1
|
Muir A, Paudyal B, Schmidt S, Sedaghat-Rostami E, Chakravarti S, Villanueva-Hernández S, Moffat K, Polo N, Angelopoulos N, Schmidt A, Tenbusch M, Freimanis G, Gerner W, Richard AC, Tchilian E. Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunization in the pig lung. PLoS Pathog 2024; 20:e1011910. [PMID: 39024231 PMCID: PMC11257366 DOI: 10.1371/journal.ppat.1011910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
The pig is a natural host for influenza viruses and integrally involved in virus evolution through interspecies transmissions between humans and swine. Swine have many physiological, anatomical, and immunological similarities to humans, and are an excellent model for human influenza. Here, we employed single cell RNA-sequencing (scRNA-seq) and flow cytometry to characterize the major leukocyte subsets in bronchoalveolar lavage (BAL), twenty-one days after H1N1pdm09 infection or respiratory immunization with an adenoviral vector vaccine expressing hemagglutinin and nucleoprotein with or without IL-1β. Mapping scRNA-seq clusters from BAL onto those previously described in peripheral blood facilitated annotation and highlighted differences between tissue resident and circulating immune cells. ScRNA-seq data and functional assays revealed lasting impacts of immune challenge on BAL populations. First, mucosal administration of IL-1β reduced the number of functionally active Treg cells. Second, influenza infection upregulated IFI6 in BAL cells and decreased their susceptibility to virus replication in vitro. Our data provide a reference map of porcine BAL cells and reveal lasting immunological consequences of influenza infection and respiratory immunization in a highly relevant large animal model for respiratory virus infection.
Collapse
Affiliation(s)
- Andrew Muir
- Immunology Programme, The Babraham Institute, Cambridge, United Kingdom
| | | | | | | | | | | | - Katy Moffat
- The Pirbright Institute, Pirbright, United Kingdom
| | - Noemi Polo
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Anna Schmidt
- Virologisches Institut-Klinische und Molekulare Virologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- FAU Profilzentrum Immunmedizin (FAU I-MED), Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Tenbusch
- Virologisches Institut-Klinische und Molekulare Virologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- FAU Profilzentrum Immunmedizin (FAU I-MED), Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | | | | | | | | |
Collapse
|
2
|
Hoang MH, Skidmore ZL, Rindt H, Chu S, Fisk B, Foltz JA, Fronick C, Fulton R, Zhou M, Bivens NJ, Reinero CN, Fehniger TA, Griffith M, Bryan JN, Griffith OL. Single-cell T-cell receptor repertoire profiling in dogs. Commun Biol 2024; 7:484. [PMID: 38649520 PMCID: PMC11035579 DOI: 10.1038/s42003-024-06174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Spontaneous cancers in companion dogs are robust models of human disease. Tracking tumor-specific immune responses in these models requires reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). scTCRseq and integration with scRNA data have not been demonstrated on companion dogs with cancer. Here, five healthy dogs, two dogs with T cell lymphoma and four dogs with melanoma are selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. Single-cell suspensions of PBMCs or lymph node aspirates are profiled using scRNA and dog-specific scTCRseq primers. In total, 77,809 V(D)J-expressing cells are detected, with an average of 3498 (348 - 5,971) unique clonotypes identified per sample. In total, 29/34, 40/40, 22/22 and 9/9 known functional TRAV, TRAJ, TRBV and TRBJ gene segments are observed respectively. Pseudogene or otherwise defective gene segments are also detected supporting re-annotation of several as functional. Healthy dogs exhibit highly diverse repertoires, T cell lymphomas exhibit clonal repertoires, and vaccine-treated melanoma dogs are dominated by a small number of highly abundant clonotypes. scRNA libraries define large clusters of V(D)J-expressing CD8+ and CD4 + T cells. Dominant clonotypes observed in melanoma PBMCs are predominantly CD8 + T cells, with activated phenotypes, suggesting possible anti-tumor T cell populations.
Collapse
Affiliation(s)
- My H Hoang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Hans Rindt
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Shirley Chu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Bryan Fisk
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Jennifer A Foltz
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Mingyi Zhou
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Carol N Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Todd A Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
3
|
London CA, Gardner H, Zhao S, Knapp DW, Utturkar SM, Duval DL, Chambers MR, Ostrander E, Trent JM, Kuffel G. Leading the pack: Best practices in comparative canine cancer genomics to inform human oncology. Vet Comp Oncol 2023; 21:565-577. [PMID: 37778398 DOI: 10.1111/vco.12935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Pet dogs develop spontaneous cancers at a rate estimated to be five times higher than that of humans, providing a unique opportunity to study disease biology and evaluate novel therapeutic strategies in a model system that possesses an intact immune system and mirrors key aspects of human cancer biology. Despite decades of interest, effective utilization of pet dog cancers has been hindered by a limited repertoire of necessary cellular and molecular reagents for both in vitro and in vivo studies, as well as a dearth of information regarding the genomic landscape of these cancers. Recently, many of these critical gaps have been addressed through the generation of a highly annotated canine reference genome, the creation of several tools necessary for multi-omic analysis of canine tumours, and the development of a centralized repository for key genomic and associated clinical information from canine cancer patients, the Integrated Canine Data Commons. Together, these advances have catalysed multidisciplinary efforts designed to integrate the study of pet dog cancers more effectively into the translational continuum, with the ultimate goal of improving human outcomes. The current review summarizes this recent progress and provides a guide to resources and tools available for comparative study of pet dog cancers.
Collapse
Affiliation(s)
- Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Heather Gardner
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Shaying Zhao
- University of Georgia Cancer Center, University of Georgia, Athens, Georgia, USA
| | - Deborah W Knapp
- College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Sagar M Utturkar
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Dawn L Duval
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | | | - Elaine Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Gina Kuffel
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
4
|
Miguelena Chamorro B, Hameed SA, Dechelette M, Claude JB, Piney L, Chapat L, Swaminathan G, Poulet H, Longet S, De Luca K, Mundt E, Paul S. Characterization of Canine Peyer's Patches by Multidimensional Analysis: Insights from Immunofluorescence, Flow Cytometry, and Single-Cell RNA Sequencing. Immunohorizons 2023; 7:788-805. [PMID: 38015460 PMCID: PMC10696420 DOI: 10.4049/immunohorizons.2300091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
The oral route is effective and convenient for vaccine administration to stimulate a protective immune response. GALT plays a crucial role in mucosal immune responses, with Peyer's patches (PPs) serving as the primary site of induction. A comprehensive understanding of the structures and functions of these structures is crucial for enhancing vaccination strategies and comprehending disease mechanisms; nonetheless, our current knowledge of these structures in dogs remains incomplete. We performed immunofluorescence and flow cytometry studies on canine PPs to identify cell populations and structures. We also performed single-cell RNA sequencing (scRNA-seq) to investigate the immune cell subpopulations present in PPs at steady state in dogs. We generated and validated an Ab specifically targeting canine M cells, which will be a valuable tool for elucidating Ag trafficking into the GALT of dogs. Our findings will pave the way for future studies of canine mucosal immune responses to oral vaccination and enteropathies. Moreover, they add to the growing body of knowledge in canine immunology, further expanding our understanding of the complex immune system of dogs.
Collapse
Affiliation(s)
- Beatriz Miguelena Chamorro
- Centre International de Recherche en Infectiologie, Team GIMAP (Saint-Etienne), Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, UJM, F69007 Lyon, France
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | | | | | | | - Lauriane Piney
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | - Ludivine Chapat
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | | | - Hervé Poulet
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | - Stéphanie Longet
- Centre International de Recherche en Infectiologie, Team GIMAP (Saint-Etienne), Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, UJM, F69007 Lyon, France
| | - Karelle De Luca
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | - Egbert Mundt
- Global Innovation, Boehringer Ingelheim, Saint-Priest, France
| | - Stéphane Paul
- Centre International de Recherche en Infectiologie, Team GIMAP (Saint-Etienne), Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, UJM, F69007 Lyon, France
- International Center for Infectiology Research, INSERM 1408 Vaccinology, Saint-Etienne, France
| |
Collapse
|
5
|
Zhou Q, Huang L, Liu Y, Huang J, Wen L, Yang J, Liang J, Chen Y, Chen C. Single-cell RNA sequencing depicts metabolic changes in children with aplastic anemia. Front Oncol 2023; 13:1075408. [PMID: 37064094 PMCID: PMC10090469 DOI: 10.3389/fonc.2023.1075408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
IntroductionAplastic anemia (AA) is a bone marrow hematopoietic failure syndrome mediated by immune cells. The mechanism of this immune disorder is not well understood and therapeutic strategies still need to be improved.MethodsStudies have found that abnormalities in metabolisms promote the survival of AA cells. In recent years, an increasing number of studies have reported the immunosuppressive therapy for the treatment of AA. In this study, we analyzed the transcriptome of AA from peripheral blood compared with healthy donors by single-cell sequencing and identified the affected metabolic pathways including lysine degradation. We demonstrated that the metabolic abnormalities of T lymphocytes mainly focus on glycolysis/gluconeogenesis. In addition, the metabolic abnormalities of natural killer cells concentrated in oxidative phosphorylation.ResultsThe key genes involved in abnormal metabolic processes were Neustein neurotrophic factor (NENF), inositol polyphosphate-4-phosphatase type II B (INPP4B), aldo-keto reductase family 1, member C3 (AKR1C3), and carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 (CHST2) by differential gene expression analysis.DiscussionMolecule interaction analysis showed that tumor necrosis factor superfamily, member 12 (TNFSM12) in tumor necrosis factor (TNF) signaling was broadly activated in AA. In conclusion, we suppose that the treatment of the immune cells’ abnormal metabolic pathway may contribute to the development of novel strategies to treat AA.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jintang Liang
- *Correspondence: Chun Chen, ; Yun Chen, ; Jintang Liang,
| | - Yun Chen
- *Correspondence: Chun Chen, ; Yun Chen, ; Jintang Liang,
| | - Chun Chen
- *Correspondence: Chun Chen, ; Yun Chen, ; Jintang Liang,
| |
Collapse
|
6
|
Kouki S, Viitanen SJ, Koho N, Laurila HP, Lilja‐Maula L, Holopainen S, Neuvonen M, Niemi M, Fastrès A, Clercx C, Rajamäki MM. Extraesophageal reflux and reflux aspiration in dogs with respiratory diseases and in healthy dogs. Vet Med (Auckl) 2023; 37:268-276. [PMID: 36655626 PMCID: PMC9889628 DOI: 10.1111/jvim.16622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/15/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Salivary bile acids are used to diagnose extraesophageal reflux (EER) and to evaluate the risk of reflux aspiration that is associated with respiratory diseases in dogs. OBJECTIVES To study total bile acid (TBA) concentrations in saliva and in bronchoalveolar lavage fluid (BALF) to investigate EER and reflux aspiration in dogs with respiratory diseases and in healthy dogs. ANIMALS Thirty-one West Highland White Terriers (WHWTs) with idiopathic pulmonary fibrosis (IPF), 12 dogs with inflammatory airway disease (IAD), 6 dogs with recurrent pneumonia (RP), 26 brachycephalic dogs (BD), 27 healthy WHWTs (HW), 52 healthy dogs (HD). All privately-owned dogs. METHODS Saliva and BALF were collected from dogs in each group. RESULTS Salivary TBA concentrations were higher in IPF (median 0.1692 μM, interquartile range [IQR] 0.1115-0.2925 μM, Cohen's d 3.4, 95% confidence interval [CI] 2.2-4.0, P < .001) and BD (0.0256 μM, IQR 0.0086-0.0417 μM, d 0.5, CI -0.1 to 1.1, P = .003) compared to HD (0 μM, IQR not quantifiable [n.q.]-0.0131 μM). Bronchoalveolar lavage fluid TBA concentrations were higher in IPF (0.0117 μM, IQR 0.0048-0.0361 μM, d 0.5, CI 0-1.1, P < .001) compared to HD (0 μM, IQR n.q.-0.0074 μM). CONCLUSION AND CLINICAL IMPORTANCE Extraesophageal reflux and reflux aspiration occur in healthy dogs and those with respiratory diseases.
Collapse
Affiliation(s)
- Sirkku Kouki
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Sanna J. Viitanen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Ninna Koho
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Henna P. Laurila
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Liisa Lilja‐Maula
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Saila Holopainen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Mikko Neuvonen
- Department of Clinical Pharmacology, Faculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Mikko Niemi
- Department of Clinical Pharmacology, Faculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Aline Fastrès
- Department of Clinical Sciences, Faculty of Veterinary MedicineUniversity of LiègeLiègeBelgium
| | - Cécile Clercx
- Department of Clinical Sciences, Faculty of Veterinary MedicineUniversity of LiègeLiègeBelgium
| | - Minna M. Rajamäki
- Department of Equine and Small Animal Medicine, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| |
Collapse
|
7
|
Eschke M, Moore PF, Chang H, Alber G, Keller SM. Canine peripheral blood TCRαβ T cell atlas: Identification of diverse subsets including CD8A + MAIT-like cells by combined single-cell transcriptome and V(D)J repertoire analysis. Front Immunol 2023; 14:1123366. [PMID: 36911660 PMCID: PMC9995359 DOI: 10.3389/fimmu.2023.1123366] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023] Open
Abstract
The dog is valued as a companion animal and increasingly recognized as a model for human disorders. Given the importance of T cells in health and disease, comprehensive knowledge of canine T cells can contribute to our understanding of pathogenesis mechanisms and inform the development of new treatment strategies. However, the diversity of canine T cells is still poorly understood mainly due to the lack of species-reactive antibodies for use in flow cytometry. The aim of this study was to generate a detailed atlas of peripheral blood TCRαβ+ T cells of healthy dogs using single-cell RNA-sequencing (scRNAseq) combined with immune repertoire sequencing. A total of 22 TCRαβ+ T cell clusters were identified, which were classified into three major groups: CD4-dominant (11 clusters), CD8A-dominant (8 clusters), and CD4/CD8A-mixed (3 clusters). Based on differential gene expression, distinct differentiation states (naïve, effector, memory, exhausted) and lineages (e.g. CD4 T helper and regulatory T cells) could be distinguished. Importantly, several T cell populations were identified, which have not been described in dogs before. Of particular note, our data provide first evidence for the existence of canine mucosa-associated invariant T cell (MAIT)-like cells, representing one of three newly identified FCER1G+ innate-like CD8A+ T cell populations in the peripheral blood of healthy dogs. In conclusion, using scRNAseq combined with immune repertoire sequencing we were able to resolve canine TCRαβ+ T cell populations at unprecedented resolution. The peripheral blood TCRαβ+ T cell atlas of healthy dogs generated here represents an important reference data set for future studies and is of relevance for identifying new targets for T cell-specific therapies.
Collapse
Affiliation(s)
- Maria Eschke
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
| | - Gottfried Alber
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| |
Collapse
|
8
|
Sage SE, Nicholson P, Peters LM, Leeb T, Jagannathan V, Gerber V. Single-cell gene expression analysis of cryopreserved equine bronchoalveolar cells. Front Immunol 2022; 13:929922. [PMID: 36105804 PMCID: PMC9467276 DOI: 10.3389/fimmu.2022.929922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/08/2022] [Indexed: 12/21/2022] Open
Abstract
The transcriptomic profile of a cell population can now be studied at the cellular level using single-cell mRNA sequencing (scRNA-seq). This novel technique provides the unprecedented opportunity to explore the cellular composition of the bronchoalveolar lavage fluid (BALF) of the horse, a species for which cell type markers are poorly described. Here, scRNA-seq technology was applied to cryopreserved equine BALF cells. Analysis of 4,631 cells isolated from three asthmatic horses in remission identified 16 cell clusters belonging to six major cell types: monocytes/macrophages, T cells, B/plasma cells, dendritic cells, neutrophils and mast cells. Higher resolution analysis of the constituents of the major immune cell populations allowed deep annotation of monocytes/macrophages, T cells and B/plasma cells. A significantly higher lymphocyte/macrophage ratio was detected with scRNA-seq compared to conventional cytological differential cell count. For the first time in horses, we detected a transcriptomic signature consistent with monocyte-lymphocyte complexes. Our findings indicate that scRNA-seq technology is applicable to cryopreserved equine BALF cells, allowing the identification of its major (cytologically differentiated) populations as well as previously unexplored T cell and macrophage subpopulations. Single-cell gene expression analysis has the potential to facilitate understanding of the immunological mechanisms at play in respiratory disorders of the horse, such as equine asthma.
Collapse
Affiliation(s)
- Sophie E. Sage
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- *Correspondence: Sophie E. Sage,
| | - Pamela Nicholson
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
| | - Laureen M. Peters
- Clinical Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| |
Collapse
|
9
|
Fastrès A, Pirottin D, Fievez L, Tutunaru AC, Bolen G, Merveille AC, Marichal T, Desmet CJ, Bureau F, Clercx C. Identification of Pro-Fibrotic Macrophage Populations by Single-Cell Transcriptomic Analysis in West Highland White Terriers Affected With Canine Idiopathic Pulmonary Fibrosis. Front Immunol 2020; 11:611749. [PMID: 33384697 PMCID: PMC7770158 DOI: 10.3389/fimmu.2020.611749] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Canine idiopathic pulmonary fibrosis (CIPF) affects old dogs from the West Highland white terrier (WHWT) breed and mimics idiopathic pulmonary fibrosis (IPF) in human. The disease results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure. Recent studies in IPF using single-cell RNA sequencing (scRNA-seq) revealed the presence of profibrotic macrophage populations in the lung, which could be targeted for therapeutic purpose. In dogs, scRNA-seq was recently validated for the detection of cell populations in bronchoalveolar lavage fluid (BALF) from healthy dogs. Here we used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes (Ma/Mo) in the BALF from five WHWTs affected with CIPF in comparison with three healthy WHWTs. Gene set enrichment analysis was also used to assess pro-fibrotic capacities of Ma/Mo populations. Five clusters of Ma/Mo were identified. Gene set enrichment analyses revealed the presence of pro-fibrotic monocytes in higher proportion in CIPF WHWTs than in healthy WHWTs. In addition, monocyte-derived macrophages enriched in pro-fibrotic genes in CIPF compared with healthy WHWTs were also identified. These results suggest the implication of Ma/Mo clusters in CIPF processes, although, further research is needed to understand their role in disease pathogenesis. Overexpressed molecules associated with pulmonary fibrosis processes were also identified that could be used as biomarkers and/or therapeutic targets in the future.
Collapse
Affiliation(s)
- Aline Fastrès
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - Dimitri Pirottin
- Laboratory of Cellular and Molecular Immunology, Department Functional Sciences and GIGA-Inflammation, Infection & Immunity, University of Liège, Liège, Belgium
| | - Laurence Fievez
- Laboratory of Cellular and Molecular Immunology, Department Functional Sciences and GIGA-Inflammation, Infection & Immunity, University of Liège, Liège, Belgium
| | - Alexandru-Cosmin Tutunaru
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - Géraldine Bolen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - Anne-Christine Merveille
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - Thomas Marichal
- Laboratory of Cellular and Molecular Immunology, Department Functional Sciences and GIGA-Inflammation, Infection & Immunity, University of Liège, Liège, Belgium
| | - Christophe J Desmet
- Laboratory of Cellular and Molecular Immunology, Department Functional Sciences and GIGA-Inflammation, Infection & Immunity, University of Liège, Liège, Belgium
| | - Fabrice Bureau
- Laboratory of Cellular and Molecular Immunology, Department Functional Sciences and GIGA-Inflammation, Infection & Immunity, University of Liège, Liège, Belgium
| | - Cécile Clercx
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health (FARAH), University of Liège, Liège, Belgium
| |
Collapse
|