences at the midgraft versus anastomosis may suggest unique mechanisms of reepithelialization. At the recipient-donor interface, there may be a faster direct migration of recipient-derived epithelial cells, in line with preclinical studies. The midgraft, in contrast, responds with epithelial proliferation from the donor basal cells or dedifferentiated mucous cells. LEVEL OF EVIDENCE N/A Laryngoscope, 134:2664-2671, 2024.
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Affiliation(s)
- Benjamin M Laitman
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A
| | - Pamela Cruz-Encarnacion
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A
| | - Ronald E Gordon
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A
| | - Eric M Genden
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A
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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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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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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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40
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Qiu Y, Yang L, Jiang H, Zou Q. scTPC: a novel semisupervised deep clustering model for scRNA-seq data. Bioinformatics 2024; 40:btae293. [PMID: 38684178 PMCID: PMC11091743 DOI: 10.1093/bioinformatics/btae293] [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: 01/04/2024] [Revised: 04/14/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
MOTIVATION Continuous advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled researchers to further explore the study of cell heterogeneity, trajectory inference, identification of rare cell types, and neurology. Accurate scRNA-seq data clustering is crucial in single-cell sequencing data analysis. However, the high dimensionality, sparsity, and presence of "false" zero values in the data can pose challenges to clustering. Furthermore, current unsupervised clustering algorithms have not effectively leveraged prior biological knowledge, making cell clustering even more challenging. RESULTS This study investigates a semisupervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint, and cross-entropy constraint based on deep learning. Specifically, the model begins by pretraining a denoising autoencoder based on a zero-inflated negative binomial distribution. Deep clustering is then performed in the learned latent feature space using triplet constraints and pairwise constraints generated from partial labeled cells. Finally, to address imbalanced cell-type datasets, a weighted cross-entropy loss is introduced to optimize the model. A series of experimental results on 10 real scRNA-seq datasets and five simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework. AVAILABILITY AND IMPLEMENTATION scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.
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Affiliation(s)
- Yushan Qiu
- School of Mathematical Sciences, Shenzhen University, Shenzhen, Guangdong 518000, China
| | - Lingfei Yang
- School of Mathematical Sciences, Shenzhen University, Shenzhen, Guangdong 518000, China
| | - Hao Jiang
- School of Mathematics, Renmin University of China, Haidian District, Beijing 100872, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610056, China
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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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42
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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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43
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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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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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45
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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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46
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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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47
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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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48
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Liu Y, Lv W, Wang W. Uncovering the Cellular Microenvironment in Chronic Rhinosinusitis via Single-Cell RNA Sequencing: Application and Future Directions. Clin Rev Allergy Immunol 2024; 66:210-222. [PMID: 38687404 DOI: 10.1007/s12016-024-08992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Chronic rhinosinusitis (CRS) is a heterogenic disease characterized by persistent mucosal inflammation of the upper airway. Researches of CRS have progressed from phenotype-based to endotype-based, looking more deeply into molecular biomarkers, signaling pathways, and immune microenvironment. Single-cell RNA sequencing is an effective tool in analyzing composition, function, and interaction of cells in disease microenvironment at transcriptome level, showing great advantage in analyzing potential biomarkers, pathogenesis, and heterogeneity of chronic airway inflammation in an unbiased manner. In this article, we will review the latest advances in scRNA-seq studies of CRS to provide new perspectives for the diagnosis and treatment of this heterogeneous disease.
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Affiliation(s)
- Yuzhuo Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
| | - Wei Lv
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China.
| | - Weiqing Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China.
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49
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Gao FF, Chen DQ, Jiang YT, Han CF, Lin BY, Yang Z, Quan JH, Xiong YH, Chen XT. Functional roles of circular RNAs in lung injury. Front Pharmacol 2024; 15:1354806. [PMID: 38601461 PMCID: PMC11004487 DOI: 10.3389/fphar.2024.1354806] [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: 12/13/2023] [Accepted: 01/16/2024] [Indexed: 04/12/2024] Open
Abstract
Lung injury leads to respiratory dysfunction, low quality of life, and even life-threatening conditions. Circular RNAs (circRNAs) are endogenous RNAs produced by selective RNA splicing. Studies have reported their involvement in the progression of lung injury. Understanding the roles of circRNAs in lung injury may aid in elucidating the underlying mechanisms and provide new therapeutic targets. Thus, in this review, we aimed to summarize and discuss the characteristics and biological functions of circRNAs, and their roles in lung injury from existing research, to provide a theoretical basis for the use of circRNAs as a diagnostic and therapeutic target for lung injury.
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Affiliation(s)
- Fei-Fei Gao
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Dian-Qing Chen
- Department of Hand and Foot Surgery, Armed Police Corps Hospital of Hebei, Shijiazhuang, Hebei, China
| | - Yue-Tong Jiang
- Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Cui-Fei Han
- Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Bi-Yun Lin
- Biotissue Repository, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Zhan Yang
- Biotissue Repository, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Juan-Hua Quan
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Ying-Huan Xiong
- Biotissue Repository, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Xin-Tian Chen
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
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50
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Brody SL, Pan J, Huang T, Xu J, Xu H, Koenitizer J, Brennan SK, Nanjundappa R, Saba TG, Berical A, Hawkins FJ, Wang X, Zhang R, Mahjoub MR, Horani A, Dutcher SK. Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585965. [PMID: 38562900 PMCID: PMC10983967 DOI: 10.1101/2024.03.20.585965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Motile cilia have essential cellular functions in development, reproduction, and homeostasis. Genetic causes for motile ciliopathies have been identified, but the consequences on cellular functions beyond impaired motility remain unknown. Variants in CCDC39 and CCDC40 cause severe disease not explained by loss of motility. Using human cells with pathological variants in these genes, Chlamydomonas genetics, cryo-electron microscopy, single cell RNA transcriptomics, and proteomics, we identified perturbations in multiple cilia-independent pathways. Absence of the axonemal CCDC39/CCDC40 heterodimer results in loss of a connectome of over 90 proteins. The undocked connectome activates cell quality control pathways, switches multiciliated cell fate, impairs microtubule architecture, and creates a defective periciliary barrier. Both cilia-dependent and independent defects are likely responsible for the disease severity. Our findings provide a foundation for reconsidering the broad cellular impact of pathologic variants in ciliopathies and suggest new directions for therapies.
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Affiliation(s)
- Steven L Brody
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jiehong Pan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Tao Huang
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jian Xu
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Huihui Xu
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jeffrey Koenitizer
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Steven K Brennan
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rashmi Nanjundappa
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Thomas G Saba
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
| | - Andrew Berical
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Moe R Mahjoub
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Amjad Horani
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Susan K Dutcher
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
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