1
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Lee HJ, Bernau K, Harr TJ, Rosenkrans ZT, Kessler GA, Stott K, Oler AT, Rahar B, Zhu T, Medina-Guevara Y, Gupta N, Cho I, Gari MK, Burkel BM, Jeffery JJ, Weichmann AM, Tomasini-Johansson BR, Ponik SM, Engle JW, Hernandez R, Kwon GS, Sandbo N. [ 64Cu]Cu-PEG-FUD peptide for noninvasive and sensitive detection of murine pulmonary fibrosis. Sci Adv 2024; 10:eadj1444. [PMID: 38598637 PMCID: PMC11006221 DOI: 10.1126/sciadv.adj1444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/05/2024] [Indexed: 04/12/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease resulting in irreversible scarring within the lungs. However, the lack of biomarkers that enable real-time assessment of disease activity remains a challenge in providing efficient clinical decision-making and optimal patient care in IPF. Fibronectin (FN) is highly expressed in fibroblastic foci of the IPF lung where active extracellular matrix (ECM) deposition occurs. Functional upstream domain (FUD) tightly binds the N-terminal 70-kilodalton domain of FN that is crucial for FN assembly. In this study, we first demonstrate the capacity of PEGylated FUD (PEG-FUD) to target FN deposition in human IPF tissue ex vivo. We subsequently radiolabeled PEG-FUD with 64Cu and monitored its spatiotemporal biodistribution via μPET/CT imaging in mice using the bleomycin-induced model of pulmonary injury and fibrosis. We demonstrated [64Cu]Cu-PEG-FUD uptake 3 and 11 days following bleomycin treatment, suggesting that radiolabeled PEG-FUD holds promise as an imaging probe in aiding the assessment of fibrotic lung disease activity.
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Affiliation(s)
- Hye Jin Lee
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Ksenija Bernau
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Thomas J. Harr
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Zachary T. Rosenkrans
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Grace A. Kessler
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Kristen Stott
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Angie Tebon Oler
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Babita Rahar
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Terry Zhu
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Yadira Medina-Guevara
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Nikesh Gupta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Inyoung Cho
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Metti K. Gari
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Brian M. Burkel
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Justin J. Jeffery
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, USA
| | - Ashley M. Weichmann
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, USA
| | - Bianca R. Tomasini-Johansson
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
- Arrowhead Pharmaceuticals, 502 S. Rosa Rd., Madison, WI 53719, USA
| | - Suzanne M. Ponik
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, USA
| | - Jonathan W. Engle
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Reinier Hernandez
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, USA
| | - Glen S. Kwon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, USA
| | - Nathan Sandbo
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
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2
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Patel M, Post Y, Hill N, Sura A, Ye J, Fisher T, Suen N, Zhang M, Cheng L, Pribluda A, Chen H, Yeh WC, Li Y, Baribault H, Fletcher RB. A WNT mimetic with broad spectrum FZD-specificity decreases fibrosis and improves function in a pulmonary damage model. Respir Res 2024; 25:153. [PMID: 38566174 PMCID: PMC10985870 DOI: 10.1186/s12931-024-02786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Wnt/β-catenin signaling is critical for lung development and AT2 stem cell maintenance in adults, but excessive pathway activation has been associated with pulmonary fibrosis, both in animal models and human diseases such as idiopathic pulmonary fibrosis (IPF). IPF is a detrimental interstitial lung disease, and although two approved drugs limit functional decline, transplantation is the only treatment that extends survival, highlighting the need for regenerative therapies. METHODS Using our antibody-based platform of Wnt/β-catenin modulators, we investigated the ability of a pathway antagonist and pathway activators to reduce pulmonary fibrosis in the acute bleomycin model, and we tested the ability of a WNT mimetic to affect alveolar organoid cultures. RESULTS A WNT mimetic agonist with broad FZD-binding specificity (FZD1,2,5,7,8) potently expanded alveolar organoids. Upon therapeutic dosing, a broad FZD-binding specific Wnt mimetic decreased pulmonary inflammation and fibrosis and increased lung function in the bleomycin model, and it impacted multiple lung cell types in vivo. CONCLUSIONS Our results highlight the unexpected capacity of a WNT mimetic to effect tissue repair after lung damage and support the continued development of Wnt/β-catenin pathway modulation for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Mehaben Patel
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Yorick Post
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Natalie Hill
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Asmiti Sura
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Jay Ye
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Trevor Fisher
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Nicholas Suen
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Mengrui Zhang
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Leona Cheng
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Ariel Pribluda
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Hui Chen
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Wen-Chen Yeh
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Yang Li
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Hélène Baribault
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Russell B Fletcher
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA.
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3
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Shakarchy A, Zarfati G, Hazak A, Mealem R, Huk K, Ziv T, Avinoam O, Zaritsky A. Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion. Mol Syst Biol 2024; 20:217-241. [PMID: 38238594 PMCID: PMC10912675 DOI: 10.1038/s44320-024-00010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 03/06/2024] Open
Abstract
Cells modify their internal organization during continuous state transitions, supporting functions from cell division to differentiation. However, tools to measure dynamic physiological states of individual transitioning cells are lacking. We combined live-cell imaging and machine learning to monitor ERK1/2-inhibited primary murine skeletal muscle precursor cells, that transition rapidly and robustly from proliferating myoblasts to post-mitotic myocytes and then fuse, forming multinucleated myotubes. Our models, trained using motility or actin intensity features from single-cell tracking data, effectively tracked real-time continuous differentiation, revealing that differentiation occurs 7.5-14.5 h post induction, followed by fusion ~3 h later. Co-inhibition of ERK1/2 and p38 led to differentiation without fusion. Our model inferred co-inhibition leads to terminal differentiation, indicating that p38 is specifically required for transitioning from terminal differentiation to fusion. Our model also predicted that co-inhibition leads to changes in actin dynamics. Mass spectrometry supported these in silico predictions and suggested novel fusion and maturation regulators downstream of differentiation. Collectively, this approach can be adapted to various biological processes to uncover novel links between dynamic single-cell states and their functional outcomes.
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Affiliation(s)
- Amit Shakarchy
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Giulia Zarfati
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Adi Hazak
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Reut Mealem
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Karina Huk
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Tamar Ziv
- The Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel.
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel.
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4
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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: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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.
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5
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Mayr CH, Sengupta A, Asgharpour S, Ansari M, Pestoni JC, Ogar P, Angelidis I, Liontos A, Rodriguez-Castillo JA, Lang NJ, Strunz M, Porras-Gonzalez D, Gerckens M, De Sadeleer LJ, Oehrle B, Viteri-Alvarez V, Fernandez IE, Tallquist M, Irmler M, Beckers J, Eickelberg O, Stoleriu GM, Behr J, Kneidinger N, Wuyts WA, Wasnick RM, Yildirim AÖ, Ahlbrecht K, Morty RE, Samakovlis C, Theis FJ, Burgstaller G, Schiller HB. Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts. Eur Respir J 2024; 63:2301326. [PMID: 38212077 PMCID: PMC10850614 DOI: 10.1183/13993003.01326-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Fibroblast-to-myofibroblast conversion is a major driver of tissue remodelling in organ fibrosis. Distinct lineages of fibroblasts support homeostatic tissue niche functions, yet their specific activation states and phenotypic trajectories during injury and repair have remained unclear. METHODS We combined spatial transcriptomics, multiplexed immunostainings, longitudinal single-cell RNA-sequencing and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. Our findings were validated in idiopathic pulmonary fibrosis patient tissues in situ as well as in cell differentiation and invasion assays using patient lung fibroblasts. Cell differentiation and invasion assays established a function of SFRP1 in regulating human lung fibroblast invasion in response to transforming growth factor (TGF)β1. MEASUREMENTS AND MAIN RESULTS We discovered a transitional fibroblast state characterised by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1 + cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage-specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1 + transitional fibroblasts and Cthrc1 + myofibroblasts. TGFβ1 downregulated SFRP1 in noninvasive transitional cells and induced their switch to an invasive CTHRC1+ myofibroblast identity. Finally, using loss-of-function studies we showed that SFRP1 modulates TGFβ1-induced fibroblast invasion and RHOA pathway activity. CONCLUSIONS Our study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies SFRP1 as a modulator of TGFβ1-driven fibroblast phenotypes in fibrogenesis. These findings are relevant in the context of therapeutic interventions that aim at limiting or reversing fibroblast foci formation.
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Affiliation(s)
- Christoph H Mayr
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- C.H. Mayr and A. Sengupta contributed equally to this work
| | - Arunima Sengupta
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- C.H. Mayr and A. Sengupta contributed equally to this work
| | - Sara Asgharpour
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Munich, Germany
| | - Jeanine C Pestoni
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Paulina Ogar
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ilias Angelidis
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Andreas Liontos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | | | - Niklas J Lang
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Maximilian Strunz
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Diana Porras-Gonzalez
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael Gerckens
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Laurens J De Sadeleer
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium
| | - Bettina Oehrle
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Valeria Viteri-Alvarez
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Isis E Fernandez
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michelle Tallquist
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Chair of Experimental Genetics, Technical University of Munich, Freising, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabriel Mircea Stoleriu
- Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Jürgen Behr
- Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Nikolaus Kneidinger
- Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium
| | - Roxana Maria Wasnick
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Katrin Ahlbrecht
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Rory E Morty
- Department of Translational Pulmonology, University Hospital Heidelberg, and Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christos Samakovlis
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, Munich, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- G. Burgstaller and H.B. Schiller contributed equally to this article as lead authors and supervised the work
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
- G. Burgstaller and H.B. Schiller contributed equally to this article as lead authors and supervised the work
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6
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Yeo HJ, Ha M, Shin DH, Lee HR, Kim YH, Cho WH. Development of a Novel Biomarker for the Progression of Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2024; 25:599. [PMID: 38203769 PMCID: PMC10779374 DOI: 10.3390/ijms25010599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
The progression of idiopathic pulmonary fibrosis (IPF) is diverse and unpredictable. We identified and validated a new biomarker for IPF progression. To identify a candidate gene to predict progression, we assessed differentially expressed genes in patients with advanced IPF compared with early IPF and controls in three lung sample cohorts. Candidate gene expression was confirmed using immunohistochemistry and Western blotting of lung tissue samples from an independent IPF clinical cohort. Biomarker potential was assessed using an enzyme-linked immunosorbent assay of serum samples from the retrospective validation cohort. We verified that the final candidate gene reflected the progression of IPF in a prospective validation cohort. In the RNA-seq comparative analysis of lung tissues, CD276, COL7A1, CTSB, GLI2, PIK3R2, PRAF2, IGF2BP3, and NUPR1 were up-regulated, and ADAMTS8 was down-regulated in the samples of advanced IPF. Only CTSB showed significant differences in expression based on Western blotting (n = 12; p < 0.001) and immunohistochemistry between the three groups of the independent IPF cohort. In the retrospective validation cohort (n = 78), serum CTSB levels were higher in the progressive group (n = 25) than in the control (n = 29, mean 7.37 ng/mL vs. 2.70 ng/mL, p < 0.001) and nonprogressive groups (n = 24, mean 7.37 ng/mL vs. 2.56 ng/mL, p < 0.001). In the prospective validation cohort (n = 129), serum CTSB levels were higher in the progressive group than in the nonprogressive group (mean 8.30 ng/mL vs. 3.00 ng/mL, p < 0.001). After adjusting for baseline FVC, we found that CTSB was independently associated with IPF progression (adjusted OR = 2.61, p < 0.001). Serum CTSB levels significantly predicted IPF progression (AUC = 0.944, p < 0.001). Serum CTSB level significantly distinguished the progression of IPF from the non-progression of IPF or healthy control.
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Affiliation(s)
- Hye Ju Yeo
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (D.H.S.); (H.R.L.)
| | - Mihyang Ha
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Busan 46241, Republic of Korea;
- Department of Nuclear Medicine, Pusan National University Medical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea
| | - Dong Hoon Shin
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (D.H.S.); (H.R.L.)
- Department of Pathology, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Hye Rin Lee
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (D.H.S.); (H.R.L.)
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Woo Hyun Cho
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (D.H.S.); (H.R.L.)
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7
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Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B. Discovery of sparse, reliable omic biomarkers with Stabl. Nat Biotechnol 2024:10.1038/s41587-023-02033-x. [PMID: 38168992 DOI: 10.1038/s41587-023-02033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/16/2023] [Indexed: 01/05/2024]
Abstract
Adoption of high-content omic technologies in clinical studies, coupled with computational methods, has yielded an abundance of candidate biomarkers. However, translating such findings into bona fide clinical biomarkers remains challenging. To facilitate this process, we introduce Stabl, a general machine learning method that identifies a sparse, reliable set of biomarkers by integrating noise injection and a data-driven signal-to-noise threshold into multivariable predictive modeling. Evaluation of Stabl on synthetic datasets and five independent clinical studies demonstrates improved biomarker sparsity and reliability compared to commonly used sparsity-promoting regularization methods while maintaining predictive performance; it distills datasets containing 1,400-35,000 features down to 4-34 candidate biomarkers. Stabl extends to multi-omic integration tasks, enabling biological interpretation of complex predictive models, as it hones in on a shortlist of proteomic, metabolomic and cytometric events predicting labor onset, microbial biomarkers of pre-term birth and a pre-operative immune signature of post-surgical infections. Stabl is available at https://github.com/gregbellan/Stabl .
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Affiliation(s)
- Julien Hédou
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Ivana Marić
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Grégoire Bellan
- Télécom Paris, Institut Polytechnique de Paris, Paris, France
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Dyani K Gaudillière
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | | | - Franck Verdonk
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Sorbonne University, GRC 29, AP-HP, DMU DREAM, Department of Anesthesiology and Intensive Care, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Maximilian Sabayev
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Joshua Gillard
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jonas Amar
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Amelie Cambriel
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Alennie Roldan
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan L Golob
- Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas A Bonham
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Masaki Sato
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Maïgane Diop
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Xavier Durand
- École Polytechnique, Institut Polytechnique de Paris, Paris, France
| | - Martin S Angst
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrea Montanari
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA.
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
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8
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Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis. Sci Transl Med 2023; 15:eadh0908. [PMID: 38055803 DOI: 10.1126/scitranslmed.adh0908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT-staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type-specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.
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Affiliation(s)
- Niklas J Lang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Janine Gote-Schniering
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Rheumatology and Immunology, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Lung Precision Medicine Program, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Diana Porras-Gonzalez
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lin Yang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Laurens J De Sadeleer
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - R Christoph Jentzsch
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Vladimir A Shitov
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Shuhong Zhou
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Ahmed Agami
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Christoph H Mayr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Baharak Hooshiar Kashani
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Yuexin Chen
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lukas Heumos
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Jeanine C Pestoni
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Eszter Sarolta Molnar
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | | | | | | | - Melanie Wögrath
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Michael Gerckens
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Mareike Lehmann
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), 35043 Marburg, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Rudolf Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Jürgen Behr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - Mircea-Gabriel Stoleriu
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Malte D Luecken
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
- Department of Mathematics, Technische Universität München, 85748 Garching bei München, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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
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10
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Wang N, Wang H. Identification of metabolism-related gene signature in lung adenocarcinoma. Medicine (Baltimore) 2023; 102:e36267. [PMID: 38013279 PMCID: PMC10681599 DOI: 10.1097/md.0000000000036267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
AIM Lung cancer is one of the most common cancers in China and has a high mortality rate. Most patients who are diagnosed have lost the opportunity to undergo surgery. Aberrant metabolism is closely associated with tumorigenesis. We aimed to identify an effective metabolism-related prediction model for assessing prognosis based on the cancer genome atlas (TCGA) and GSE116959 databases. METHODS TCGA and GSE116959 datasets from Gene Expression Omnibus were used to obtain lung adenocarcinoma (LUAD) data. Additionally, we captured metabolism-related genes (MRGs) from the GeneCards database. First, we extracted differentially expressed genes using R to analyze the LUAD data. We then selected the same differentially expressed genes, including 168 downregulated and 77 upregulated genes. Finally, 218 differentially expressed MRGs (DEMRGs) were included to perform functional enrichment analysis and construct a protein-protein interaction network with the help of Cytoscape and Search Tool for the Retrieval of Interacting Genes database. Cytoscape was used to visualize the intensive intervals in the network. Then univariate and Least Absolute Shrinkage and Selection Operator Cox regression analyses, which assisted in identifying the overall survival (OS)-related DEMRGs and building a 10-DEMRG prognosis model, were performed. The prognostic values, tumor immunity relevance, and molecular mechanism were further investigated. A nomogram incorporating signature, age, gender, and TNM stage was established. RESULTS A 10-DEMRG model was established to forecast the OS of LUAD through Least Absolute Shrinkage and Selection Operator regression analysis. This prognostic signature stratified LUAD patients into low-risk and high-risk groups. The receiver operating characteristic curve and K-M analysis indicated good performance of the DEMRGs signature at predicting OS in the TCGA dataset. Univariate and multivariate Cox regression also revealed that the DEMRGs signature was an independent prognosis factor in LUAD. We noticed that the risk score was substantially related to the clinical parameters of LUAD patients, covering age and stage. Immune analysis results showed that risk score was associated with some immune cells and immune checkpoints. Nomogram also verified the clinical value of the DEMRGs signature. CONCLUSION In this study, we constructed a DEMRGs signature and established a prognostic nomogram that is robust and reliable to predict OS in LUAD. Overall, the findings could help with therapeutic customization and personalized therapies.
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Affiliation(s)
- Ning Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Shandong University, Shandong University, Jinan, Shandong, China
| | - Hui Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Shandong University, Shandong University, Jinan, Shandong, China
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11
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Leuschner G, Semenova A, Mayr CH, Kapellos TS, Ansari M, Seeliger B, Frankenberger M, Kneidinger N, Hatz RA, Hilgendorff A, Prasse A, Behr J, Mann M, Schiller HB. Mass spectrometry-based autoimmune profiling reveals predictive autoantigens in idiopathic pulmonary fibrosis. iScience 2023; 26:108345. [PMID: 38026226 PMCID: PMC10661358 DOI: 10.1016/j.isci.2023.108345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmunity plays a role in certain types of lung fibrosis, notably connective tissue disease-associated interstitial lung disease (CTD-ILD). In idiopathic pulmonary fibrosis (IPF), an incurable and fatal lung disease, diagnosis typically requires clinical exclusion of autoimmunity. However, autoantibodies of unknown significance have been detected in IPF patients. We conducted computational analysis of B cell transcriptomes in published transcriptomics datasets and developed a proteomic Differential Antigen Capture (DAC) assay that captures plasma antibodies followed by affinity purification of lung proteins coupled to mass spectrometry. We analyzed antibody capture in two independent cohorts of IPF and CTL-ILD patients over two disease progression time points. Our findings revealed significant upregulation of specific immunoglobulins with V-segment bias in IPF across multiple cohorts. We identified a predictive autoimmune signature linked to reduced transplant-free survival in IPF, persisting over time. Notably, autoantibodies against thrombospondin-1 were associated with decreased survival, suggesting their potential as predictive biomarkers.
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Affiliation(s)
- Gabriela Leuschner
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Anna Semenova
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Christoph H. Mayr
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Theodore S. Kapellos
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Meshal Ansari
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Benjamin Seeliger
- Department of Pneumology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Marion Frankenberger
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Nikolaus Kneidinger
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Rudolf A. Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU), Munich, and Asklepios Medical Center, Member of the German Center for Lung Research (DZL), Gauting, Germany
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Center for Comprehensive Developmental Care (CDeCLMU), Hospital of the Ludwig-Maximilians University (LMU), Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Antje Prasse
- Department of Pneumology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Jürgen Behr
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany
| | - Herbert B. Schiller
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
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12
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Lv W, Mao H, Ruan Y, Li S, Shimizu K, Zhang L, Zhang C. Identification and immunological characterization of PLA2G2A and cell death-associated molecular clusters in idiopathic pulmonary fibrosis. Life Sci 2023; 331:122071. [PMID: 37673297 DOI: 10.1016/j.lfs.2023.122071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
AIMS Idiopathic pulmonary fibrosis (IPF) is a severe pulmonary interstitial pneumonia. Our study focuses on the role of PLA2 enzyme in the IPF to explore a more effective diagnosis and treatment mechanism of IPF. MAIN METHODS Transcriptome data of IPF from GEO database and bleomycin-induced pulmonary fibrosis mice were analyzed to identify PLA2 enzyme and their metabolite, lysophosphatidylcholines 18:0, in IPF. Based on PLA2G2A and PLA2G2D / PLA2G2A-associated cell death genes (PCDs), the consensus clustering analysis was used to identify the subtypes of IPF and the correlation between PLA2G2A and prognosis was analyzed. The machine learning (ML) models and artificial neural network (ANN) model was used to validate the diagnostic accuracy of PLA2s and PCDs in diagnosing IPF. The gene and protein expression of NLRP3, GSDMD, and CASP-1 was estimated in recombinant PLA2G2A protein induced MLE-12 cells. KEY FINDINGS The expression of PLA2G2D, PLA2G2A, and LPC18 significantly changed in IPF. Furtherly, PLA2G2A has a significant correlation with poor patient prognosis, which could predict the 2 or 3-years mortality rates of IPF. Two subtypes of IPF patients, identified based on PCDs, showed significant different immunoinfiltration. Recombinant PLA2G2A protein could induce the pyrotosis in the MLE-12 cell. The generalized linear model and ANN model of PLA2s or PCDs accurate diagnosis IPF. SIGNIFICANCE PLA2G2A is the most robustly associated gene with IPF among the PLA2s, which demonstrates a potential in diagnosing and prognostic value in IPF, and provides a foundation for further understanding and breakthroughs in IPF diagnosis and treatment.
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Affiliation(s)
- Weichao Lv
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hongcai Mao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yang Ruan
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Shuaiyu Li
- Saigo Laboratory, School of Information Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Kuniyoshi Shimizu
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Louqian Zhang
- Department of Thoratic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China.
| | - Chaofeng Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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13
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Galaris A, Fanidis D, Tsitoura E, Kanellopoulou P, Barbayianni I, Ntatsoulis K, Touloumi K, Gramenoudi S, Karampitsakos T, Tzouvelekis A, Antoniou K, Aidinis V. Increased lipocalin-2 expression in pulmonary inflammation and fibrosis. Front Med (Lausanne) 2023; 10:1195501. [PMID: 37746070 PMCID: PMC10513431 DOI: 10.3389/fmed.2023.1195501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive interstitial lung disease with dismal prognosis. The underlying pathogenic mechanisms are poorly understood, resulting in a lack of effective treatments. However, recurrent epithelial damage is considered critical for disease initiation and perpetuation, via the secretion of soluble factors that amplify inflammation and lead to fibroblast activation and exuberant deposition of ECM components. Lipocalin-2 (LCN2) is a neutrophil gelatinase-associated lipocalin (NGAL) that has been suggested as a biomarker of kidney damage. LCN2 has been reported to modulate innate immunity, including the recruitment of neutrophils, and to protect against bacterial infections by sequestering iron. Methods In silico analysis of publicly available transcriptomic datasets; ELISAs on human IPF patients' bronchoalveolar lavage fluids (BALFs); bleomycin (BLM)-induced pulmonary inflammation and fibrosis and LPS-induced acute lung injury (ALI) in mice: pulmonary function tests, histology, Q-RT-PCR, western blot, and FACS analysis. Results and discussion Increased LCN2 mRNA expression was detected in the lung tissue of IPF patients negatively correlating with respiratory functions, as also shown for BALF LCN2 protein levels in a cohort of IPF patients. Increased Lcn2 expression was also detected upon BLM-induced pulmonary inflammation and fibrosis, especially at the acute phase correlating with neutrophilic infiltration, as well as upon LPS-induced ALI, an animal model characterized by neutrophilic infiltration. Surprisingly, and non withstanding the limitations of the study and the observed trends, Lcn2-/- mice were found to still develop BLM- or LPS-induced pulmonary inflammation and fibrosis, thus questioning a major pathogenic role for Lcn2 in mice. However, LCN2 qualifies as a surrogate biomarker of pulmonary inflammation and a possible indicator of compromised pulmonary functions, urging for larger studies.
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Affiliation(s)
- Apostolos Galaris
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Dionysios Fanidis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Eliza Tsitoura
- Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Paraskevi Kanellopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Ilianna Barbayianni
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Konstantinos Ntatsoulis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Katerina Touloumi
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Sofia Gramenoudi
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Theodoros Karampitsakos
- Department of Respiratory Medicine, School of Medicine, University of Patras, Patras, Greece
| | - Argyrios Tzouvelekis
- Department of Respiratory Medicine, School of Medicine, University of Patras, Patras, Greece
| | - Katerina Antoniou
- Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Vassilis Aidinis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
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14
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Johansson MW, Balnis J, Muehlbauer LK, Bukhman YV, Stefely MS, Overmyer KA, Vancavage R, Tiwari A, Adhikari AR, Feustel PJ, Schwartz BS, Coon JJ, Stewart R, Jaitovich A, Mosher DF. Decreased plasma cartilage acidic protein 1 in COVID-19. Physiol Rep 2023; 11:e15814. [PMID: 37667413 PMCID: PMC10477339 DOI: 10.14814/phy2.15814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 09/06/2023] Open
Abstract
Cartilage acidic protein-1 (CRTAC1) is produced by several cell types, including Type 2 alveolar epithelial (T2AE) cells that are targeted by SARS-CoV2. Plasma CRTAC1 is known based on proteomic surveys to be low in patients with severe COVID-19. Using an ELISA, we found that patients treated for COVID-19 in an ICU almost uniformly had plasma concentrations of CRTAC1 below those of healthy controls. Magnitude of decrease in CRTAC1 distinguished COVID-19 from other causes of acute respiratory decompensation and correlated with established metrics of COVID-19 severity. CRTAC1 concentrations below those of controls were found in some patients a year after hospitalization with COVID-19, long COVID after less severe COVID-19, or chronic obstructive pulmonary disease. Decreases in CRTAC1 in severe COVID-19 correlated (r = 0.37, p = 0.0001) with decreases in CFP (properdin), which interacts with CRTAC1. Thus, decreases of CRTAC1 associated with severe COVID-19 may result from loss of production by T2AE cells or co-depletion with CFP. Determination of significance of and reasons behind decreased CRTAC1 concentration in a subset of patients with long COVID will require analysis of roles of preexisting lung disease, impact of prior acute COVID-19, age, and other confounding variables in a larger number of patients.
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Affiliation(s)
- Mats W Johansson
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, New York, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, USA
| | - Laura K Muehlbauer
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yury V Bukhman
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Rachel Vancavage
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, New York, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, New York, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, USA
| | - Anish Raj Adhikari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, New York, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, USA
| | - Paul J Feustel
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Bradford S Schwartz
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, New York, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, USA
| | - Deane F Mosher
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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15
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Jin Z, Zhao L, Chang Y, Jin R, Hu F, Wu S, Xue Z, Ma Y, Chen C, Zheng M, Chang Y, Jin H, Xie Q, Huang C, Huang H. CRTAC1 enhances the chemosensitivity of non-small cell lung cancer to cisplatin by eliciting RyR-mediated calcium release and inhibiting Akt1 expression. Cell Death Dis 2023; 14:563. [PMID: 37633993 PMCID: PMC10460435 DOI: 10.1038/s41419-023-06088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023]
Abstract
Sensitivity to platinum-based combination chemotherapy is associated with a favorable prognosis in patients with non-small cell lung cancer (NSCLC). Here, our results obtained from analyses of the Gene Expression Omnibus database of NSCLC patients showed that cartilage acidic protein 1 (CRTAC1) plays a role in the response to platinum-based chemotherapy. Overexpression of CRTAC1 increased sensitivity to cisplatin in vitro, whereas knockdown of CRTAC1 decreased chemosensitivity of NSCLC cells. In vivo mouse experiments showed that CRTAC1 overexpression increased the antitumor effects of cisplatin. CRTAC1 overexpression promoted NFAT transcriptional activation by increasing intracellular Ca2+ levels, thereby inducing its regulated STUB1 mRNA transcription and protein expression, accelerating Akt1 protein degradation and, in turn, enhancing cisplatin-induced apoptosis. Taken together, the present results indicate that CRTAC1 overexpression increases the chemosensitivity of NSCLC to cisplatin treatment by inducing Ca2+-dependent Akt1 degradation and apoptosis, suggesting the potential of CRTAC1 as a biomarker for predicting cisplatin chemosensitivity. Our results further reveal that modulating the expression of CRTAC1 could be a new strategy for increasing the efficacy of cisplatin in chemotherapy of NSCLC patients.
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Affiliation(s)
- Zihui Jin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
- Center for Molecular Diagnosis and Precision Medicine, and The Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, 17 Yongwai Zhengjie, 330006, Nanchang, China
| | - Lingling Zhao
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Yixin Chang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Rongjia Jin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Fangyu Hu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Shuang Wu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Zixuan Xue
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Yimeng Ma
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Chenglin Chen
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Minghui Zheng
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Yuanyuan Chang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Qipeng Xie
- Department of Laboratory Medicine, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, 325035, Wenzhou, Zhejiang, People's Republic of China
| | - Chuanshu Huang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), 325035, Wenzhou, Zhejiang, China.
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China.
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16
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Ptasinski V, Monkley SJ, Öst K, Tammia M, Alsafadi HN, Overed-Sayer C, Hazon P, Wagner DE, Murray LA. Modeling fibrotic alveolar transitional cells with pluripotent stem cell-derived alveolar organoids. Life Sci Alliance 2023; 6:e202201853. [PMID: 37230801 PMCID: PMC10213712 DOI: 10.26508/lsa.202201853] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Repeated injury of the lung epithelium is proposed to be the main driver of idiopathic pulmonary fibrosis (IPF). However, available therapies do not specifically target the epithelium and human models of fibrotic epithelial damage with suitability for drug discovery are lacking. We developed a model of the aberrant epithelial reprogramming observed in IPF using alveolar organoids derived from human-induced pluripotent stem cells stimulated with a cocktail of pro-fibrotic and inflammatory cytokines. Deconvolution of RNA-seq data of alveolar organoids indicated that the fibrosis cocktail rapidly increased the proportion of transitional cell types including the KRT5 - /KRT17 + aberrant basaloid phenotype recently identified in the lungs of IPF patients. We found that epithelial reprogramming and extracellular matrix (ECM) production persisted after removal of the fibrosis cocktail. We evaluated the effect of the two clinically approved compounds for IPF, nintedanib and pirfenidone, and found that they reduced the expression of ECM and pro-fibrotic mediators but did not completely reverse epithelial reprogramming. Thus, our system recapitulates key aspects of IPF and is a promising system for drug discovery.
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Affiliation(s)
- Victoria Ptasinski
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Experimental Medical Sciences, Lung Bioengineering and Regeneration, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Susan J Monkley
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Karolina Öst
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Markus Tammia
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Hani N Alsafadi
- Department of Experimental Medical Sciences, Lung Bioengineering and Regeneration, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Catherine Overed-Sayer
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Petra Hazon
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Darcy E Wagner
- Department of Experimental Medical Sciences, Lung Bioengineering and Regeneration, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Lynne A Murray
- Bioscience COPD/IPF, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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17
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Exarchos KP, Gkrepi G, Kostikas K, Gogali A. Recent Advances of Artificial Intelligence Applications in Interstitial Lung Diseases. Diagnostics (Basel) 2023; 13:2303. [PMID: 37443696 DOI: 10.3390/diagnostics13132303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Interstitial lung diseases (ILDs) comprise a rather heterogeneous group of diseases varying in pathophysiology, presentation, epidemiology, diagnosis, treatment and prognosis. Even though they have been recognized for several years, there are still areas of research debate. In the majority of ILDs, imaging modalities and especially high-resolution Computed Tomography (CT) scans have been the cornerstone in patient diagnostic approach and follow-up. The intricate nature of ILDs and the accompanying data have led to an increasing adoption of artificial intelligence (AI) techniques, primarily on imaging data but also in genetic data, spirometry and lung diffusion, among others. In this literature review, we describe the most prominent applications of AI in ILDs presented approximately within the last five years. We roughly stratify these studies in three categories, namely: (i) screening, (ii) diagnosis and classification, (iii) prognosis.
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Affiliation(s)
- Konstantinos P Exarchos
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Georgia Gkrepi
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Konstantinos Kostikas
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Athena Gogali
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
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18
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Lipman D, Safo SE, Chekouo T. Integrative multi-omics approach for identifying molecular signatures and pathways and deriving and validating molecular scores for COVID-19 severity and status. BMC Genomics 2023; 24:319. [PMID: 37308820 PMCID: PMC10259816 DOI: 10.1186/s12864-023-09410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND There is still more to learn about the pathobiology of COVID-19. A multi-omic approach offers a holistic view to better understand the mechanisms of COVID-19. We used state-of-the-art statistical learning methods to integrate genomics, metabolomics, proteomics, and lipidomics data obtained from 123 patients experiencing COVID-19 or COVID-19-like symptoms for the purpose of identifying molecular signatures and corresponding pathways associated with the disease. RESULTS We constructed and validated molecular scores and evaluated their utility beyond clinical factors known to impact disease status and severity. We identified inflammation- and immune response-related pathways, and other pathways, providing insights into possible consequences of the disease. CONCLUSIONS The molecular scores we derived were strongly associated with disease status and severity and can be used to identify individuals at a higher risk for developing severe disease. These findings have the potential to provide further, and needed, insights into why certain individuals develop worse outcomes.
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Affiliation(s)
- Danika Lipman
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Sandra E Safo
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, USA.
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada.
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, USA.
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19
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Van de Sande B, Lee JS, Mutasa-Gottgens E, Naughton B, Bacon W, Manning J, Wang Y, Pollard J, Mendez M, Hill J, Kumar N, Cao X, Chen X, Khaladkar M, Wen J, Leach A, Ferran E. Applications of single-cell RNA sequencing in drug discovery and development. Nat Rev Drug Discov 2023; 22:496-520. [PMID: 37117846 PMCID: PMC10141847 DOI: 10.1038/s41573-023-00688-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 04/30/2023]
Abstract
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery and development. New opportunities are emerging in target identification owing to improved disease understanding through cell subtyping, and highly multiplexed functional genomics screens incorporating scRNA-seq are enhancing target credentialling and prioritization. ScRNA-seq is also aiding the selection of relevant preclinical disease models and providing new insights into drug mechanisms of action. In clinical development, scRNA-seq can inform decision-making via improved biomarker identification for patient stratification and more precise monitoring of drug response and disease progression. Here, we illustrate how scRNA-seq methods are being applied in key steps in drug discovery and development, and discuss ongoing challenges for their implementation in the pharmaceutical industry.
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Affiliation(s)
| | | | | | - Bart Naughton
- Computational Neurobiology, Eisai, Cambridge, MA, USA
| | - Wendi Bacon
- EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- The Open University, Milton Keynes, UK
| | | | - Yong Wang
- Precision Bioinformatics, Prometheus Biosciences, San Diego, CA, USA
| | | | - Melissa Mendez
- Genomic Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Jon Hill
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Namit Kumar
- Informatics & Predictive Sciences, Bristol Myers Squibb, San Diego, CA, USA
| | - Xiaohong Cao
- Genomic Research Center, AbbVie Inc., Cambridge, MA, USA
| | - Xiao Chen
- Magnet Biomedicine, Cambridge, MA, USA
| | - Mugdha Khaladkar
- Human Genetics and Computational Biology, GlaxoSmithKline, Collegeville, PA, USA
| | - Ji Wen
- Oncology Research and Development Unit, Pfizer, La Jolla, CA, USA
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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Blackburn JB, Li NF, Bartlett NW, Richmond BW. An update in club cell biology and its potential relevance to chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2023; 324:L652-L665. [PMID: 36942863 PMCID: PMC10110710 DOI: 10.1152/ajplung.00192.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
Club cells are found in human small airways where they play an important role in immune defense, xenobiotic metabolism, and repair after injury. Over the past few years, data from single-cell RNA sequencing (scRNA-seq) studies has generated new insights into club cell heterogeneity and function. In this review, we integrate findings from scRNA-seq experiments with earlier in vitro, in vivo, and microscopy studies and highlight the many ways club cells contribute to airway homeostasis. We then discuss evidence for loss of club cells or club cell products in the airways of patients with chronic obstructive pulmonary disease (COPD) and discuss potential mechanisms through which this might occur.
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Affiliation(s)
- Jessica B Blackburn
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, United States
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
| | - Ngan Fung Li
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - Nathan W Bartlett
- Viral Immunology and Respiratory Disease Group, University of Newcastle, Callaghan, New South Wales, Australia
| | - Bradley W Richmond
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, United States
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States
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22
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Fanidis D, Pezoulas VC, Fotiadis DΙ, Aidinis V. An explainable machine learning-driven proposal of pulmonary fibrosis biomarkers. Comput Struct Biotechnol J 2023; 21:2305-2315. [PMID: 37007651 PMCID: PMC10049879 DOI: 10.1016/j.csbj.2023.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Pulmonary fibrosing diseases are in the very epicenter of biomedical research both due to their increasing prevalence and their association with SARS-CoV-2 infections. Research of idiopathic pulmonary fibrosis, the most lethal among the interstitial lung diseases, is in need for new biomarkers and potential disease targets, a goal that could be accelerated using machine learning techniques. In this study, we have used Shapley values to explain the decisions made by an ensemble learning model trained to classify samples to an either pulmonary fibrosis or steady state based on the expression values of deregulated genes. This process resulted in a full and a laconic set of features capable of separating phenotypes to an at least equal degree as previously published marker sets. Indicatively, a maximum increase of 6% in specificity and 5% in Mathew's correlation coefficient was achieved. Evaluation with an additional independent dataset showed our feature set having a greater generalization potential than the rest. Ultimately, the proposed gene lists are expected not only to serve as new sets of diagnostic marker elements, but also as a target pool for future research initiatives.
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Affiliation(s)
- Dionysios Fanidis
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari GR16672, Greece
| | - Vasileios C. Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
| | - Dimitrios Ι. Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
- Biomedical Research Institute, FORTH, Ioannina GR45110, Greece
| | - Vassilis Aidinis
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari GR16672, Greece
- Corresponding author.
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23
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Kim JW, Jeong MH, Yu HT, Park YJ, Kim HS, Chung KH. Fibrinogen on extracellular vesicles derived from polyhexamethylene guanidine phosphate-exposed mice induces inflammatory effects via integrin β. Ecotoxicol Environ Saf 2023; 252:114600. [PMID: 36736230 DOI: 10.1016/j.ecoenv.2023.114600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Polyhexamethylene guanidine phosphate (PHMG-p), used as a humidifier disinfectant, causes interstitial lung disease, obliterative bronchiolitis, and lung fibrosis; however, little is known about its effect on intercellular interactions. Extracellular vesicles (EVs), which carry diverse compounds including proteins, RNA, and DNA to mediate cell-to-cell communication through their paracrine effects, have been highlighted as novel factors in lung fibrogenesis. This study aimed to identify the effect of proteins on small EVs (sEVs) from bronchoalveolar lavage fluid (BALF) of the recipient cells after PHMG-p exposure. A week after intratracheal administration of PHMG-p, sEVs were isolated from BALF of tissue showing overexpressed inflammatory and fibrosis markers. To investigate the role of sEVs in inflammation, naïve macrophages were cultured with sEVs, which induced their activation. To identify sEV proteins that are associated with these responses, proteomics analysis was performed. In the gene ontology analysis, coagulation, fibrinolysis, and hemostasis were associated with the upregulated proteins in sEVs. The highest increase was observed in fibrinogen levels, which was also related to those gene ontologies. We validated role of exosomal fibrinogen in inflammation using recombinant fibrinogen and an inhibitor of the integrin, which is the binding receptor for fibrinogen. Overall, we elucidated that increased fibrinogen levels in the early sEVs-PHMG activated inflammatory response during early fibrosis. These results suggest that sEVs from the BALF of PHMG-p-exposed mice could aggravate fibrogenesis by activating naïve macrophages via various proteins in the sEVs, Furthermore, this finding will be broadening the spectrum of communicating mediators.
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Affiliation(s)
- Jun Woo Kim
- Sungkyunkwan University, School of Pharmacy, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Mi Ho Jeong
- Massachusetts General Hospital, Center for Systems Biology, Boston, MA 02114, USA
| | - Hyeong Tae Yu
- Sungkyunkwan University, School of Pharmacy, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Yong Joo Park
- Kyungsung University, College of Pharmacy, Busan 48434, Republic of Korea
| | - Hyung Sik Kim
- Sungkyunkwan University, School of Pharmacy, Suwon, Gyeonggi-do 16419, Republic of Korea.
| | - Kyu Hyuck Chung
- Sungkyunkwan University, School of Pharmacy, Suwon, Gyeonggi-do 16419, Republic of Korea.
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24
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Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Bonham TA, Sato M, Diop M, Angst MS, Stevenson D, Aghaeepour N, Montanari A, Gaudillière B. Stabl: sparse and reliable biomarker discovery in predictive modeling of high-dimensional omic data. Res Sq 2023:rs.3.rs-2609859. [PMID: 36909508 PMCID: PMC10002850 DOI: 10.21203/rs.3.rs-2609859/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
High-content omic technologies coupled with sparsity-promoting regularization methods (SRM) have transformed the biomarker discovery process. However, the translation of computational results into a clinical use-case scenario remains challenging. A rate-limiting step is the rigorous selection of reliable biomarker candidates among a host of biological features included in multivariate models. We propose Stabl, a machine learning framework that unifies the biomarker discovery process with multivariate predictive modeling of clinical outcomes by selecting a sparse and reliable set of biomarkers. Evaluation of Stabl on synthetic datasets and four independent clinical studies demonstrates improved biomarker sparsity and reliability compared to commonly used SRMs at similar predictive performance. Stabl readily extends to double- and triple-omics integration tasks and identifies a sparser and more reliable set of biomarkers than those selected by state-of-the-art early- and late-fusion SRMs, thereby facilitating the biological interpretation and clinical translation of complex multi-omic predictive models. The complete package for Stabl is available online at https://github.com/gregbellan/Stabl.
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Affiliation(s)
- Julien Hédou
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Ivana Marić
- Department of Pediatrics, Stanford University, Stanford, CA
| | | | - Jakob Einhaus
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Dyani K. Gaudillière
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University, Stanford, CA
| | | | - Franck Verdonk
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
- Sorbonne University, GRC 29, AP-HP, DMU DREAM, Department of Anesthesiology and Intensive Care, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris; Paris, France
| | - Ina A. Stelzer
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Amy S. Tsai
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Edward A. Ganio
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Maximilian Sabayev
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Joshua Gillard
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Thomas A. Bonham
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Masaki Sato
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Maïgane Diop
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Andrea Montanari
- Department of Statistics, Stanford University, Stanford, CA
- Department of Electrical Engineering, Stanford University, Stanford, CA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
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25
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Lu TC, Sun YM, Zhong Y, Lin XH, Lei Y, Liu AL. Electrochemical immunosensor based on AuNPs/ERGO@CNT nanocomposites by one-step electrochemical co-reduction for sensitive detection of P-glycoprotein in serum. Biosens Bioelectron 2023; 222:115001. [PMID: 36516634 DOI: 10.1016/j.bios.2022.115001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
P-glycoprotein (P-gp), a transmembrane glycoprotein widely expressed on the surface of various cells, is highly associated with multidrug resistance (MDR) that heralds the malignant progress of disease after drug treatment. Notably, there have been reported that serum P-gp is a potential marker for assessing the progression of disease resistance. Currently, there are few methods for point-of-care serum P-gp detection. In this study, we proposed a gold nanoparticles/electrochemically reduced graphene oxide@carbon nanotube (AuNPs/ERGO@CNT) modified immunosensor based on a one-step electrochemical co-reduction method. The limit of detection (LOD) of our constructed electrochemical immunosensor for P-gp detection reached 0.13 ng/mL, and the detection results in serum were consistent with ELISA. The developed immunosensor is expected to provide a scientific basis for the clinical application of serum P-gp monitoring and integrated medicine.
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26
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Ćorović A, Wall C, Nus M, Gopalan D, Huang Y, Imaz M, Zulcinski M, Peverelli M, Uryga A, Lambert J, Bressan D, Maughan RT, Pericleous C, Dubash S, Jordan N, Jayne DR, Hoole SP, Calvert PA, Dean AF, Rassl D, Barwick T, Iles M, Frontini M, Hannon G, Manavaki R, Fryer TD, Aloj L, Graves MJ, Gilbert FJ, Dweck MR, Newby DE, Fayad ZA, Reynolds G, Morgan AW, Aboagye EO, Davenport AP, Jørgensen HF, Mallat Z, Bennett MR, Peters JE, Rudd JHF, Mason JC, Tarkin JM. Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis. J Am Coll Cardiol 2023; 81:336-354. [PMID: 36697134 PMCID: PMC9883634 DOI: 10.1016/j.jacc.2022.10.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Assessing inflammatory disease activity in large vessel vasculitis (LVV) can be challenging by conventional measures. OBJECTIVES We aimed to investigate somatostatin receptor 2 (SST2) as a novel inflammation-specific molecular imaging target in LVV. METHODS In a prospective, observational cohort study, in vivo arterial SST2 expression was assessed by positron emission tomography/magnetic resonance imaging (PET/MRI) using 68Ga-DOTATATE and 18F-FET-βAG-TOCA. Ex vivo mapping of the imaging target was performed using immunofluorescence microscopy; imaging mass cytometry; and bulk, single-cell, and single-nucleus RNA sequencing. RESULTS Sixty-one participants (LVV: n = 27; recent atherosclerotic myocardial infarction of ≤2 weeks: n = 25; control subjects with an oncologic indication for imaging: n = 9) were included. Index vessel SST2 maximum tissue-to-blood ratio was 61.8% (P < 0.0001) higher in active/grumbling LVV than inactive LVV and 34.6% (P = 0.0002) higher than myocardial infarction, with good diagnostic accuracy (area under the curve: ≥0.86; P < 0.001 for both). Arterial SST2 signal was not elevated in any of the control subjects. SST2 PET/MRI was generally consistent with 18F-fluorodeoxyglucose PET/computed tomography imaging in LVV patients with contemporaneous clinical scans but with very low background signal in the brain and heart, allowing for unimpeded assessment of nearby coronary, myocardial, and intracranial artery involvement. Clinically effective treatment for LVV was associated with a 0.49 ± 0.24 (standard error of the mean [SEM]) (P = 0.04; 22.3%) reduction in the SST2 maximum tissue-to-blood ratio after 9.3 ± 3.2 months. SST2 expression was localized to macrophages, pericytes, and perivascular adipocytes in vasculitis specimens, with specific receptor binding confirmed by autoradiography. SSTR2-expressing macrophages coexpressed proinflammatory markers. CONCLUSIONS SST2 PET/MRI holds major promise for diagnosis and therapeutic monitoring in LVV. (PET Imaging of Giant Cell and Takayasu Arteritis [PITA], NCT04071691; Residual Inflammation and Plaque Progression Long-Term Evaluation [RIPPLE], NCT04073810).
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Affiliation(s)
- Andrej Ćorović
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christopher Wall
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Meritxell Nus
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Deepa Gopalan
- Department of Radiology, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom; Department of Radiology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - Yuan Huang
- Engineering and Physical Sciences Research Council Centre for Mathematical Imaging in Healthcare, University of Cambridge, Cambridge, United Kingdom
| | - Maria Imaz
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michal Zulcinski
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Marta Peverelli
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom; Vascular Sciences, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Anna Uryga
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jordi Lambert
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Dario Bressan
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Robert T Maughan
- Vascular Sciences, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Charis Pericleous
- Vascular Sciences, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Suraiya Dubash
- Department of Oncology, University College London NHS Trust, London, United Kingdom; Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Natasha Jordan
- Department of Rheumatology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - David R Jayne
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephen P Hoole
- Department of Cardiology, Royal Papworth Hospital NHS Trust, Cambridge, United Kingdom
| | - Patrick A Calvert
- Department of Cardiology, Royal Papworth Hospital NHS Trust, Cambridge, United Kingdom
| | - Andrew F Dean
- Department of Histopathology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - Doris Rassl
- Department of Histopathology, Royal Papworth Hospital NHS Trust, Cambridge, United Kingdom
| | - Tara Barwick
- Department of Radiology, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom; Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Mark Iles
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Mattia Frontini
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Greg Hannon
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Roido Manavaki
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Tim D Fryer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Luigi Aloj
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Martin J Graves
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Fiona J Gilbert
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Marc R Dweck
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - David E Newby
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Zahi A Fayad
- BioMedical Engineering & Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gary Reynolds
- Department of Rheumatology, University of Newcastle, Newcastle, United Kingdom
| | - Ann W Morgan
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Eric O Aboagye
- Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Anthony P Davenport
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Helle F Jørgensen
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ziad Mallat
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martin R Bennett
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James E Peters
- Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - James H F Rudd
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Justin C Mason
- Vascular Sciences, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Jason M Tarkin
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, United Kingdom; Vascular Sciences, National Heart & Lung Institute, Imperial College London, London, United Kingdom.
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27
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Asghar S, Monkley S, Smith DJF, Hewitt RJ, Grime K, Murray LA, Overed-Sayer CL, Molyneaux PL. Epithelial senescence in idiopathic pulmonary fibrosis is propagated by small extracellular vesicles. Respir Res 2023; 24:51. [PMID: 36788603 PMCID: PMC9930250 DOI: 10.1186/s12931-023-02333-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease that affects 3 million people worldwide. Senescence and small extracellular vesicles (sEVs) have been implicated in the pathogenesis of IPF, although how sEVs promote disease remains unclear. Here, we profile sEVs from bronchial epithelial cells and determine small RNA (smRNA) content. METHODS Conditioned media was collected and sEVs were isolated from normal human bronchial epithelial cells (NHBEs) and IPF-diseased human bronchial epithelial cells (DHBEs). RESULTS Increased sEV release from DHBEs compared to NHBEs (n = 4; p < 0.05) was detected by nanoparticle tracking analysis. NHBEs co-cultured with DHBE-derived sEVs for 72 h expressed higher levels of SA-β-Gal and γH2AX protein, p16 and p21 RNA and increased secretion of IL6 and IL8 proteins (all n = 6-8; p < 0.05). sEVs were also co-cultured with healthy air-liquid interface (ALI) cultures and similar results were observed, with increases in p21 and p16 gene expression and IL6 and IL8 (basal and apical) secretion (n = 6; p < 0.05). Transepithelial electrical resistance (TEER) measurements, a reflection of epithelial barrier integrity, were decreased upon the addition of DHBE-derived sEVs (n = 6; p < 0.05). smRNA-sequencing identified nineteen significantly differentially expressed miRNA in DHBE-derived sEVs compared to NHBE-derived sEVs, with candidate miRNAs validated by qPCR (all n = 5; p < 0.05). Four of these miRNAs were upregulated in NHBEs co-cultured with DHBE-derived sEVs and three in healthy ALI cultures co-cultured with DHBE-derived sEVs (n = 3-4; p < 0.05). CONCLUSIONS This data demonstrates that DHBE-derived sEVs transfer senescence to neighbouring healthy cells, promoting the disease state in IPF.
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Affiliation(s)
- Sabha Asghar
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
| | - Susan Monkley
- grid.418151.80000 0001 1519 6403Translational Sciences & Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - David J. F. Smith
- grid.7445.20000 0001 2113 8111National Heart & Lung Institute, Imperial College London, London, UK ,grid.420545.20000 0004 0489 3985Royal Brompton & Harefield Hospitals, Guy’s & St Thomas’ NHS Foundation Trust, London, UK
| | - Richard J. Hewitt
- grid.7445.20000 0001 2113 8111National Heart & Lung Institute, Imperial College London, London, UK ,grid.420545.20000 0004 0489 3985Royal Brompton & Harefield Hospitals, Guy’s & St Thomas’ NHS Foundation Trust, London, UK
| | - Ken Grime
- grid.418151.80000 0001 1519 6403Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lynne A. Murray
- grid.417815.e0000 0004 5929 4381Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Catherine L. Overed-Sayer
- grid.417815.e0000 0004 5929 4381Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Philip L. Molyneaux
- grid.7445.20000 0001 2113 8111National Heart & Lung Institute, Imperial College London, London, UK ,grid.420545.20000 0004 0489 3985Royal Brompton & Harefield Hospitals, Guy’s & St Thomas’ NHS Foundation Trust, London, UK
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28
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Glenn LM, Troy LK, Corte TJ. Novel diagnostic techniques in interstitial lung disease. Front Med (Lausanne) 2023; 10:1174443. [PMID: 37188089 PMCID: PMC10175799 DOI: 10.3389/fmed.2023.1174443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Research into novel diagnostic techniques and targeted therapeutics in interstitial lung disease (ILD) is moving the field toward increased precision and improved patient outcomes. An array of molecular techniques, machine learning approaches and other innovative methods including electronic nose technology and endobronchial optical coherence tomography are promising tools with potential to increase diagnostic accuracy. This review provides a comprehensive overview of the current evidence regarding evolving diagnostic methods in ILD and to consider their future role in routine clinical care.
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Affiliation(s)
- Laura M. Glenn
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
- *Correspondence: Laura M. Glenn,
| | - Lauren K. Troy
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
| | - Tamera J. Corte
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
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29
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Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G, Panizzolo E, Martowicz A, Trebo M, Pall G, Gamerith G, Sykora M, Augustin F, Schmitz K, Finotello F, Rieder D, Perner S, Sopper S, Wolf D, Pircher A, Trajanoski Z. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 2022; 40:1503-1520.e8. [PMID: 36368318 PMCID: PMC9767679 DOI: 10.1016/j.ccell.2022.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/26/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and resistance. However, full understanding of how immune cell phenotypes vary across different patient subgroups is lacking. Here, we dissect the NSCLC tumor microenvironment at high resolution by integrating 1,283,972 single cells from 556 samples and 318 patients across 29 datasets, including our dataset capturing cells with low mRNA content. We stratify patients into immune-deserted, B cell, T cell, and myeloid cell subtypes. Using bulk samples with genomic and clinical information, we identify cellular components associated with tumor histology and genotypes. We then focus on the analysis of tissue-resident neutrophils (TRNs) and uncover distinct subpopulations that acquire new functional properties in the tissue microenvironment, providing evidence for the plasticity of TRNs. Finally, we show that a TRN-derived gene signature is associated with anti-programmed cell death ligand 1 (PD-L1) treatment failure.
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Affiliation(s)
- Stefan Salcher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lena Horvath
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Christiane Kuempers
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisa Panizzolo
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria; Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - Manuel Trebo
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Pall
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriele Gamerith
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Sykora
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Augustin
- Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Innsbruck, Austria
| | - Katja Schmitz
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria; INNPATH GmbH, Institute of Pathology, Innsbruck, Austria
| | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria; Digital Science Center, University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany; Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Lung Research (DZL), Luebeck and Borstel, Germany
| | - Sieghart Sopper
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Pircher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria.
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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Engelbrecht E, Kooistra T, Knipe RS. The Vasculature in Pulmonary Fibrosis. Curr Tissue Microenviron Rep 2022; 3:83-97. [PMID: 36712832 PMCID: PMC9881604 DOI: 10.1007/s43152-022-00040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
Abstract
Purpose of Review The current paradigm of idiopathic pulmonary fibrosis (IPF) pathogenesis involves recurrent injury to a sensitive alveolar epithelium followed by impaired repair responses marked by fibroblast activation and deposition of extracellular matrix. Multiple cell types are involved in this response with potential roles suggested by advances in single-cell RNA sequencing and lung developmental biology. Notably, recent work has better characterized the cell types present in the pulmonary endothelium and identified vascular changes in patients with IPF. Recent Findings Lung tissue from patients with IPF has been examined at single-cell resolution, revealing reductions in lung capillary cells and expansion of a population of vascular cells expressing markers associated with bronchial endothelium. In addition, pre-clinical models have demonstrated a fundamental role for aging and vascular permeability in the development of pulmonary fibrosis. Summary Mounting evidence suggests that the endothelium undergoes changes in the context of fibrosis, and these changes may contribute to the development and/or progression of pulmonary fibrosis. Additional studies will be needed to further define the functional role of these vascular changes.
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Affiliation(s)
| | - Tristan Kooistra
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Rachel S. Knipe
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Pesold VV, Wendler O, Morgenthaler L, Gröhn F, Mueller SK. Analysis of CRSsNP Proteome Using a Highly Multiplexed Approach in Nasal Mucus. Am J Rhinol Allergy 2022; 37:348-359. [PMID: 36341722 DOI: 10.1177/19458924221136651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Chronic rhinosinusitis without nasal polyps (CRSsNP) represents a phenotype of CRS, whose immunological mechanisms are still unclear. So far there are neither suitable biomarkers to determine the course of the disease nor an individual therapy. OBJECTIVE The purpose of this study was to characterize the CRSsNP endotype by identifying and validating non-invasive proteomic biomarkers. METHODS A highly-multiplexed proteomic array consisting of antibodies against 2000 proteins was used to identify proteins that are differentially expressed in the nasal mucus of the CRSsNP and control groups (n = 7 per group). The proteins identified to be most differentially expressed were validated in matched nasal mucus samples using western blots and enzyme-linked immunosorbent assay (ELISA). Validation was also done in a second cohort using western blots (CRSsNP n = 25, control n = 23) and ELISA (n = 30 per group). Additionally, immunohistochemistry in CRSsNP and control tissue samples was performed to characterize the selected proteins further. RESULTS Out of the 2000 proteins examined, 7 from the most differentially expressed proteins were chosen to be validated. The validation results showed that 4 proteins were significantly upregulated in CRSsNP mucus, including macrophage inflammatory protein-1beta (MIP-1β), resistin, high mobility group box 1 (HMGB1), and forkhead box protein 3 (FOXP3). Cartilage acidic protein 1 (CRTAC1) was not significantly upregulated. Two proteins were significantly downregulated including scavenger receptor class F member 2 (SCARF2) and P-selectin. All proteins selected are mainly associated with inflammation, cell proliferation/differentiation, apoptosis and cell-cell or cell-matrix interaction. CONCLUSION Proteomic analysis of CRSsNP and control mucus has confirmed known and revealed novel disease-associated proteins that could potentially serve as a new biosignature for CRSsNP. Analysis of the associated pathways will specify endotypes of CRSsNP and will lead to an improved understanding of the pathophysiology of CRSsNP. Furthermore, our data contribute to the development of a reproducible, non-invasive, and quantitative "liquid biopsy" for rhinosinusitis.
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Affiliation(s)
- Vanessa-Vivien Pesold
- Department of Otolaryngology, Head and Neck Surgery, 9171Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Olaf Wendler
- Department of Otolaryngology, Head and Neck Surgery, 9171Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lisa Morgenthaler
- Department of Otolaryngology, Head and Neck Surgery, 9171Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy, Interdisciplinary Center for Molecular Materials, 9171Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sarina K Mueller
- Department of Otolaryngology, Head and Neck Surgery, 9171Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Li X, Kolling FW, Aridgides D, Mellinger D, Ashare A, Jakubzick CV. ScRNA-seq expression of IFI27 and APOC2 identifies four alveolar macrophage superclusters in healthy BALF. Life Sci Alliance 2022; 5:e202201458. [PMID: 35820705 PMCID: PMC9275597 DOI: 10.26508/lsa.202201458] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
Alveolar macrophages (AMs) reside on the luminal surface of the airways and alveoli, ensuring proper gas exchange by ingesting cellular debris and pathogens, and regulating inflammatory responses. Therefore, understanding the heterogeneity and diverse roles played by AMs, interstitial macrophages, and recruited monocytes is critical for treating airway diseases. We performed single-cell RNA sequencing on 113,213 bronchoalveolar lavage cells from four healthy and three uninflamed cystic fibrosis subjects and identified two MARCKS+LGMN+IMs, FOLR2+SELENOP+ and SPP1+PLA2G7+ IMs, monocyte subtypes, DC1, DC2, migDCs, plasmacytoid DCs, lymphocytes, epithelial cells, and four AM superclusters (families) based on the gene expression of IFI27 and APOC2 These four AM families have at least eight distinct functional members (subclusters) named after their differentially expressed gene(s): IGF1, CCL18, CXCL5, cholesterol, chemokine, metallothionein, interferon, and small-cluster AMs. Interestingly, the chemokine cluster further divides with each subcluster selectively expressing a unique combination of chemokines. One of the most striking observations, besides the heterogeneity, is the conservation of AM family members in relatively equal ratio across all AM superclusters and individuals. Transcriptional data and TotalSeq technology were used to investigate cell surface markers that distinguish resident AMs from recruited monocytes. Last, other AM datasets were projected onto our dataset. Similar AM superclusters and functional subclusters were observed, along with a significant increase in chemokine and IFN AM subclusters in individuals infected with COVID-19. Overall, functional specializations of the AM subclusters suggest that there are highly regulated AM niches with defined programming states, highlighting a clear division of labor.
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Affiliation(s)
- Xin Li
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Fred W Kolling
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Daniel Aridgides
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Diane Mellinger
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Alix Ashare
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Claudia V Jakubzick
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
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Abstract
Single-cell sequencing is a powerful approach that can detect genetic alterations and their phenotypic consequences in the context of human development, with cellular resolution. Humans start out as single-cell zygotes and undergo fission and differentiation to develop into multicellular organisms. Before fertilisation and during development, the cellular genome acquires hundreds of mutations that propagate down the cell lineage. Whether germline or somatic in nature, some of these mutations may have significant genotypic impact and lead to diseased cellular phenotypes, either systemically or confined to a tissue. Single-cell sequencing enables the detection and monitoring of the genotype and the consequent molecular phenotypes at a cellular resolution. It offers powerful tools to compare the cellular lineage between 'normal' and 'diseased' conditions and to establish genotype-phenotype relationships. By preserving cellular heterogeneity, single-cell sequencing, unlike bulk-sequencing, allows the detection of even small, diseased subpopulations of cells within an otherwise normal tissue. Indeed, the characterisation of biopsies with cellular resolution can provide a mechanistic view of the disease. While single-cell approaches are currently used mainly in basic research, it can be expected that applications of these technologies in the clinic may aid the detection, diagnosis and eventually the treatment of rare genetic diseases as well as cancer. This review article provides an overview of the single-cell sequencing technologies in the context of human genetics, with an aim to empower clinicians to understand and interpret the single-cell sequencing data and analyses. We discuss the state-of-the-art experimental and analytical workflows and highlight current challenges/limitations. Notably, we focus on two prospective applications of the technology in human genetics, namely the annotation of the non-coding genome using single-cell functional genomics and the use of single-cell sequencing data for in silico variant prioritisation.
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Affiliation(s)
- Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Byeon SK, Madugundu AK, Garapati K, Ramarajan MG, Saraswat M, Kumar-M P, Hughes T, Shah R, Patnaik MM, Chia N, Ashrafzadeh-Kian S, Yao JD, Pritt BS, Cattaneo R, Salama ME, Zenka RM, Kipp BR, Grebe SKG, Singh RJ, Sadighi Akha AA, Algeciras-Schimnich A, Dasari S, Olson JE, Walsh JR, Venkatakrishnan AJ, Jenkinson G, O'Horo JC, Badley AD, Pandey A. Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study. Lancet Digit Health 2022; 4:e632-45. [PMID: 35835712 DOI: 10.1016/S2589-7500(22)00112-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/26/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND COVID-19 is a multi-system disorder with high variability in clinical outcomes among patients who are admitted to hospital. Although some cytokines such as interleukin (IL)-6 are believed to be associated with severity, there are no early biomarkers that can reliably predict patients who are more likely to have adverse outcomes. Thus, it is crucial to discover predictive markers of serious complications. METHODS In this retrospective cohort study, we analysed samples from 455 participants with COVID-19 who had had a positive SARS-CoV-2 RT-PCR result between April 14, 2020, and Dec 1, 2020 and who had visited one of three Mayo Clinic sites in the USA (Minnesota, Arizona, or Florida) in the same period. These participants were assigned to three subgroups depending on disease severity as defined by the WHO ordinal scale of clinical improvement (outpatient, severe, or critical). Our control cohort comprised of 182 anonymised age-matched and sex-matched plasma samples that were available from the Mayo Clinic Biorepository and banked before the COVID-19 pandemic. We did a deep profiling of circulatory cytokines and other proteins, lipids, and metabolites from both cohorts. Most patient samples were collected before, or around the time of, hospital admission, representing ideal samples for predictive biomarker discovery. We used proximity extension assays to quantify cytokines and circulatory proteins and tandem mass spectrometry to measure lipids and metabolites. Biomarker discovery was done by applying an AutoGluon-tabular classifier to a multiomics dataset, producing a stacked ensemble of cutting-edge machine learning algorithms. Global proteomics and glycoproteomics on a subset of patient samples with matched pre-COVID-19 plasma samples was also done. FINDINGS We quantified 1463 cytokines and circulatory proteins, along with 902 lipids and 1018 metabolites. By developing a machine-learning-based prediction model, a set of 102 biomarkers, which predicted severe and clinical COVID-19 outcomes better than the traditional set of cytokines, were discovered. These predictive biomarkers included several novel cytokines and other proteins, lipids, and metabolites. For example, altered amounts of C-type lectin domain family 6 member A (CLEC6A), ether phosphatidylethanolamine (P-18:1/18:1), and 2-hydroxydecanoate, as reported here, have not previously been associated with severity in COVID-19. Patient samples with matched pre-COVID-19 plasma samples showed similar trends in muti-omics signatures along with differences in glycoproteomics profile. INTERPRETATION A multiomic molecular signature in the plasma of patients with COVID-19 before being admitted to hospital can be exploited to predict a more severe course of disease. Machine learning approaches can be applied to highly complex and multidimensional profiling data to reveal novel signatures of clinical use. The absence of validation in an independent cohort remains a major limitation of the study. FUNDING Eric and Wendy Schmidt.
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Wu S, Xu Y, Zhang J, Ran X, Jia X, Wang J, Sun L, Yang H, Li Y, Fu B, Huang C, Liao P, Sun W. Longitudinal Serum Proteome Characterization of COVID-19 Patients With Different Severities Revealed Potential Therapeutic Strategies. Front Immunol 2022; 13:893943. [PMID: 35958562 PMCID: PMC9361788 DOI: 10.3389/fimmu.2022.893943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is exerting huge pressure on global healthcare. Understanding of the molecular pathophysiological alterations in COVID-19 patients with different severities during disease is important for effective treatment. In this study, we performed proteomic profiling of 181 serum samples collected at multiple time points from 79 COVID-19 patients with different severity levels (asymptomatic, mild, moderate, and severe/critical) and 27 serum samples from non-COVID-19 control individuals. Dysregulation of immune response and metabolic reprogramming was found in severe/critical COVID-19 patients compared with non-severe/critical patients, whereas asymptomatic patients presented an effective immune response compared with symptomatic COVID-19 patients. Interestingly, the moderate COVID-19 patients were mainly grouped into two distinct clusters using hierarchical cluster analysis, which demonstrates the molecular pathophysiological heterogeneity in COVID-19 patients. Analysis of protein-level alterations during disease progression revealed that proteins involved in complement activation, the coagulation cascade and cholesterol metabolism were restored at the convalescence stage, but the levels of some proteins, such as anti-angiogenesis protein PLGLB1, would not recovered. The higher serum level of PLGLB1 in COVID-19 patients than in control groups was further confirmed by parallel reaction monitoring (PRM). These findings expand our understanding of the pathogenesis and progression of COVID-19 and provide insight into the discovery of potential therapeutic targets and serum biomarkers worth further validation.
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Affiliation(s)
- Songfeng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yuan Xu
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Chongqing Medical University, Chongqing, China
| | - Jian Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaoju Ran
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xue Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jing Wang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing, China
| | - Longqin Sun
- Beijing Qinglian Biotech Co., Ltd, Beijing, China
| | - Huan Yang
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Yulei Li
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bin Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Changwu Huang
- Department of Clinical Laboratory, Chongqing Fifth People’s Hospital, Chongqing, China
- *Correspondence: Wei Sun, ; Pu Liao, ; Changwu Huang,
| | - Pu Liao
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
- *Correspondence: Wei Sun, ; Pu Liao, ; Changwu Huang,
| | - Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- *Correspondence: Wei Sun, ; Pu Liao, ; Changwu Huang,
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De Sadeleer LJ, Verleden SE, Schupp JC, McDonough JE, Goos T, Yserbyt J, Bargagli E, Rottoli P, Kaminski N, Prasse A, Wuyts WA. BAL Transcriptomes Characterize Idiopathic Pulmonary Fibrosis Endotypes With Prognostic Impact. Chest 2022; 161:1576-1588. [PMID: 35063449 PMCID: PMC9424328 DOI: 10.1016/j.chest.2021.12.668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Given the plethora of pathophysiologic mechanisms described in idiopathic pulmonary fibrosis (IPF), we hypothesize that the mechanisms driving fibrosis in IPF may be different from one patient to another. RESEARCH QUESTION Do IPF endotypes exist and are they associated with outcome? STUDY DESIGN AND METHODS Using a publicly available gene expression dataset retrieved from BAL samples of patients with IPF and control participants (GSE70867), we clustered IPF samples based on a dimension reduction algorithm specifically designed for -omics data, called DDR Tree. After clustering, gene set enrichment analysis was performed for functional annotation, associations with clinical variables and prognosis were investigated, and differences in transcriptional regulation were determined using motif enrichment analysis. The findings were validated in three independent publicly available gene expression datasets retrieved from IPF blood samples. RESULTS One hundred seventy-six IPF samples from three centers were clustered in six IPF clusters, with distinct functional enrichment. Although clinical characteristics did not differ between the clusters, one cluster conferred worse sex-age-physiology score-corrected survival, whereas another showed a numeric trend toward worse survival (P = .08). The first was enriched for increased epithelial and innate and adaptive immunity signatures, whereas the other showed important telomere and mitochondrial dysfunction, loss of proteostasis, and increased myofibroblast signatures. The existence of these two endotypes, including the impact on survival of the immune endotype, was validated in three independent validation cohorts. Finally, we identified transcription factors regulating the expression of endotype-specific survival-associated genes. INTERPRETATION Gene expression-based endotyping in IPF is feasible and can inform clinical evolution. As endotype-specific pathways and survival-associated transcription factors are identified, endotyping may open up the possibility of endotype-tailored therapy.
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Affiliation(s)
- Laurens J De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.
| | - Stijn E Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Antwerp Surgical Training, Anatomy and Research Centre, Antwerp University, Antwerp, Belgium
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT; Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - John E McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Jonas Yserbyt
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium
| | - Elena Bargagli
- Respiratory Diseases and Lung Transplantation Unit, AOUS and Siena University, Siena, Italy
| | - Paola Rottoli
- Specialization School in Respiratory Diseases, Siena University, Siena, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT
| | - Antje Prasse
- Department of Pulmonology, Hannover Medical School, Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany; German Centre for Lung Research, BREATH, Hannover, Germany; Department of Pneumology, University Medical Centre, Freiburg, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
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Peisker F, Halder M, Nagai J, Ziegler S, Kaesler N, Hoeft K, Li R, Bindels EMJ, Kuppe C, Moellmann J, Lehrke M, Stoppe C, Schaub MT, Schneider RK, Costa I, Kramann R. Mapping the cardiac vascular niche in heart failure. Nat Commun 2022; 13:3027. [PMID: 35641541 DOI: 10.1038/s41467-022-30682-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2022] [Indexed: 02/08/2023] Open
Abstract
The cardiac vascular and perivascular niche are of major importance in homeostasis and during disease, but we lack a complete understanding of its cellular heterogeneity and alteration in response to injury as a major driver of heart failure. Using combined genetic fate tracing with confocal imaging and single-cell RNA sequencing of this niche in homeostasis and during heart failure, we unravel cell type specific transcriptomic changes in fibroblast, endothelial, pericyte and vascular smooth muscle cell subtypes. We characterize a specific fibroblast subpopulation that exists during homeostasis, acquires Thbs4 expression and expands after injury driving cardiac fibrosis, and identify the transcription factor TEAD1 as a regulator of fibroblast activation. Endothelial cells display a proliferative response after injury, which is not sustained in later remodeling, together with transcriptional changes related to hypoxia, angiogenesis, and migration. Collectively, our data provides an extensive resource of transcriptomic changes in the vascular niche in hypertrophic cardiac remodeling. The cardiac vascular niche is of major importance in homeostasis and disease, but knowledge of its complexity in response to injury remains limited. Here we combine lineage tracing with single cell RNA sequencing to show alterations in fibroblasts, endothelial and mural cells in hypertrophic remodeling.
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Ghandikota S, Sharma M, Ediga HH, Madala SK, Jegga AG. Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. Int J Mol Sci 2022; 23. [PMID: 35628257 DOI: 10.3390/ijms23105447] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic data from independent IPF cohorts using weighted gene co-expression network analysis (WGCNA) to identify gene modules based on their preservation status in these cohorts. The consensus gene modules were characterized by leveraging existing clinical and molecular data such as lung function, biological processes, pathways, and lung cell types. From a total of 32 consensus gene modules identified, two modules were found to be significantly correlated with the disease, lung function, and preserved in other IPF datasets. The upregulated gene module was enriched for extracellular matrix, collagen metabolic process, and BMP signaling while the downregulated module consisted of genes associated with tube morphogenesis, blood vessel development, and cell migration. Using a combination of connectivity-based and trait-based significance measures, we identified and prioritized 103 "hub" genes (including 25 secretory candidate biomarkers) by their similarity to known IPF genetic markers. Our validation studies demonstrate the dysregulated expression of CRABP2, a retinol-binding protein, in multiple lung cells of IPF, and its correlation with the decline in lung function.
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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Burgy O, Loriod S, Beltramo G, Bonniaud P. Extracellular Lipids in the Lung and Their Role in Pulmonary Fibrosis. Cells 2022; 11:1209. [PMID: 35406772 PMCID: PMC8997955 DOI: 10.3390/cells11071209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Lipids are major actors and regulators of physiological processes within the lung. Initial research has described their critical role in tissue homeostasis and in orchestrating cellular communication to allow respiration. Over the past decades, a growing body of research has also emphasized how lipids and their metabolism may be altered, contributing to the development and progression of chronic lung diseases such as pulmonary fibrosis. In this review, we first describe the current working model of the mechanisms of lung fibrogenesis before introducing lipids and their cellular metabolism. We then summarize the evidence of altered lipid homeostasis during pulmonary fibrosis, focusing on their extracellular forms. Finally, we highlight how lipid targeting may open avenues to develop therapeutic options for patients with lung fibrosis.
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Chakraborty A, Mastalerz M, Ansari M, Schiller HB, Staab-Weijnitz CA. Emerging Roles of Airway Epithelial Cells in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:cells11061050. [PMID: 35326501 PMCID: PMC8947093 DOI: 10.3390/cells11061050] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with incompletely understood aetiology and limited treatment options. Traditionally, IPF was believed to be mainly caused by repetitive injuries to the alveolar epithelium. Several recent lines of evidence, however, suggest that IPF equally involves an aberrant airway epithelial response, which contributes significantly to disease development and progression. In this review, based on recent clinical, high-resolution imaging, genetic, and single-cell RNA sequencing data, we summarize alterations in airway structure, function, and cell type composition in IPF. We furthermore give a comprehensive overview on the genetic and mechanistic evidence pointing towards an essential role of airway epithelial cells in IPF pathogenesis and describe potentially implicated aberrant epithelial signalling pathways and regulation mechanisms in this context. The collected evidence argues for the investigation of possible therapeutic avenues targeting these processes, which thus represent important future directions of research.
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Zhou HY, Sui H, Zhao YJ, Qian HJ, Yang N, Liu L, Guan Q, Zhou Y, Lin HL, Wang DP. The Impact of Inflammatory Immune Reactions of the Vascular Niche on Organ Fibrosis. Front Pharmacol 2021; 12:750509. [PMID: 34776968 PMCID: PMC8585779 DOI: 10.3389/fphar.2021.750509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
Inflammation is a type of defense response against tissue damage, and can be mediated by lymphocytes and macrophages. Fibrosis is induced by tissue injury and inflammation, which leads to an increase in fibrous connective tissue in organs and a decrease in organ parenchyma cells, finally leading to organ dysfunction or even failure. The vascular niche is composed of endothelial cells, pericytes, macrophages, and hematopoietic stem cells. It forms a guiding microenvironment for the behavior of adjacent cells, and mainly exists in the microcirculation, including capillaries. When an organ is damaged, the vascular niche regulates inflammation and affects the repair of organ damage in a variety of ways, such as via its angiocrine function and transformation of myofibroblasts. In this paper, the main roles of vascular niche in the process of organ fibrosis and its mechanism of promoting the progress of fibrosis through inflammatory immunoregulation are summarized. It was proposed that the vascular niche should be regarded as a new therapeutic target for organ fibrosis, suggesting that antifibrotic effects could be achieved by regulating macrophages, inhibiting endothelial-mesenchymal transition, interfering with the angiocrine function of endothelial cells, and inhibiting the transformation of pericytes into myofibroblasts, thus providing new ideas for antifibrosis drug research.
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Affiliation(s)
- Hong-Yan Zhou
- The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Hua Sui
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Yang-Jianing Zhao
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Hong-Jie Qian
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Nan Yang
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Lu Liu
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Qing Guan
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Yue Zhou
- Department of Nephrology, The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Hong-Li Lin
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China.,Department of Nephrology, The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Da-Peng Wang
- Institude college of Integrative Medicine, Dalian Medical University, Dalian, China.,Department of Nephrology, The First Affiliated Hospital, Dalian Medical University, Dalian, China
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Fanidis D, Moulos P, Aidinis V. Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. Sci Rep 2021; 11:21712. [PMID: 34741074 PMCID: PMC8571330 DOI: 10.1038/s41598-021-01069-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/21/2021] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application (http://www.fibromine.com/Fibromine) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.
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Affiliation(s)
- Dionysios Fanidis
- Institute for Bioinnovation, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece.
| | - Vassilis Aidinis
- Institute for Bioinnovation, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece.
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Renzoni EA, Poletti V, Mackintosh JA. Disease pathology in fibrotic interstitial lung disease: is it all about usual interstitial pneumonia? Lancet 2021; 398:1437-1449. [PMID: 34499865 DOI: 10.1016/s0140-6736(21)01961-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022]
Abstract
The interstitial pneumonias comprise a diverse group of diseases that are typically defined by their cause (either idiopathic or non-idiopathic) and their distinct histopathological features, for which radiology, in the form of high-resolution CT, is often used as a surrogate. One trend, fuelled by the failure of conventional therapies in a subset of patients and the broad-spectrum use of antifibrotic therapies, has been the focus on the progressive fibrosing phenotype of interstitial lung disease. The histological pattern, known as usual interstitial pneumonia, is the archetype of progressive fibrosis. However, it is clear that progressive fibrosis is not exclusive to this histological entity. Techniques including immunohistochemistry and single-cell RNA sequencing are providing pathogenetic insights and, if integrated with traditional histopathology, are likely to have an effect on the pathological classification of interstitial lung disease. This review, which focuses on the histopathology of interstitial lung disease and its relationship with progressive fibrosis, asks the question: is it all about usual interstitial pneumonia?
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Affiliation(s)
- Elisabetta A Renzoni
- Interstitial Lung Disease Unit, Royal Brompton and Harefield Clinical Group, Guy's and St Thomas' NHS Foundation Trust, London, UK; Margaret Turner Warwick Centre for Fibrosing Lung Diseases, National Heart and Lung Institute, Imperial College London, London, UK
| | - Venerino Poletti
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark; Thoracic Diseases Department, GB Morgagni Hospital/University of Bologna, Forlì, Italy
| | - John A Mackintosh
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia.
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