1
|
Berdnikovs S, Newcomb DC, McKernan KE, Kuehnle SN, Haruna NF, Gebretsadik T, McKennan C, Ma S, Cephus JY, Rosas-Salazar C, Anderson LJ, Gern JE, Hartert T. Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602506. [PMID: 39026695 PMCID: PMC11257436 DOI: 10.1101/2024.07.08.602506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Although childhood asthma is in part an airway epithelial disorder, the development of the airway epithelium in asthma is not understood. We sought to characterize airway epithelial developmental phenotypes in those with and without recurrent wheeze and the impact of infant infection with respiratory syncytial virus (RSV). Nasal airway epithelial cells (NAECs) were collected at age 2-3 years from an a priori designed nested birth cohort of children from four mutually exclusive groups of wheezers/non-wheezers and RSV-infected/uninfected in the first year of life. NAECs were cultured in air-liquid interface differentiation conditions followed by a combined analysis of single cell RNA sequencing (scRNA-seq) and in vitro infection with respiratory syncytial virus (RSV). NAECs from children with a wheeze phenotype were characterized by abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation and a delayed onset of maturation. NAECs from children with wheeze also had increased diversity of currently known RSV receptors and blunted anti-viral immune responses to in vitro infection. The most dramatic changes in differentiation of cultured epithelium were observed in NAECs derived from children that had both wheeze and RSV in the first year of life. Together this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and increased RSV receptors, which may predispose to and amplify the effects of RSV infection in infancy and susceptibility to other asthma risk factors that interact with the airway mucosa. SUMMARY Nasal airway epithelial cells from children with wheeze are characterized by altered development and increased susceptibility to RSV infection.
Collapse
|
2
|
Skibba ME, Brasier AR. NF-κB/RelA signaling in secretoglobin progenitors mediates plasticity and MMP-induced barrier disruption in house dust mite-induced allergic asthma. Am J Physiol Lung Cell Mol Physiol 2024; 327:L86-L101. [PMID: 38713619 DOI: 10.1152/ajplung.00066.2024] [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: 02/20/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024] Open
Abstract
The mechanisms how aeroallergens induce sensitization are incompletely understood. The house dust mite (HDM) Dermatophagoides pteronyssius (Der p) is a ubiquitous aeroallergen that represents a major cause of allergic rhinitis and asthma. Herein, we tested whether HDM-induced aeroallergen exposure sensitivity is caused by the innate-immune response in small airway epithelial cells. HDM exposure is a rapid activator of NF-κB/RelA in the Secretoglobin (Scgb1a1+) lineage associated with upregulation of NF-κB/RelA-dependent markers of epithelial plasticity. To determine the effect of epithelial NF-κB signaling, NF-κB was depleted in a tamoxifen (TMX)-inducible Scgb1a1-CreERTM mouse within a CL57B/L6 background. Corn oil or TMX-treated/RelA-depleted [RelA knockdown (KD)] mice were repetitively exposed to airway HDM challenges to induce airway hyperresponsiveness (AHR). Strikingly, we observed that HDM induces hallmarks of epithelial plasticity through upregulation of the mesenchymal core factors SNAI1 and ZEB1 and production of metalloproteinase (MMP)9 that are RelA-dependent. Downstream, HDM-induced mucous metaplasia, Th2 polarization, allergen sensitivity, and airway hyperreactivity were all reduced in the RelA-depleted mice. Mechanistically, HDM-induced functional and structural barrier disruption was dependent on RelA signaling and associated with active MMP secretion into the bronchoalveolar lavage fluid. To establish the role of MMP2/9 in barrier disruption, we observe that a small-molecule MMP inhibitor (SB-3CT) blocked HDM-induced barrier disruption and activation of plasticity in naïve wild-type (WT) mice. Loss of functional barrier was associated with MMP disruption of zona occludens (ZO)-1 containing adherens junctions. Overall, this data indicates that host innate signaling in the Scgb1a1+ progenitors is directly linked to epithelial plasticity, MMP9 secretion, and enhanced barrier permeability that allows allergen penetration, sensitization producing allergic asthma (AA) in vivo. We propose that maintenance of epithelial integrity may reduce allergic sensitization and AA.NEW & NOTEWORTHY Allergic asthma from house dust mite (HDM) allergy causes substantial morbidity. This study examines the dynamic changes in small airway epithelial cells in a mouse model of HDM exposure. Our findings indicate that NF-κB/RelA signaling mediates matrix metalloproteinase production, disrupting the epithelial barrier resulting in allergic sensitization. Our findings bring new insight into mechanisms for epithelial cell-state change in the allergen response, creating a potential therapeutic pathway for maintaining barrier function in asthma.
Collapse
Affiliation(s)
- Melissa E Skibba
- School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States
| | - Allan R Brasier
- School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States
- Institute for Clinical and Translational Research, Madison, Wisconsin, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O'Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal influenza infection rewires tissue-scale memory response dynamics. Immunity 2024:S1074-7613(24)00311-X. [PMID: 38964332 DOI: 10.1016/j.immuni.2024.06.005] [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: 05/05/2023] [Revised: 03/14/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
The nasal mucosa is often the initial site of respiratory viral infection, replication, and transmission. Understanding how infection shapes tissue-scale primary and memory responses is critical for designing mucosal therapeutics and vaccines. We generated a single-cell RNA-sequencing atlas of the murine nasal mucosa, sampling three regions during primary influenza infection and rechallenge. Compositional analysis revealed restricted infection to the respiratory mucosa with stepwise changes in immune and epithelial cell subsets and states. We identified and characterized a rare subset of Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells, which concurrently increased with tissue-resident memory T (TRM)-like cells. Proportionality analysis, cell-cell communication inference, and microscopy underscored the CXCL16-CXCR6 axis between KNIIFE and TRM cells. Secondary influenza challenge induced accelerated and coordinated myeloid and lymphoid responses without epithelial proliferation. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses.
Collapse
Affiliation(s)
- Samuel W Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O'Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
6
|
Marriott H, Duchesne M, Moitra S, Okoye I, Gerla L, Mayers I, Moolji J, Adatia A, Lacy P. Upper Airway Alarmin Cytokine Expression in Asthma of Different Severities. J Clin Med 2024; 13:3721. [PMID: 38999286 PMCID: PMC11242732 DOI: 10.3390/jcm13133721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Background: The secretion of alarmin cytokines by epithelial cells, including thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33, initiates inflammatory cascades in asthma. However, alarmin cytokine expression in the upper airways in asthma remains largely unknown. Methods: We recruited 40 participants with asthma into four groups as per the Global Initiative for Asthma (GINA) steps (10 in each group of GINA 1/2, 3, 4, and 5). Cells were derived from nasal, buccal, and throat brushings. Intracellular cytokine expression (TSLP, IL-25, and IL-33) was assessed by flow cytometry in cytokeratin 8+ (Ck8+) epithelial cells immediately following collection. Results: TSLP was significantly increased (p < 0.001) in GINA 5 patients across nasal, buccal, and throat Ck8+ epithelial cells, while IL-25 was elevated in nasal and throat samples (p < 0.003), and IL-33 levels were variable, compared with GINA 1-4 patients. Individual GINA subgroup comparison showed that TSLP levels in nasal samples from GINA 5 patients were significantly (p = 0.03) elevated but did not differ between patients with and without nasal comorbidities. IL-25 and IL-33 (obtained from nasal, buccal, and throat samples) were not significantly different in individual groups. Conclusions: Our study demonstrates for the first time that Ck8+ nasal epithelial cells from GINA 5 asthma patients express elevated levels of TSLP.
Collapse
Affiliation(s)
- Hazel Marriott
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Marc Duchesne
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Subhabrata Moitra
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Isobel Okoye
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Luke Gerla
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Irvin Mayers
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jalal Moolji
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Adil Adatia
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Paige Lacy
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Chang JJY, Grimley SL, Tran BM, Deliyannis G, Tumpach C, Nguyen AN, Steinig E, Zhang J, Schröder J, Caly L, McAuley J, Wong SL, Waters SA, Stinear TP, Pitt ME, Purcell D, Vincan E, Coin LJ. Uncovering strain- and age-dependent innate immune responses to SARS-CoV-2 infection in air-liquid-interface cultured nasal epithelia. iScience 2024; 27:110009. [PMID: 38868206 PMCID: PMC11166695 DOI: 10.1016/j.isci.2024.110009] [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: 05/19/2023] [Revised: 04/03/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Continuous assessment of the impact of SARS-CoV-2 on the host at the cell-type level is crucial for understanding key mechanisms involved in host defense responses to viral infection. We investigated host response to ancestral-strain and Alpha-variant SARS-CoV-2 infections within air-liquid-interface human nasal epithelial cells from younger adults (26-32 Y) and older children (12-14 Y) using single-cell RNA-sequencing. Ciliated and secretory-ciliated cells formed the majority of highly infected cell-types, with the latter derived from ciliated lineages. Strong innate immune responses were observed across lowly infected and uninfected bystander cells and heightened in Alpha-infection. Alpha highly infected cells showed increased expression of protein-refolding genes compared with ancestral-strain-infected cells in children. Furthermore, oxidative phosphorylation-related genes were down-regulated in bystander cells versus infected and mock-control cells, underscoring the importance of these biological functions for viral replication. Overall, this study highlights the complexity of cell-type-, age- and viral strain-dependent host epithelial responses to SARS-CoV-2.
Collapse
Affiliation(s)
- Jessie J.-Y. Chang
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Samantha L. Grimley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Bang M. Tran
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Georgia Deliyannis
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Carolin Tumpach
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - An N.T. Nguyen
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Eike Steinig
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - JianShu Zhang
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jan Schröder
- Computational Sciences Initiative (CSI), The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sharon L. Wong
- Molecular and Integrative Cystic Fibrosis Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shafagh A. Waters
- Molecular and Integrative Cystic Fibrosis Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Respiratory Medicine, Sydney Children’s Hospital, Sydney, NSW 2031, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Miranda E. Pitt
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Damian Purcell
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Lachlan J.M. Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
Collapse
Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Chingpan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
11
|
Ding M, Wei X, Liu C, Tan X. Mahuang Fuzi Xixin decoction alleviates allergic rhinitis by inhibiting NLRP3/Caspase-1/GSDMD-N-mediated pyroptosis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 327:118041. [PMID: 38479543 DOI: 10.1016/j.jep.2024.118041] [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: 11/03/2023] [Revised: 02/28/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Allergic rhinitis (AR) is a prevalent nasal inflammatory disorder, and pyroptosis plays a crucial role in aggravating AR. Current medications for AR treatment still have deficiencies, and finding new agents is of great interest. Mahuang Fuzi Xixin decoction (MFXD), an ancient Chinese medicine, is now commonly used to treat AR, which has anti-inflammatory and immunomodulatory effects, but its underlying mechanism is unknown. AIM OF THIS STUDY This study aims to evaluate the effects of MFXD on AR and explore its potential mechanisms in view of the regulatory effect on pyroptosis. METHODS MFXD, Mahuang, Fuzi, and Xixin water extracts were analyzed using ultra high performance liquid chromatography-Orbitrap-high-resolution accurate mass spectrometry. In in vivo study, the effects of MFXD on AR treatment were evaluated in an ovalbumin-induced mouse model. Mice were administered saline (control and model groups), MFXD (1.375, 2.75 g/kg), and dexamethasone (2.5 mg/kg) for 13 days. AR symptoms were evaluated by blinded observers. Immunoglobulin E (IgE) and histamine levels were measured using enzyme-linked immunosorbent assays. Expression of pyroptosis-related proteins (NLRP3, ASC, Caspase-1 p10/p20, GSDMD-N and IL-1β) in AR mouse nasal mucosa were estimated by immunohistochemistry. In in vivtro study, the effects of MFXD on pyroptosis were assessed in human nasal epithelial cells (HNEpCs) stimulated with lipopolysaccharide (LPS) and adenosine triphosphate (ATP), and incubated with MFXD (12.5, 25, and 50 μg/mL). Pyroptosis-related protein expression was measured by western blotting. RESULTS Thirty-three compounds in MFXD were identified, including ephedrine, pseudoephedrine, higenamine, aconine, aconitine, benzoylmesaconitine, benzoylhypaconine and hypaconitine. In the in vivo study, oral taken of MFXD/dexamethasone significantly ameliorated AR symptoms, reduced swelling of the nasal mucosa, and decreased the levels of IgE and histamine in AR mice serum. MFXD/dexamethasone attenuated histopathological changes and reduced the expression of pyroptosis-related proteins in nasal mucosa, indicating the inhibitory effect on nasal epithelial pyroptosis. In the in vitro study, MFXD (50 μg/mL) significantly alleviated cytotoxicity, protected cells from swelling and rupture, and downregulated the expression of pyroptosis-related proteins in LPS/ATP-induced HNEpCs. CONCLUSION MFXD suppressed nasal epithelial pyroptosis by inhibiting the NLRP3/Caspase-1/GSDMD-N signaling pathway, which alleviates AR. Our results offer valuable insights into potential AR therapies and provide evidence for the clinical utilization of MFXD to treat AR.
Collapse
Affiliation(s)
- Mengze Ding
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China; Guangzhou Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation, Technology, Guangzhou, 510515, China.
| | - Xiaohan Wei
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Changshun Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China; Guangzhou Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation, Technology, Guangzhou, 510515, China.
| | - Xiaomei Tan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China; Guangzhou Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation, Technology, Guangzhou, 510515, China.
| |
Collapse
|
12
|
Mérignac-Lacombe J, Kornbausch N, Sivarajan R, Boichot V, Berg K, Oberwinkler H, Saliba AE, Loos HM, Ehret Kasemo T, Scherzad A, Bodem J, Buettner A, Neiers F, Erhard F, Hackenberg S, Heydel JM, Steinke M. Characterization of a Human Respiratory Mucosa Model to Study Odorant Metabolism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12696-12706. [PMID: 38775624 DOI: 10.1021/acs.jafc.4c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Nasal xenobiotic metabolizing enzymes (XMEs) are important for the sense of smell because they influence odorant availability and quality. Since the major part of the human nasal cavity is lined by a respiratory mucosa, we hypothesized that this tissue contributed to nasal odorant metabolism through XME activity. Thus, we built human respiratory tissue models and characterized the XME profiles using single-cell RNA sequencing. We focused on the XMEs dicarbonyl and l-xylulose reductase, aldehyde dehydrogenase (ALDH) 1A1, and ALDH3A1, which play a role in food odorant metabolism. We demonstrated protein abundance and localization in the tissue models and showed the metabolic activity of the corresponding enzyme families by exposing the models to the odorants 3,4-hexandione and benzaldehyde. Using gas chromatography coupled with mass spectrometry, we observed, for example, a significantly higher formation of the corresponding metabolites 4-hydroxy-3-hexanone (39.03 ± 1.5%, p = 0.0022), benzyl alcohol (10.05 ± 0.88%, p = 0.0008), and benzoic acid (8.49 ± 0.57%, p = 0.0004) in odorant-treated tissue models compared to untreated controls (0 ± 0, 0.12 ± 0.12, and 0.18 ± 0.18%, respectively). This is the first study that reveals the XME profile of tissue-engineered human respiratory mucosa models and demonstrates their suitability to study nasal odorant metabolism.
Collapse
Affiliation(s)
- Jeanne Mérignac-Lacombe
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Nicole Kornbausch
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
| | - Rinu Sivarajan
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Valentin Boichot
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Kevin Berg
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, 93053 Regensburg, Germany
| | - Heike Oberwinkler
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Helene M Loos
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
- Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354 Freising, Germany
- FAU Research Center "New Bioactive Compounds", Schlossplatz 4, 91054 Erlangen, Germany
| | - Totta Ehret Kasemo
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Agmal Scherzad
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Andrea Buettner
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
- Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354 Freising, Germany
- FAU Research Center "New Bioactive Compounds", Schlossplatz 4, 91054 Erlangen, Germany
| | - Fabrice Neiers
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, 93053 Regensburg, Germany
| | - Stephan Hackenberg
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Jean-Marie Heydel
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Maria Steinke
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
- Fraunhofer Institute for Silicate Research ISC, Röntgenring 12, 97070 Würzburg, Germany
| |
Collapse
|
13
|
Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
Collapse
Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| |
Collapse
|
14
|
Brownell J, Lee KE, Chasman D, Gangnon R, Bendixsen CG, Barnes K, Grindle K, Pappas T, Bochkov YA, Dresen A, Hou C, Haslam DB, Seroogy CM, Ong IM, Gern JE. Farm animal exposure, respiratory illnesses, and nasal cell gene expression. J Allergy Clin Immunol 2024; 153:1647-1654. [PMID: 38309597 PMCID: PMC11162314 DOI: 10.1016/j.jaci.2024.01.019] [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: 05/16/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. OBJECTIVE We hypothesized that children raised in farm environments have a lower incidence of respiratory illnesses over the first 2 years of life than nonfarm children. We also analyzed whether farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. METHODS The Wisconsin Infant Study Cohort included farm (n = 156) and nonfarm (n = 155) families with children followed to age 2 years. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression in a subset of 64 children at age 2 years was compared to farm exposure and respiratory illness history. RESULTS Farm versus nonfarm children had nominally lower rates of respiratory illnesses (rate ratio 0.82 [95% CI, 0.69, 0.97]) with a stepwise reduction in illness rates in children exposed to 0, 1, or ≥2 animal species, but these trends were nonsignificant in a multivariable model. Farm exposures and preceding respiratory illnesses were positively related to nasal cell gene signatures for mononuclear cells and innate and antimicrobial responses. CONCLUSIONS Maternal and infant exposure to farms and farm animals was associated with nonsignificant trends for reduced respiratory illnesses. Nasal cell gene expression in a subset of children suggests that farm exposures and respiratory illnesses in early life are associated with distinct patterns of mucosal immune expression.
Collapse
Affiliation(s)
- Joshua Brownell
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Kristine E Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Deborah Chasman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis; Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wis
| | - Ronald Gangnon
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, Wis
| | - Katherine Barnes
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, Wis
| | - Kristine Grindle
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Tressa Pappas
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Amy Dresen
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Christine Hou
- Department of Statistics, University of Wisconsin-Madison, Madison
| | - David B Haslam
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | | | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis; Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wis
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
van Woudenbergh E, van Rooijen DM, Veldman-Wolf JJ, Nicolaie MA, Huynen MA, van der Klis FRM, de Jonge MI, den Hartog G. Effect of age and season on respiratory mucosal immune marker profiles. J Allergy Clin Immunol 2024; 153:1681-1691.e12. [PMID: 38142822 DOI: 10.1016/j.jaci.2023.12.009] [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: 07/12/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
BACKGROUND The upper respiratory tract is continuously exposed to microorganisms and noxious elements, leading to local immune responses and the secretion of immune markers. While several studies describe immune marker profiles in respiratory mucosal samples in defined patient cohorts, mucosal immune profiles from the general population during the different seasons are lacking. Such baseline profiles are essential to understand the effect of various exposures to the mucosal immune system throughout life. OBJECTIVE We sought to establish baseline local upper respiratory mucosal immune profiles in the general population and assess these profiles with regard to age, sex, seasonality, and basic health and lifestyle factors. METHODS We measured the concentrations of 35 immune markers involved in a broad range of immunological processes at the mucosa in nasopharyngeal swab samples from 951 individuals, aged 0 to 86 years, from a nationwide study. RESULTS Clustering analysis showed that immune marker profiles clearly reflected immunological functions, such as tissue regeneration and antiviral responses. Immune marker concentrations changed strongly with seasonality and age, with the most profound changes occurring in the first 25 years of life; they were also associated with sex, body mass index, smoking, mild symptoms of airway infection, and chronic asthma and hay fever. CONCLUSION Immunological analyses of noninvasive mucosal samples provide insight into mucosal immune responses to microbial and noxious element exposure in the general population. These data provide a baseline for future studies on respiratory mucosal immune responses and for the development of mucosal immune-based diagnostics.
Collapse
Affiliation(s)
- Esther van Woudenbergh
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Debbie M van Rooijen
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Janine J Veldman-Wolf
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mioara A Nicolaie
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Fiona R M van der Klis
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Gerco den Hartog
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.
| |
Collapse
|
17
|
Stoleriu MG, Ansari M, Strunz M, Schamberger A, Heydarian M, Ding Y, Voss C, Schneider JJ, Gerckens M, Burgstaller G, Castelblanco A, Kauke T, Fertmann J, Schneider C, Behr J, Lindner M, Stacher-Priehse E, Irmler M, Beckers J, Eickelberg O, Schubert B, Hauck SM, Schmid O, Hatz RA, Stoeger T, Schiller HB, Hilgendorff A. COPD basal cells are primed towards secretory to multiciliated cell imbalance driving increased resilience to environmental stressors. Thorax 2024; 79:524-537. [PMID: 38286613 PMCID: PMC11137452 DOI: 10.1136/thorax-2022-219958] [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: 12/18/2022] [Accepted: 01/03/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Environmental pollutants injure the mucociliary elevator, thereby provoking disease progression in chronic obstructive pulmonary disease (COPD). Epithelial resilience mechanisms to environmental nanoparticles in health and disease are poorly characterised. METHODS We delineated the impact of prevalent pollutants such as carbon and zinc oxide nanoparticles, on cellular function and progeny in primary human bronchial epithelial cells (pHBECs) from end-stage COPD (COPD-IV, n=4), early disease (COPD-II, n=3) and pulmonary healthy individuals (n=4). After nanoparticle exposure of pHBECs at air-liquid interface, cell cultures were characterised by functional assays, transcriptome and protein analysis, complemented by single-cell analysis in serial samples of pHBEC cultures focusing on basal cell differentiation. RESULTS COPD-IV was characterised by a prosecretory phenotype (twofold increase in MUC5AC+) at the expense of the multiciliated epithelium (threefold reduction in Ac-Tub+), resulting in an increased resilience towards particle-induced cell damage (fivefold reduction in transepithelial electrical resistance), as exemplified by environmentally abundant doses of zinc oxide nanoparticles. Exposure of COPD-II cultures to cigarette smoke extract provoked the COPD-IV characteristic, prosecretory phenotype. Time-resolved single-cell transcriptomics revealed an underlying COPD-IV unique basal cell state characterised by a twofold increase in KRT5+ (P=0.018) and LAMB3+ (P=0.050) expression, as well as a significant activation of Wnt-specific (P=0.014) and Notch-specific (P=0.021) genes, especially in precursors of suprabasal and secretory cells. CONCLUSION We identified COPD stage-specific gene alterations in basal cells that affect the cellular composition of the bronchial elevator and may control disease-specific epithelial resilience mechanisms in response to environmental nanoparticles. The identified phenomena likely inform treatment and prevention strategies.
Collapse
Affiliation(s)
- Mircea Gabriel Stoleriu
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Meshal Ansari
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Maximilian Strunz
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Andrea Schamberger
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Motaharehsadat Heydarian
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Yaobo Ding
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Carola Voss
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Juliane Josephine Schneider
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Michael Gerckens
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine V, University Hospital, LMU Munich and Asklepios Medical Center, Munich, Germany
| | - Gerald Burgstaller
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Alejandra Castelblanco
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Teresa Kauke
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Jan Fertmann
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Christian Schneider
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Juergen Behr
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine V, University Hospital, LMU Munich and Asklepios Medical Center, Munich, Germany
| | - Michael Lindner
- Department of Visceral and Thoracic Surgery Salzburg, Paracelsus Medical University, Salzburg, Austria
| | | | - Martin Irmler
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Experimental Genetics, Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Experimental Genetics, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Life Sciences, Chair of Experimental Genetics, Technical University Munich, Freising, Germany
| | - Oliver Eickelberg
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Medicine, Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Benjamin Schubert
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Department of Mathematics, Technische Universität München, Garching bei München, München, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Otmar Schmid
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Rudolf A Hatz
- Division for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich, Germany
| | - Tobias Stoeger
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Herbert B Schiller
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
| | - Anne Hilgendorff
- Institute for Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Lung Research Center (DZL), Munich, Germany
- Center for Comprehensive Developmental Care at the iSPZ Hauner, Dr. von Haunersches Children's University Hospital, Ludwig-Maximilians-University of Munich (LMU); Member of the German Lung Research Center (DZL), Munich, Germany
| |
Collapse
|
18
|
Ruysseveldt E, Steelant B, Wils T, Cremer J, Bullens DMA, Hellings PW, Martens K. The nasal basal cell population shifts toward a diseased phenotype with impaired barrier formation capacity in allergic rhinitis. J Allergy Clin Immunol 2024:S0091-6749(24)00454-8. [PMID: 38705259 DOI: 10.1016/j.jaci.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The integrity of the airway epithelium is guarded by the airway basal cells that serve as progenitor cells and restore wounds in case of injury. Basal cells are a heterogenous population, and specific changes in their behavior are associated with chronic barrier disruption-mechanisms that have not been studied in detail in allergic rhinitis (AR). OBJECTIVE We aimed to study basal cell subtypes in AR and healthy controls. METHODS Single-cell RNA sequencing (scRNA-Seq) of the nasal epithelium was performed on nonallergic and house dust mite-allergic AR patients to reveal basal cell diversity and to identify allergy-related alterations. Flow cytometry, immunofluorescence staining, and in vitro experiments using primary basal cells were performed to confirm phenotypic findings at the protein level and functionally. RESULTS The scRNA-Seq, flow cytometry, and immunofluorescence staining revealed that basal cells are abundantly and heterogeneously present in the nasal epithelium, suggesting specialized subtypes. The total basal cell fraction within the epithelium in AR is increased compared to controls. scRNA-Seq demonstrated that potentially beneficial basal cells are missing in AR epithelium, while an activated population of allergy-associated basal cells is more dominantly present. Furthermore, our in vitro proliferation, wound healing assay and air-liquid interface cultures show that AR-associated basal cells have altered progenitor capacity compared to nonallergic basal cells. CONCLUSIONS The nasal basal cell population is abundant and diverse, and it shifts toward a diseased state in AR. The absence of potentially protective subtypes and the rise of a proinflammatory population suggest that basal cells are important players in maintaining epithelial barrier defects in AR.
Collapse
Affiliation(s)
- Emma Ruysseveldt
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium.
| | - Brecht Steelant
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Tine Wils
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Dominique M A Bullens
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Clinical Department of Paediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Peter W Hellings
- 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; Upper Airways Research Laboratory, University of Ghent, Ghent, Belgium
| | - Katleen Martens
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
19
|
Emanuel E, Arifuzzaman M, Artis D. Epithelial-neuronal-immune cell interactions: Implications for immunity, inflammation, and tissue homeostasis at mucosal sites. J Allergy Clin Immunol 2024; 153:1169-1180. [PMID: 38369030 PMCID: PMC11070312 DOI: 10.1016/j.jaci.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
The epithelial lining of the respiratory tract and intestine provides a critical physical barrier to protect host tissues against environmental insults, including dietary antigens, allergens, chemicals, and microorganisms. In addition, specialized epithelial cells communicate directly with hematopoietic and neuronal cells. These epithelial-immune and epithelial-neuronal interactions control host immune responses and have important implications for inflammatory conditions associated with defects in the epithelial barrier, including asthma, allergy, and inflammatory bowel diseases. In this review, we discuss emerging research that identifies the mechanisms and impact of epithelial-immune and epithelial-neuronal cross talk in regulating immunity, inflammation, and tissue homeostasis at mucosal barrier surfaces. Understanding the regulation and impact of these pathways could provide new therapeutic targets for inflammatory diseases at mucosal sites.
Collapse
Affiliation(s)
- Elizabeth Emanuel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY; Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Allen Discovery Center for Neuroimmune Interactions, New York, NY; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY.
| |
Collapse
|
20
|
Lin B, Shah VS, Chernoff C, Sun J, Shipkovenska GG, Vinarsky V, Waghray A, Xu J, Leduc AD, Hintschich CA, Surve MV, Xu Y, Capen DE, Villoria J, Dou Z, Hariri LP, Rajagopal J. Airway hillocks are injury-resistant reservoirs of unique plastic stem cells. Nature 2024; 629:869-877. [PMID: 38693267 DOI: 10.1038/s41586-024-07377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Airway hillocks are stratified epithelial structures of unknown function1. Hillocks persist for months and have a unique population of basal stem cells that express genes associated with barrier function and cell adhesion. Hillock basal stem cells continually replenish overlying squamous barrier cells. They exhibit dramatically higher turnover than the abundant, largely quiescent classic pseudostratified airway epithelium. Hillocks resist a remarkably broad spectrum of injuries, including toxins, infection, acid and physical injury because hillock squamous cells shield underlying hillock basal stem cells from injury. Hillock basal stem cells are capable of massive clonal expansion that is sufficient to resurface denuded airway, and eventually regenerate normal airway epithelium with each of its six component cell types. Hillock basal stem cells preferentially stratify and keratinize in the setting of retinoic acid signalling inhibition, a known cause of squamous metaplasia2,3. Here we show that mouse hillock expansion is the cause of vitamin A deficiency-induced squamous metaplasia. Finally, we identify human hillocks whose basal stem cells generate functional squamous barrier structures in culture. The existence of hillocks reframes our understanding of airway epithelial regeneration. Furthermore, we show that hillocks are one origin of 'squamous metaplasia', which is long thought to be a precursor of lung cancer.
Collapse
Affiliation(s)
- Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA.
- Department of Developmental, Molecular and Chemical Biology, School of Medicine, Tufts University, Boston, MA, USA.
| | - Viral S Shah
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chaim Chernoff
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Developmental and Regenerative Biology Program, Harvard, Cambridge, MA, USA
| | - Jiawei Sun
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Gergana G Shipkovenska
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Jiajie Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Andrew D Leduc
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Constantin A Hintschich
- Department of Developmental, Molecular and Chemical Biology, School of Medicine, Tufts University, Boston, MA, USA
- Department of Otorhinolaryngology, Regensburg University Hospital, Regensburg, Germany
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Manalee Vishnu Surve
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Diane E Capen
- Program in Membrane Biology and Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Villoria
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Lida P Hariri
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA.
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Developmental and Regenerative Biology Program, Harvard, Cambridge, MA, USA.
| |
Collapse
|
21
|
Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
Collapse
Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
| |
Collapse
|
22
|
Roth D, Şahin AT, Ling F, Senger CN, Quiroz EJ, Calvert BA, van der Does AM, Güney TG, Tepho N, Glasl S, van Schadewijk A, von Schledorn L, Olmer R, Kanso E, Nawroth JC, Ryan AL. STRUCTURE-FUNCTION RELATIONSHIPS OF MUCOCILIARY CLEARANCE IN HUMAN AIRWAYS. RESEARCH SQUARE 2024:rs.3.rs-4164522. [PMID: 38746209 PMCID: PMC11092836 DOI: 10.21203/rs.3.rs-4164522/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Our study focuses on the intricate connection between tissue-level organization and ciliated organ function in humans, particularly in understanding the morphological organization of airways and their role in mucociliary clearance. Mucociliary clearance is a key mechanical defense mechanism of human airways, and clearance failure is associated with many respiratory diseases, including chronic obstructive pulmonary disease (COPD) and asthma. While single-cell transcriptomics have unveiled the cellular complexity of the human airway epithelium, our understanding of the mechanics that link epithelial structure to clearance function mainly stem from animal models. This reliance on animal data limits crucial insights into human airway barrier function and hampers the human-relevant in vitro modeling of airway diseases. This study, for the first time, maps the distribution of ciliated and secretory cell types along the airway tree in both rats and humans, noting species-specific differences in ciliary function and elucidates structural parameters of airway epithelia that predict clearance function in both native and in vitro tissues alike. By uncovering how tissue organization influences ciliary function, we can better understand disruptions in mucociliary clearance, which could have implications for various ciliated organs beyond the airways.
Collapse
Affiliation(s)
- Doris Roth
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Ayşe Tuğçe Şahin
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Feng Ling
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Christiana N. Senger
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Erik J. Quiroz
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ben A. Calvert
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anne M. van der Does
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tankut G. Güney
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Niels Tepho
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Sarah Glasl
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Annemarie van Schadewijk
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura von Schledorn
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Hannover, D-30625, Germany
- Biomedical Research in End stage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, D-30625, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, D-30625, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Hannover, D-30625, Germany
- Biomedical Research in End stage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, D-30625, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, D-30625, Germany
| | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Janna C. Nawroth
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Amy L. Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA 52242, USA
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Kicic-Starcevich E, Hancock DG, Iosifidis T, Agudelo-Romero P, Caparros-Martin JA, Karpievitch YV, Silva D, Turkovic L, Le Souef PN, Bosco A, Martino DJ, Kicic A, Prescott SL, Stick SM. Airway epithelium respiratory illnesses and allergy (AERIAL) birth cohort: study protocol. FRONTIERS IN ALLERGY 2024; 5:1349741. [PMID: 38666051 PMCID: PMC11043573 DOI: 10.3389/falgy.2024.1349741] [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: 12/05/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life. Methods The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to 5 years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to 6 weeks, 1, 3, and 5 years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal sampling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses. Discussion The AERIAL study will provide a comprehensive longitudinal assessment of factors influencing the association between epithelial dysfunction and respiratory morbidity in early life, and hopefully identify novel targets for diagnosis and early intervention.
Collapse
Affiliation(s)
| | - David G. Hancock
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA, Australia
- School of Medicine, The University of Western Australia, Nedlands, WA, Australia
| | - Thomas Iosifidis
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine, The University of Western Australia, Nedlands, WA, Australia
| | - Patricia Agudelo-Romero
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- European Virus Bioinformatics Centre, Jena, Germany
| | | | | | - Desiree Silva
- School of Medicine, The University of Western Australia, Nedlands, WA, Australia
- Telethon Kids Institute, Perth, WA, Australia
- Department of Paediatrics and Neonatology, Joondalup Health Campus, Joondalup, WA, Australia
- School of Medicine and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | | | - Peter N. Le Souef
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA, Australia
| | - Anthony Bosco
- School of Population Health, Curtin University, Bentley, WA, Australia
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
- Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, United States
| | - David J. Martino
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anthony Kicic
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine, The University of Western Australia, Nedlands, WA, Australia
| | - Susan L. Prescott
- School of Medicine, The University of Western Australia, Nedlands, WA, Australia
- European Virus Bioinformatics Centre, Jena, Germany
| | - Stephen M. Stick
- Wal-yan RespiratoryResearch Centre, Telethon Kids Institute, Perth, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine, The University of Western Australia, Nedlands, WA, Australia
| |
Collapse
|
25
|
Ding Y, Wang Z, Zhang Z, You R, Wu Y, Bian T. GLUT3-mediated cigarette smoke-induced epithelial-mesenchymal transition in chronic obstructive pulmonary disease through the NF-kB/ZEB1 pathway. Respir Res 2024; 25:158. [PMID: 38594707 PMCID: PMC11005242 DOI: 10.1186/s12931-024-02785-3] [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: 01/10/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Airway remodelling plays an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Epithelial-mesenchymal transition (EMT) is a significant process during the occurrence of airway remodelling. Increasing evidence suggests that glucose transporter 3 (GLUT3) is involved in the epithelial mesenchymal transition (EMT) process of various diseases. However, the role of GLUT3 in EMT in the airway epithelial cells of COPD patients remains unclear. METHODS We detected the levels of GLUT3 in the peripheral lung tissue of COPD patients and cigarette smoke (CS)-exposed mice. Two Gene Expression Omnibus GEO datasets were utilised to analyse GLUT3 gene expression profiles in COPD. Western blot and immunofluorescence were used to detect GLUT3 expression. In addition, we used the AAV9-GLUT3 inhibitor to reduce GLUT3 expression in the mice model. Masson's staining and lung function measurement were used detect the collagen deposition and penh in the mice. A cell study was performed to confirm the regulatory effect of GLUT3. Inhibition of GLUT3 expression with siRNA, Western blot, and immunofluorescence were used to detect the expression of E-cadherin, N-cadherin, vimentin, p65, and ZEB1. RESULTS Based on the GEO data set analysis, GLUT3 expression in COPD patients was higher than in non-smokers. Moreover, GLUT3 was highly expressed in COPD patients, CS exposed mice, and BEAS-2B cells treated with CS extract (CSE). Further research revealed that down-regulation of GLUT3 significantly alleviated airway remodelling in vivo and in vitro. Lung function measurement showed that GLUT3 reduction reduced airway resistance in experimental COPD mice. Mechanistically, our study showed that reduction of GLUT3 inhibited CSE-induced EMT by down-regulating the NF-κB/ZEB1 pathway. CONCLUSION We demonstrate that CS enhances the expression of GLUT3 in COPD and further confirm that GLUT3 may regulate airway remodelling in COPD through the NF-κB/ZEB1 pathway; these findings have potential value in the diagnosis and treatment of COPD. The down-regulation of GLUT3 significantly alleviated airway remodelling and reduced airway resistance in vivo. Our observations uncover a key role of GLUT3 in modulating airway remodelling and shed light on the development of GLUT3-targeted therapeutics for COPD.
Collapse
Affiliation(s)
- Yu Ding
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China
| | - Ziteng Wang
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China
| | - Zheming Zhang
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China
| | - Rong You
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China
| | - Yan Wu
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China.
| | - Tao Bian
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, Jiangsu, 214023, People's Republic of China.
| |
Collapse
|
26
|
Simonin JL, Tomba C, Mercier V, Bacchetta M, Idris T, Badaoui M, Roux A, Chanson M. Apical dehydration impairs the cystic fibrosis airway epithelium barrier via a β1-integrin/YAP1 pathway. Life Sci Alliance 2024; 7:e202302449. [PMID: 38336456 PMCID: PMC10858171 DOI: 10.26508/lsa.202302449] [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: 10/19/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Defective hydration of airway surface mucosa is associated with lung infection in cystic fibrosis (CF), partly caused by disruption of the epithelial barrier integrity. Although rehydration of the CF airway surface liquid (ASL) alleviates epithelium vulnerability to infection by junctional protein expression, the mechanisms linking ASL to barrier integrity are unknown. We show here the strong degradation of YAP1 and TAZ proteins in well-polarized CF human airway epithelial cells (HAECs), a process that was prevented by ASL rehydration. Conditional silencing of YAP1 in rehydrated CF HAECs indicated that YAP1 expression was necessary for the maintenance of junctional complexes. A higher plasma membrane tension in CF HAECs reduced endocytosis, concurrent with the maintenance of active β1-integrin ectopically located at the apical membrane. Pharmacological inhibition of β1-integrin accumulation restored YAP1 expression in CF HAECs. These results indicate that dehydration of the CF ASL affects epithelial plasma membrane tension, resulting in ectopic activation of a β1-integrin/YAP1 signaling pathway associated with degradation of junctional proteins.
Collapse
Affiliation(s)
- Juliette L Simonin
- https://ror.org/01swzsf04 Department of Cell Physiology and Metabolism, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Caterina Tomba
- https://ror.org/01swzsf04 Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Vincent Mercier
- https://ror.org/01swzsf04 Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Marc Bacchetta
- https://ror.org/01swzsf04 Department of Cell Physiology and Metabolism, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Tahir Idris
- https://ror.org/01swzsf04 Department of Cell Physiology and Metabolism, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Mehdi Badaoui
- https://ror.org/01swzsf04 Department of Cell Physiology and Metabolism, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Aurélien Roux
- https://ror.org/01swzsf04 Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Marc Chanson
- https://ror.org/01swzsf04 Department of Cell Physiology and Metabolism, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Roth D, Şahin AT, Ling F, Senger CN, Quiroz EJ, Calvert BA, van der Does AM, Güney TG, Tepho N, Glasl S, van Schadewijk A, von Schledorn L, Olmer R, Kanso E, Nawroth JC, Ryan AL. STRUCTURE-FUNCTION RELATIONSHIPS OF MUCOCILIARY CLEARANCE IN HUMAN AIRWAYS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.24.572054. [PMID: 38187619 PMCID: PMC10769450 DOI: 10.1101/2023.12.24.572054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mucociliary clearance is a key mechanical defense mechanism of human airways, and clearance failure is linked to major respiratory diseases, such as chronic obstructive pulmonary disease (COPD) and asthma. While single-cell transcriptomics have unveiled the cellular complexity of the human airway epithelium, our understanding of the mechanics that link epithelial structure to clearance function mainly stem from animal models. This reliance on animal data limits crucial insights into human airway barrier function and hampers the human-relevant in vitro modeling of airway diseases. Our study fills this crucial knowledge gap and for the first time (1) maps the distribution of ciliated and secretory cell types on the mucosal surface along the proximo-distal axis of the rat and human airway tree, (2) identifies species-specific differences in ciliary beat and clearance function, and (3) elucidates structural parameters of airway epithelia that predict clearance function in both native and in vitro tissues alike. Our broad range of experimental approaches and physics-based modeling translate into generalizable parameters to quantitatively benchmark the human-relevancy of mucociliary clearance in experimental models, and to characterize distinct disease states.
Collapse
Affiliation(s)
- Doris Roth
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Ayşe Tuğçe Şahin
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Feng Ling
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Christiana N. Senger
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Erik J. Quiroz
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ben A. Calvert
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anne M. van der Does
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tankut G. Güney
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Niels Tepho
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Sarah Glasl
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
| | - Annemarie van Schadewijk
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura von Schledorn
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Hannover, D-30625, Germany
- Biomedical Research in End stage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, D-30625, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, D-30625, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Hannover, D-30625, Germany
- Biomedical Research in End stage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, D-30625, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, D-30625, Germany
| | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Janna C. Nawroth
- Helmholtz Pioneer Campus, Institute of Biological and Medical Imaging, and Member of the German Lung Research Center (DZL CPC-M), Helmholtz Zentrum München, Neuherberg, D-85764, Germany
- Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, D-81675, Germany
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Amy L. Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, IA 52242, USA
| |
Collapse
|
29
|
Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O’Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal viral infection rewires the tissue-scale memory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.539887. [PMID: 38562902 PMCID: PMC10983857 DOI: 10.1101/2023.05.11.539887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission. Recent work has started to clarify the independent responses of epithelial, myeloid, and lymphoid cells to viral infection in the nasal mucosa, but their spatiotemporal coordination and relative contributions remain unclear. Furthermore, understanding whether and how primary infection shapes tissue-scale memory responses to secondary challenge is critical for the rational design of nasal-targeting therapeutics and vaccines. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in cell type, subset, and state composition over time. Type I Interferon (IFN)-responsive neutrophils appeared 2 days post infection (dpi) and preceded transient IFN-responsive/cycling epithelial cell responses 5 dpi, which coincided with broader antiviral monocyte and NK cell accumulation. By 8 dpi, monocyte-derived macrophages (MDMs) expressing Cxcl9 and Cxcl16 arose alongside effector cytotoxic CD8 and Ifng-expressing CD4 T cells. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16-CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses upon rechallenge.
Collapse
Affiliation(s)
- Samuel W. Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M. Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O’Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H. von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| |
Collapse
|
30
|
Minařík M, Modrell MS, Gillis JA, Campbell AS, Fuller I, Lyne R, Micklem G, Gela D, Pšenička M, Baker CVH. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Front Cell Dev Biol 2024; 12:1327924. [PMID: 38562141 PMCID: PMC10982350 DOI: 10.3389/fcell.2024.1327924] [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: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
Collapse
Affiliation(s)
- Martin Minařík
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Melinda S. Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - J. Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Alexander S. Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Fuller
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Gela
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Clare V. H. Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
31
|
Joulia R, Puttur F, Stölting H, Traves WJ, Entwistle LJ, Voitovich A, Garcia Martín M, Al-Sahaf M, Bonner K, Scotney E, Molyneaux PL, Hewitt RJ, Walker SA, Yates L, Saglani S, Lloyd CM. Mast cell activation disrupts interactions between endothelial cells and pericytes during early life allergic asthma. J Clin Invest 2024; 134:e173676. [PMID: 38487999 PMCID: PMC10940085 DOI: 10.1172/jci173676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024] Open
Abstract
Allergic asthma generally starts during early life and is linked to substantial tissue remodeling and lung dysfunction. Although angiogenesis is a feature of the disrupted airway, the impact of allergic asthma on the pulmonary microcirculation during early life is unknown. Here, using quantitative imaging in precision-cut lung slices (PCLSs), we report that exposure of neonatal mice to house dust mite (HDM) extract disrupts endothelial cell/pericyte interactions in adventitial areas. Central to the blood vessel structure, the loss of pericyte coverage was driven by mast cell (MC) proteases, such as tryptase, that can induce pericyte retraction and loss of the critical adhesion molecule N-cadherin. Furthermore, spatial transcriptomics of pediatric asthmatic endobronchial biopsies suggests intense vascular stress and remodeling linked with increased expression of MC activation pathways in regions enriched in blood vessels. These data provide previously unappreciated insights into the pathophysiology of allergic asthma with potential long-term vascular defects.
Collapse
Affiliation(s)
- Régis Joulia
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Franz Puttur
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Helen Stölting
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - William J. Traves
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Lewis J. Entwistle
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Anastasia Voitovich
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Minerva Garcia Martín
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - May Al-Sahaf
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Department of Thoracic Surgery, Hammersmith Hospital, London, UK
| | - Katie Bonner
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Elizabeth Scotney
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Philip L. Molyneaux
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Richard J. Hewitt
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Simone A. Walker
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Laura Yates
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| | - Sejal Saglani
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Clare M. Lloyd
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom (UK)
| |
Collapse
|
32
|
López-Posadas R, Bagley DC, Pardo-Pastor C, Ortiz-Zapater E. The epithelium takes the stage in asthma and inflammatory bowel diseases. Front Cell Dev Biol 2024; 12:1258859. [PMID: 38529406 PMCID: PMC10961468 DOI: 10.3389/fcell.2024.1258859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
The epithelium is a dynamic barrier and the damage to this epithelial layer governs a variety of complex mechanisms involving not only epithelial cells but all resident tissue constituents, including immune and stroma cells. Traditionally, diseases characterized by a damaged epithelium have been considered "immunological diseases," and research efforts aimed at preventing and treating these diseases have primarily focused on immuno-centric therapeutic strategies, that often fail to halt or reverse the natural progression of the disease. In this review, we intend to focus on specific mechanisms driven by the epithelium that ensure barrier function. We will bring asthma and Inflammatory Bowel Diseases into the spotlight, as we believe that these two diseases serve as pertinent examples of epithelium derived pathologies. Finally, we will argue how targeting the epithelium is emerging as a novel therapeutic strategy that holds promise for addressing these chronic diseases.
Collapse
Affiliation(s)
- Rocío López-Posadas
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universtiy Eralngen-Nürnberg, Erlangen, Germany
| | - Dustin C. Bagley
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Carlos Pardo-Pastor
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- Instituto Investigación Hospital Clínico-INCLIVA, Valencia, Spain
| |
Collapse
|
33
|
Jain A, Kim BR, Yu W, Moninger TO, Karp PH, Wagner BA, Welsh MJ. Mitochondrial uncoupling proteins protect human airway epithelial ciliated cells from oxidative damage. Proc Natl Acad Sci U S A 2024; 121:e2318771121. [PMID: 38416686 DOI: 10.1073/pnas.2318771121] [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: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 03/01/2024] Open
Abstract
Apical cilia on epithelial cells defend the lung by propelling pathogens and particulates out of the respiratory airways. Ciliated cells produce ATP that powers cilia beating by densely grouping mitochondria just beneath the apical membrane. However, this efficient localization comes at a cost because electrons leaked during oxidative phosphorylation react with molecular oxygen to form superoxide, and thus, the cluster of mitochondria creates a hotspot for oxidant production. The relatively high oxygen concentration overlying airway epithelia further intensifies the risk of generating superoxide. Thus, airway ciliated cells face a unique challenge of producing harmful levels of oxidants. However, surprisingly, highly ciliated epithelia produce less reactive oxygen species (ROS) than epithelia with few ciliated cells. Compared to other airway cell types, ciliated cells express high levels of mitochondrial uncoupling proteins, UCP2 and UCP5. These proteins decrease mitochondrial protonmotive force and thereby reduce production of ROS. As a result, lipid peroxidation, a marker of oxidant injury, decreases. However, mitochondrial uncoupling proteins exact a price for decreasing oxidant production; they decrease the fraction of mitochondrial respiration that generates ATP. These findings indicate that ciliated cells sacrifice mitochondrial efficiency in exchange for safety from damaging oxidation. Employing uncoupling proteins to prevent oxidant production, instead of relying solely on antioxidants to decrease postproduction oxidant levels, may offer an advantage for targeting a local area of intense ROS generation.
Collapse
Affiliation(s)
- Akansha Jain
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Department of Molecular Physiology and Biophysics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Bo Ram Kim
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Wenjie Yu
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Thomas O Moninger
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Philip H Karp
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Brett A Wagner
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Michael J Welsh
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Department of Molecular Physiology and Biophysics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| |
Collapse
|
34
|
Farinha CM, Santos L, Ferreira JF. Cell type-specific regulation of CFTR trafficking-on the verge of progress. Front Cell Dev Biol 2024; 12:1338892. [PMID: 38505263 PMCID: PMC10949533 DOI: 10.3389/fcell.2024.1338892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein is a complex process that starts with its biosynthesis and folding in the endoplasmic reticulum. Exit from the endoplasmic reticulum (ER) is coupled with the acquisition of a compact structure that can be processed and traffic through the secretory pathway. Once reaching its final destination-the plasma membrane, CFTR stability is regulated through interaction with multiple protein partners that are involved in its post-translation modification, connecting the channel to several signaling pathways. The complexity of the process is further boosted when analyzed in the context of the airway epithelium. Recent advances have characterized in detail the different cell types that compose the surface epithelium and shifted the paradigm on which cells express CFTR and on their individual and combined contribution to the total expression (and function) of this chloride/bicarbonate channel. Here we review CFTR trafficking and its relationship with the knowledge on the different cell types of the airway epithelia. We explore the crosstalk between these two areas and discuss what is still to be clarified and how this can be used to develop more targeted therapies for CF.
Collapse
Affiliation(s)
- Carlos M. Farinha
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | | | | |
Collapse
|
35
|
He ZJ, Chu C, Dickson R, Okuda K, Cai LH. A gel-coated air-liquid-interface culture system with tunable substrate stiffness matching healthy and diseased lung tissues. Am J Physiol Lung Cell Mol Physiol 2024; 326:L292-L302. [PMID: 38252871 DOI: 10.1152/ajplung.00153.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Since its invention in the late 1980s, the air-liquid-interface (ALI) culture system has been the standard in vitro model for studying human airway biology and pulmonary diseases. However, in a conventional ALI system, cells are cultured on a porous plastic membrane that is much stiffer than human airway tissues. Here, we develop a gel-ALI culture system by simply coating the plastic membrane with a thin layer of hydrogel with tunable stiffness matching that of healthy and fibrotic airway tissues. We determine the optimum gel thickness that does not impair the transport of nutrients and biomolecules essential to cell growth. We show that the gel-ALI system allows human bronchial epithelial cells (HBECs) to proliferate and differentiate into pseudostratified epithelium. Furthermore, we discover that HBECs migrate significantly faster on hydrogel substrates with stiffness matching that of fibrotic lung tissues, highlighting the importance of mechanical cues in human airway remodeling. The developed gel-ALI system provides a facile approach to studying the effects of mechanical cues in human airway biology and in modeling pulmonary diseases.NEW & NOTEWORTHY In a conventional ALI system, cells are cultured on a plastic membrane that is much stiffer than human airway tissues. We develop a gel-ALI system by coating the plastic membrane with a thin layer of hydrogel with tunable stiffness matching that of healthy and fibrotic airway tissues. We discover that human bronchial epithelial cells migrate significantly faster on hydrogel substrates with pathological stiffness, highlighting the importance of mechanical cues in human airway remodeling.
Collapse
Affiliation(s)
- Zhi-Jian He
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Catherine Chu
- Soft Biomatter Laboratory, Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Riley Dickson
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Kenichi Okuda
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Li-Heng Cai
- Soft Biomatter Laboratory, Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia, United States
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States
| |
Collapse
|
36
|
Rouhani MJ, Janes SM, Kim CF. Epithelial stem and progenitor cells of the upper airway. Cells Dev 2024; 177:203905. [PMID: 38355015 DOI: 10.1016/j.cdev.2024.203905] [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: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The upper airway acts as a conduit for the passage of air to the respiratory system and is implicated in several chronic diseases. Whilst the cell biology of the distal respiratory system has been described in great detail, less is known about the proximal upper airway. In this review, we describe the relevant anatomy of the upper airway and discuss the literature detailing the identification and roles of the progenitor cells of these regions.
Collapse
Affiliation(s)
- Maral J Rouhani
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Carla F Kim
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
37
|
Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024:10.1038/s41592-024-02191-z. [PMID: 38366243 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
Collapse
Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
| |
Collapse
|
38
|
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol 2024; 14:1282859. [PMID: 38414974 PMCID: PMC10897000 DOI: 10.3389/fimmu.2023.1282859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 02/29/2024] Open
Abstract
Introduction The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Collapse
Affiliation(s)
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Inna Kuperstein
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Marc E. Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- St. John’s University, Queens, NY, United States
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Felicia Burtscher
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Yusuke Hiki
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan
| | - Noriko F. Hiroi
- Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan
- Keio University School of Medicine, Tokyo, Japan
| | - Finterly Hu
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Nhung Pham
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Francesco Messina
- Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases’ Lazzaro Spallanzani’ - IRCCS, Rome, Italy
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Maria Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
| | - Kinza Rian
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Aurélien Naldi
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
| | | | - Viviam Bermudez
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnau Montagud
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
| | - Vincent Noël
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | | | | | - Benjamin M. Gyori
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - John A. Bachman
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - Augustin Luna
- Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Janet Piñero
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura I. Furlong
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Adrien Rougny
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
- Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
| | - Yohan Jarosz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rupert W. Overall
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Robert Phair
- Integrative Bioinformatics, Inc., Mountain View, CA, United States
| | - Livia Perfetto
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Lisa Matthews
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | | | | | - Luis Cristobal Monraz Gomez
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Jean Marie Ravel
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Guanming Wu
- Oregon Health Sciences University, Portland, OR, United States
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laurence Calzone
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Peter D’Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany
| | | | - Emmanuel Barillot
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Rudi Balling
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | |
Collapse
|
39
|
Tchoukalova YD, Phung TN, Kennedy MM, Miranda-Grandjean D, Becquer E, Chen L, Zhang N, Dinu V, Wilson MA, Lott DG. Idiopathic Subglottic Stenosis Is Associated With More Frequent and Abnormal Squamous Metaplasia. Ann Otol Rhinol Laryngol 2024; 133:214-223. [PMID: 37740367 DOI: 10.1177/00034894231201016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
OBJECTIVES Gain insights into the pathophysiology of idiopathic subglottic stenosis (iSGS) by investigating differences in transcriptome of subglottic mucosal tissue between patients with iSGS and controls, and between tracheal and subglottic tissue within patients. METHODS RNA sequencing was conducted on biopsied mucosal samples collected from subglottic and tracheal (in-patient control) regions in iSGS patients, and from subglottis in controls. The gene expression differences were validated on a protein level by (1) staining the tissue samples obtained from a second cohort of patients and controls; and (2) in vitro functional assays using primary subglottic epithelial cells from both iSGS patients and healthy donors. RESULTS We found 7 upregulated genes in the subglottic region of iSGS patients relative to both the tracheal mucosa and subglottic region of controls. A gene ontology enrichment analysis found that the epithelial cell differentiation and cornification pathways are significant, involving specifically 3 of the genes: involucrin (IVL), small proline rich protein 1B (SPRR1B), and keratin 16 (KRT16). Involvement of these pathways suggests squamous metaplasia of the epithelium. Histological analyses of epithelium in subglottic mucosal biopsies revealed squamous metaplasia in 41% of the samples from iSGS patients and in 25% from controls. Immunohistochemical evaluation of the samples presented with squamous epithelium revealed increased expression of the protein encoded by SPRR1B, hyperproliferative basal cells, shedding of apical layers, and accompanying lesions in iSGS compared to CTRL. Cultured primary subglottic epithelial cells from iSGS patients had higher proliferation rates compared to healthy donors and squamous metaplastic differentiation formed thinner epithelia with increased expression proteins encoded by INV, SPRR1B, and KRT16, suggesting intrinsic dysfunction of basal cells in iSGS. CONCLUSIONS Abnormal squamous differentiation of epithelial cells may contribute to the pathogenesis of iSGS. Patients having metaplastic epithelial phenotype may be sensitive to drugs that reverse it to a normal phenotype.
Collapse
Affiliation(s)
- Yourka D Tchoukalova
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Tanya N Phung
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Faculty of Science, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maeve M Kennedy
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Baylor College of Medicine, Houston, TX, USA
| | | | - Emanuel Becquer
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Contexture, Phoenix, AZ, USA
| | - Longwen Chen
- Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Nan Zhang
- Department of Quantitative Health Sciences, Mayo, AZ Clinic, Scottsdale, AZ, USA
| | - Valentin Dinu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Basic Medical Sciences, Arizona State University, Phoenix, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - David G Lott
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Otolaryngology-Head and Neck Surgery, Division of Laryngology, Mayo Clinic Arizona, Phoenix, AZ, USA
| |
Collapse
|
40
|
Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
Collapse
Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
| |
Collapse
|
41
|
Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 168] [Impact Index Per Article: 168.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
Collapse
Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| |
Collapse
|
42
|
Chu CY, Kim SY, Pryhuber GS, Mariani TJ, McGraw MD. Single-cell resolution of human airway epithelial cells exposed to bronchiolitis obliterans-associated chemicals. Am J Physiol Lung Cell Mol Physiol 2024; 326:L135-L148. [PMID: 38084407 DOI: 10.1152/ajplung.00304.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024] Open
Abstract
Bronchiolitis obliterans (BO) is a fibrotic lung disease characterized by progressive luminal narrowing and obliteration of the small airways. In the nontransplant population, inhalation exposure to certain chemicals is associated with BO; however, the mechanisms contributing to disease induction remain poorly understood. This study's objective was to use single-cell RNA sequencing for the identification of transcriptomic signatures common to primary human airway epithelial cells after chemical exposure to BO-associated chemicals-diacetyl or nitrogen mustard-to help explain BO induction. Primary airway epithelial cells were cultured at air-liquid interface and exposed to diacetyl, nitrogen mustard, or control vapors. Cultures were dissociated and sequenced for single-cell RNA. Differential gene expression and functional pathway analyses were compared across exposures. In total, 75,663 single cells were captured and sequenced from all exposure conditions. Unbiased clustering identified 11 discrete phenotypes, including 5 basal, 2 ciliated, and 2 secretory cell clusters. With chemical exposure, the proportion of cells assigned to keratin 5+ basal cells decreased, whereas the proportion of cells aligned to secretory cell clusters increased compared with control exposures. Functional pathway analysis identified interferon signaling and antigen processing/presentation as pathways commonly upregulated after diacetyl or nitrogen mustard exposure in a ciliated cell cluster. Conversely, the response of airway basal cells differed significantly with upregulation of the unfolded protein response in diacetyl-exposed basal cells, not seen in nitrogen mustard-exposed cultures. These new insights provide early identification of airway epithelial signatures common to BO-associated chemical exposures.NEW & NOTEWORTHY Bronchiolitis obliterans (BO) is a devastating fibrotic lung disease of the small airways, or bronchioles. This original manuscript uses single-cell RNA sequencing for identifying common signatures of chemically exposed airway epithelial cells in BO induction. Chemical exposure reduced the proportion of keratin 5+ basal cells while increasing the proportion of keratin 4+ suprabasal cells. Functional pathways contributory to these shifts differed significantly across exposures. These new results highlight similarities and differences in BO induction across exposures.
Collapse
Affiliation(s)
- Chin-Yi Chu
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - So-Young Kim
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew D McGraw
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| |
Collapse
|
43
|
Puray-Chavez M, LaPak KM, Jasuja R, Pan J, Xu J, Eschbach JE, Mohammed S, Lawson DQ, Wang Q, Brody SL, Major MB, Goldfarb D, Kutluay SB. A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574522. [PMID: 38260460 PMCID: PMC10802478 DOI: 10.1101/2024.01.07.574522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-α receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
Collapse
Affiliation(s)
- Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyle M LaPak
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ria Jasuja
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jiehong Pan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jian Xu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jenna E Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dana Q Lawson
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Qibo Wang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven L Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Otolaryngology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Institute for Informatics, Data Science & Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
44
|
Zaragosi LE, Gouleau A, Delin M, Lebrigand K, Arguel MJ, Girard-Riboulleau C, Rios G, Redman E, Plaisant M, Waldmann R, Magnone V, Marcet B, Barbry P, Ponzio G. Combination of CRISPR-Cas9-RNP and Single-Cell RNAseq to Identify Cell State-Specific FOXJ1 Functions in the Human Airway Epithelium. Methods Mol Biol 2024; 2725:1-25. [PMID: 37856015 DOI: 10.1007/978-1-0716-3507-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The study of the airway epithelium in vitro is routinely performed using air-liquid culture (ALI) models from nasal or bronchial basal cells. These 3D experimental models allow to follow the regeneration steps of fully differentiated mucociliary epithelium and to study gene function by performing gene invalidation. Recent progress made with CRISPR-based techniques has overcome the experimental difficulty of this approach, by a direct transfection of ribonucleoprotein complexes combining a mix of synthetic small guide RNAs (sgRNAs) and recombinant Cas9. The approach shows more than 95% efficiency and does not require any selection step. A limitation of this approach is that it generates cell populations that contain heterogeneous deletions, which makes the evaluation of invalidation efficiency difficult. We have successfully used Flongle sequencing (Nanopore) to quantify the number of distinct deletions. We describe the use of CRISPR-Cas9 RNP in combination with single-cell RNA sequencing to functionally characterize the impact of gene invalidation in ALI cultures. The complex ecosystem of the airway epithelium, composed of many cell types, makes single-cell approaches particularly relevant to study cell type, or cell state-specific events. This protocol describes the invalidation of FOXJ1 in ALI cultures through the following steps: (1) Establishment of basal cell cultures from nasal turbinates, (2) CRISPR-Cas9 RNP invalidation of FOXJ1, (3) Quantification of FOXJ1 invalidation efficiency by Nanopore sequencing, (4) Dissociation of ALI cultures and single-cell RNAseq, (5) Analysis of single-cell RNAseq data from FOXJ1-invalidated cells.We confirm here that FOXJ1 invalidation impairs the final differentiation step of multiciliated cells and provides a framework to explore other gene functions.
Collapse
Affiliation(s)
| | - Alizé Gouleau
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Margot Delin
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | | | - Geraldine Rios
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Elisa Redman
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| |
Collapse
|
45
|
Kitano M, Hayashi Y, Ohnishi H, Okuyama H, Yoshimatsu M, Mizuno K, Kuwata F, Tada T, Kishimoto Y, Morita S, Omori K. Changes in the Proportion of Each Cell Type After hiPSC-Derived Airway Epithelia Transplantation. Cell Transplant 2024; 33:9636897241228026. [PMID: 38372247 PMCID: PMC10878204 DOI: 10.1177/09636897241228026] [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: 11/04/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
No radical treatment is available for the regeneration of dysfunction and defects in airway epithelia. Artificial tracheae made of polypropylene and collagen sponge were used in clinical studies to reconstitute tracheae after resection. For early epithelialization of the luminal surface of the artificial trachea, a model was established, that is, an artificial trachea covered with human-induced pluripotent stem cell-derived airway epithelial cells (hiPSC-AECs) was transplanted into a tracheal defect in an immunodeficient rat. Unlike the cell types of hiPSC-derived cells that are currently used in clinical studies, AECs maintain tissues by proliferation and differentiation of basal cells into various cell types that constitute AECs constantly. Therefore, post-transplantation, the proportion of each cell type, such as ciliated and goblet cells, may change; however, no studies have examined this possibility. In this study, using our hiPSC-AEC-transplanted rat model, we investigated changes in the proportion of each cell type in hiPSC-AECs pre-transplantation and post-transplantation. As a result, the proportion of each cell type changed post-transplantation. The proportion of ciliated, basal, and club cells increased, and the proportion of goblet cells decreased post-transplantation. In addition, the proportion of each cell type in engrafted hiPSC-AECs is more similar to the proportion of each cell type in normal proximal airway tissue than the proportion of each cell type pre-transplantation. The results of this study are useful for the development of therapeutic techniques using hiPSC-AEC transplantation.
Collapse
Affiliation(s)
- Masayuki Kitano
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuyuki Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroe Ohnishi
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideaki Okuyama
- School of Communication Sciences and Disorders, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Masayoshi Yoshimatsu
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Keisuke Mizuno
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Kuwata
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Tada
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yo Kishimoto
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Morita
- Department of Biomedical Statistics and Bioinformatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
46
|
Basher ARMA, Hallinan C, Lee K. Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540686. [PMID: 38187596 PMCID: PMC10769187 DOI: 10.1101/2023.05.14.540686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The discovery of subtypes is pivotal for disease diagnosis and targeted therapy, considering the diverse responses of different cells or patients to specific treatments. Exploring the heterogeneity within disease or cell states provides insights into disease progression mechanisms and cell differentiation. The advent of high-throughput technologies has enabled the generation and analysis of various molecular data types, such as single-cell RNA-seq, proteomic, and imaging datasets, at large scales. While presenting opportunities for subtype discovery, these datasets pose challenges in finding relevant signatures due to their high dimensionality. Feature selection, a crucial step in the analysis pipeline, involves choosing signatures that reduce the feature size for more efficient downstream computational analysis. Numerous existing methods focus on selecting signatures that differentiate known diseases or cell states, yet they often fall short in identifying features that preserve heterogeneity and reveal subtypes. To identify features that can capture the diversity within each class while also maintaining the discrimination of known disease states, we employed deep metric learning-based feature embedding to conduct a detailed exploration of the statistical properties of features essential in preserving heterogeneity. Our analysis revealed that features with a significant difference in interquartile range (IQR) between classes possess crucial subtype information. Guided by this insight, we developed a robust statistical method, termed PHet (Preserving Heterogeneity) that performs iterative subsampling differential analysis of IQR and Fisher's method between classes, identifying a minimal set of heterogeneity-preserving discriminative features to optimize subtype clustering quality. Validation using public single-cell RNA-seq and microarray datasets showcased PHet's effectiveness in preserving sample heterogeneity while maintaining discrimination of known disease/cell states, surpassing the performance of previous outlier-based methods. Furthermore, analysis of a single-cell RNA-seq dataset from mouse tracheal epithelial cells revealed, through PHet-based features, the presence of two distinct basal cell subtypes undergoing differentiation toward a luminal secretory phenotype. Notably, one of these subtypes exhibited high expression of BPIFA1. Interestingly, previous studies have linked BPIFA1 secretion to the emergence of secretory cells during mucociliary differentiation of airway epithelial cells. PHet successfully pinpointed the basal cell subtype associated with this phenomenon, a distinction that pre-annotated markers and dispersion-based features failed to make due to their admixed feature expression profiles. These findings underscore the potential of our method to deepen our understanding of the mechanisms underlying diseases and cell differentiation and contribute significantly to personalized medicine.
Collapse
Affiliation(s)
- Abdur Rahman M. A. Basher
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Caleb Hallinan
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kwonmoo Lee
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
47
|
Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol 2023; 69:623-637. [PMID: 37523502 DOI: 10.1165/rcmb.2023-0077oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n = 13) and patients with COVID-19 (n = 20), sourced from six independent studies (167,280 high-quality cells in total). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I IFN signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type II (AT-II) cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by the induction of genes of the epidermal differentiation complex, including the cornified envelope protein SPRR3 (small proline-rich protein 3), upregulation of multiple KRT (keratin) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of lungs from patients with COVID-19 confirmed upregulation and colocalization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes.
Collapse
Affiliation(s)
| | - Aleksandra Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - David Thrower
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - Purushothama Rao Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | |
Collapse
|
48
|
Wang Z, Yang L, Wang W, Zhou H, Chen J, Ma Z, Wang X, Zhang Q, Liu H, Zhou C, Guo Z, Zhang X. Comparative immunological landscape between pre- and early-stage LUAD manifested as ground-glass nodules revealed by scRNA and scTCR integrated analysis. Cell Commun Signal 2023; 21:325. [PMID: 37957625 PMCID: PMC10644515 DOI: 10.1186/s12964-023-01322-x] [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: 06/18/2023] [Accepted: 09/16/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Mechanism underlying the malignant progression of precancer to early-stage lung adenocarcinoma (LUAD) as well as their indolence nature remains elusive. METHODS Single-cell RNA sequencing (scRNA) with simultaneous T cell receptor (TCR) sequencing on 5 normal lung tissues, 3 precancerous and 4 early-stage LUAD manifested as pulmonary ground-glass nodules (GGNs) were performed. RESULTS Through this integrated analysis, we have delineated five key modules that drive the malignant progression of early-stage LUAD in a disease stage-dependent manner. These modules are related to cell proliferation and metabolism, immune response, mitochondria, cilia, and cell adhesion. We also find that the tumor micro-environment (TME) of early-stage LUAD manifested as GGN are featured with regulatory T (Tregs) cells accumulation with three possible origins, and loss-functional state (decreased clonal expansion and cytotoxicity) of CD8 + T cells. Instead of exhaustion, the CD8 + T cells are featured with a shift to memory phenotype, which is significantly different from the late stage LUAD. Furthermore, we have identified monocyte-derived macrophages that undergo a lipid-phenotype transition and may contribute to the suppressive TME. Intense interaction between stromal cells, myeloid cells including lipid associated macrophages and LAMP3 + DCs, and lymphocytes were also characterized. CONCLUSIONS Our work provides new insight into the molecular and cellular mechanism underlying malignant progression of LUAD manifested as GGN, and pave way for novel immunotherapies for GGN. Video Abstract.
Collapse
Affiliation(s)
- Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Wenqiang Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Huanhuan Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Juan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zeheng Ma
- Department of Thoracic Surgery Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xiaoyan Wang
- Department of Pathological Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Quncheng Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Haiyang Liu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Chao Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Zhiping Guo
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
- Henan Provincial Key Laboratory of Chronic Diseases and Health Management, Zhengzhou, 450003, Henan, China.
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
| |
Collapse
|
49
|
Nakayama J, Yamamoto Y. Cancer-prone Phenotypes and Gene Expression Heterogeneity at Single-cell Resolution in Cigarette-smoking Lungs. CANCER RESEARCH COMMUNICATIONS 2023; 3:2280-2291. [PMID: 37910161 PMCID: PMC10637260 DOI: 10.1158/2767-9764.crc-23-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/16/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from eight public datasets, including 104 lung scRNA-seq samples with clinicopathologic information and designated a cigarette-smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking status. The scMeta-analysis paves the way to utilize publicly-available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution. SIGNIFICANCE The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking.
Collapse
Affiliation(s)
- Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
50
|
Badaoui M, Chanson M. Intercellular Communication in Airway Epithelial Cell Regeneration: Potential Roles of Connexins and Pannexins. Int J Mol Sci 2023; 24:16160. [PMID: 38003349 PMCID: PMC10671439 DOI: 10.3390/ijms242216160] [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: 09/26/2023] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Connexins and pannexins are transmembrane proteins that can form direct (gap junctions) or indirect (connexons, pannexons) intercellular communication channels. By propagating ions, metabolites, sugars, nucleotides, miRNAs, and/or second messengers, they participate in a variety of physiological functions, such as tissue homeostasis and host defense. There is solid evidence supporting a role for intercellular signaling in various pulmonary inflammatory diseases where alteration of connexin/pannexin channel functional expression occurs, thus leading to abnormal intercellular communication pathways and contributing to pathophysiological aspects, such as innate immune defense and remodeling. The integrity of the airway epithelium, which is the first line of defense against invading microbes, is established and maintained by a repair mechanism that involves processes such as proliferation, migration, and differentiation. Here, we briefly summarize current knowledge on the contribution of connexins and pannexins to necessary processes of tissue repair and speculate on their possible involvement in the shaping of the airway epithelium integrity.
Collapse
Affiliation(s)
| | - Marc Chanson
- Department of Cell Physiology & Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland;
| |
Collapse
|