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Razmara AM, Lammers M, Judge SJ, Murphy WJ, Gaskill CE, Culp WT, Gingrich AA, Morris ZS, Rebhun RB, Brown CT, Vail DM, Kent MS, Canter RJ. Single cell atlas of canine natural killer cells identifies distinct circulating and tissue resident gene profiles. Front Immunol 2025; 16:1571085. [PMID: 40443661 PMCID: PMC12119461 DOI: 10.3389/fimmu.2025.1571085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 04/22/2025] [Indexed: 06/02/2025] Open
Abstract
Introduction Natural killer (NK) cells in mice and humans are key effectors of the innate immune system with complex immunoregulatory functions, and diverse subsets have been identified with distinct characteristics and roles. Companion dogs with spontaneous cancer have been validated as models of human disease, including cancer immunology and immunotherapy, and greater understanding of NK cell heterogeneity in dogs can inform NK biology across species and optimize NK immunotherapy for both dogs and people. Methods Here, we assessed canine NK cell populations by single-cell RNA sequencing (scRNAseq) across blood, lung, liver, spleen, and placenta with comparison to human NK cells from blood and the same tissues to better characterize the differential gene expression of canine and human NK cells regarding ontogeny, heterogeneity, patterns of activation, inhibition, and tissue residence. Results Overall, we observed tissue-specific NK cell signatures consistent with immature NK cells in the placenta, mature and activated NK cells in the lung, and NK cells with a mixed activated and inhibited signature in the liver with significant cross-species homology. Discussion Together, our results point to heterogeneous canine NK populations highly comparable to human NK cells, and we provide a comprehensive atlas of canine NK cells across organs which will inform future cross-species NK studies and further substantiate the spontaneous canine model to optimize NK immunotherapy across species.
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Affiliation(s)
- Aryana M. Razmara
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Marshall Lammers
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Sean J. Judge
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
| | - William J. Murphy
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Cameron E. Gaskill
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
| | - William T.N. Culp
- Department of Surgical and Radiological Sciences, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - Alicia A. Gingrich
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Zachary S. Morris
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Robert B. Rebhun
- Department of Surgical and Radiological Sciences, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - C. Titus Brown
- Department Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - David M. Vail
- Department of Medical Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, United States
| | - Michael S. Kent
- Department of Surgical and Radiological Sciences, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - Robert J. Canter
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, United States
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Zimmermann ABE, Taskoparan B, Fuchs D, Pantelyushin S, Maheswaran M, Schnyder M, Hartnack S, Rohrer Bley C, vom Berg J. Prior corticosteroid treatment alters cPBMC composition and IFNγ response to immunotherapy in canine cancer. Front Immunol 2025; 16:1544949. [PMID: 40342421 PMCID: PMC12058859 DOI: 10.3389/fimmu.2025.1544949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Accepted: 03/24/2025] [Indexed: 05/11/2025] Open
Abstract
Background Immunotherapy using immune checkpoint inhibitors (ICIs) represents a promising therapeutic approach for canine cancer patients. Similar to human cancer patients, the concurrent use of corticosteroids may attenuate the efficacy of immune checkpoint inhibitors in dogs. In this study, we evaluated the impact of corticosteroid therapy on canine peripheral blood mononuclear cell (cPBMC) composition and the in vitro response to Programmed Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) axis blockade and recombinant human Interleukin-12 (rhIL-12) stimulation. Methods cPBMC samples were collected from 24 healthy, 44 cancer-bearing untreated, and 33 cancer-bearing corticosteroid pre-treated dogs. Lymphocytes were polyclonally stimulated with Staphylococcal Enterotoxin B (SEB) and either atezolizumab, a cross-functional anti-PD-L1 ICI, or rhIL-12. We analyzed the absolute and relative changes in canine interferon-gamma (cIFNɣ) production. Stimulation with gilvetmab, a recently developed canine anti-PD-1 ICI, revealed comparable results to atezolizumab. Moreover, we assessed the influence of corticosteroid pre-treatment on cPBMC composition by flow cytometry. Results Corticosteroid treatment significantly affected the immune profile, primarily the monocytic compartment, and functional cIFNɣ response of cPBMCs. Nevertheless, responses to immunotherapy appeared to be highly individual. Conclusions Overall, we observed trends suggesting that prior corticosteroid therapy may compromise the efficacy of PD-1/PD-L1 axis blockade and IL-12 in dogs with cancer. While the dose and timing of corticosteroid administration in this study reflected clinical reality and would not justify withholding this emerging therapeutic option, corticosteroid pretreatment may be a confounder for PD-1/PD-L1 axis blockade or IL-12 therapy in canine oncology.
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Affiliation(s)
- Anna Barbara Emilia Zimmermann
- Clinic for Radiation Oncology and Medical Oncology, University Animal Hospital, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Laboratory Animal Science, Vetsuisse Faculty, University of Zurich, Schlieren, Switzerland
| | - Betül Taskoparan
- Institute of Laboratory Animal Science, Vetsuisse Faculty, University of Zurich, Schlieren, Switzerland
| | - Daniel Fuchs
- Clinic for Radiation Oncology and Medical Oncology, University Animal Hospital, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Stanislav Pantelyushin
- Institute of Laboratory Animal Science, Vetsuisse Faculty, University of Zurich, Schlieren, Switzerland
| | - Mathischan Maheswaran
- Institute of Laboratory Animal Science, Vetsuisse Faculty, University of Zurich, Schlieren, Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sonja Hartnack
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carla Rohrer Bley
- Clinic for Radiation Oncology and Medical Oncology, University Animal Hospital, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Johannes vom Berg
- Institute of Laboratory Animal Science, Vetsuisse Faculty, University of Zurich, Schlieren, Switzerland
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Sergi CM, Burnett M, Jantuan E, Hakoum M, Beug ST, Leng R, Shen F. Digging Through the Complexities of Immunological Approaches in Emerging Osteosarcoma Therapeutics: A Comprehensive Narrative Review with Updated Clinical Trials. Biomedicines 2025; 13:664. [PMID: 40149640 PMCID: PMC11940054 DOI: 10.3390/biomedicines13030664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 02/19/2025] [Accepted: 02/28/2025] [Indexed: 03/29/2025] Open
Abstract
Osteosarcoma (OS) is the predominant mesenchymal primary malignant bone tumor in oncology and pathology, impacting a wide age range from adolescents to older adults. It frequently advances to lung metastasis, ultimately resulting in the mortality of OS patients. The precise pathological pathways responsible for OS progression and dissemination are not fully understood due to its heterogeneity. The integration of surgery with neoadjuvant and postoperative chemotherapy has significantly increased the 5-year survival rate to more than 70% for patients with localized OS tumors. However, about 30% of patients experience local recurrence and/or metastasis. Hence, there is a requirement for innovative therapeutic approaches to address the limitations of traditional treatments. Immunotherapy has garnered increasing attention as a promising avenue for tumors resistant to standard therapies, including OS, despite the underlying mechanisms of disease progression and dissemination remaining not well elucidated. Immunotherapy may not have been suitable for use in patients with OS because of the tumor's immunosuppressive microenvironment and limited immunogenicity. Nevertheless, there are immune-based treatments now being developed for clinical use, such as bispecific antibodies, chimeric antigen receptor T cells, and immune checkpoint inhibitors. Also, additional immunotherapy techniques including cytokines, vaccines, and modified-Natural Killer (NK) cells/macrophages are in the early phases of research but will certainly be popular subjects in the nearest future. Our goal in writing this review was to spark new lines of inquiry into OS immunotherapy by summarizing the findings from both preclinical and current clinical studies examining different approaches.
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Affiliation(s)
- Consolato M. Sergi
- Division of Anatomic Pathology, Department of Laboratory Medicine, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H 8L1, Canada
- Department of Laboratory Medicine, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada (E.J.); (F.S.)
| | - Mervin Burnett
- Department of Laboratory Medicine, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada (E.J.); (F.S.)
| | - Eugeniu Jantuan
- Department of Laboratory Medicine, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada (E.J.); (F.S.)
| | - Mariam Hakoum
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (M.H.)
| | - Shawn T. Beug
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (M.H.)
| | - Roger Leng
- Department of Laboratory Medicine, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada (E.J.); (F.S.)
| | - Fan Shen
- Department of Laboratory Medicine, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada (E.J.); (F.S.)
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Rizzoli E, Fievez L, Fastrès A, Roels E, Marichal T, Clercx C. A single-cell RNA sequencing atlas of the healthy canine lung: a foundation for comparative studies. Front Immunol 2025; 16:1501603. [PMID: 40114924 PMCID: PMC11922831 DOI: 10.3389/fimmu.2025.1501603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 02/13/2025] [Indexed: 03/22/2025] Open
Abstract
Single cell RNA sequencing (scRNA-seq) can be used to resolve the cellular and molecular heterogeneity within a tissue by identifying cell populations with an unprecedented granularity along with their transcriptional signatures. Yet, the single cell gene expression profiles of cell populations in the healthy canine lung tissue remain unexplored and such analysis could reveal novel cell populations or markers lacking in dogs and facilitate comparisons with lung diseases. Using fresh healthy lung biopsies from four dogs, we conducted droplet-based scRNA-seq on 26,278 cells. We characterized 46 transcriptionally distinct cell subpopulations across all lung tissue compartments including 23 immune, 13 mesenchymal, five epithelial and five endothelial cell subpopulations. Of note, we captured rare cells such as unconventional T cells or Schwann cells. Differential gene expression profiles identified specific markers across all cell subpopulations. Fibroblasts clusters exhibited a marked transcriptional heterogeneity, some of which might exert immune regulatory functions. Finally, the integration of canine lung cells with an annotated human lung atlas highlighted many similarities in gene expression profiles between species. This study thus provides an extensive molecular cell atlas of the healthy canine lung, expanding our knowledge of lung cell diversity in dogs, and providing the molecular foundation for investigating lung cell identities and functions in canine lung diseases. Besides, the occurrence of spontaneous lung diseases in pet dogs, with phenotypes closely resembling those in humans, may provide a relevant model for advancing research into human lung diseases.
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Affiliation(s)
- Elodie Rizzoli
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Laurence Fievez
- Department of Functional Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, University of Liège, Liège, Belgium
| | - Aline Fastrès
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Elodie Roels
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Thomas Marichal
- Department of Functional Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Immunophysiology, GIGA Institute, University of Liège, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Cécile Clercx
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Ammons DT, Harris RA, Chow L, Dow S. Characterization of canine tumor-infiltrating leukocyte transcriptomic signatures reveals conserved expression patterns with human osteosarcoma. Cancer Immunol Immunother 2025; 74:105. [PMID: 39932553 PMCID: PMC11813853 DOI: 10.1007/s00262-025-03950-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 01/20/2025] [Indexed: 02/14/2025]
Abstract
Immune cells play key roles in host responses to malignant tumors. The selective pressure that immune cells elicit on tumors promotes immune escape, while tumor-associated modulation of immune cells creates an environment favorable to tumor growth and progression. In this study we used publicly available single-cell RNA sequencing (scRNA-seq) data from the translationally relevant canine osteosarcoma (OS) model to compare tumor-infiltrating immune cells to circulating leukocytes. Through computational analysis we investigated the differences in cell type proportions and how the OS TME impacted infiltrating immune cell transcriptomic profiles relative to circulating leukocytes. Differential abundance analysis revealed increased proportions of follicular helper T cells, regulatory T cells, and mature regulatory dendritic cells (mregDCs) in the OS TME. Differential gene expression analysis identified exhaustion markers (LAG3, HAVCR2, PDCD1) to be upregulated in CD4 and CD8 T cells within the OS TME. Comparisons of B cell gene expression profiles revealed an enrichment of protein processing and endoplasmic reticulum pathways, suggesting infiltrating B cells were activated following tumor infiltration. Gene expression changes within myeloid cells identified increased expression of immune suppressive molecules (CD274, OSM, MSR1) in the OS TME, indicating the TME skews myeloid cells toward an immunosuppressive phenotype. Comparisons to human literature and analysis of human scRNA-seq data revealed conserved transcriptomic responses to tumor infiltration, while also identifying species differences. Overall, the analysis presented here provides new insights into how the OS TME impacts the transcriptional programs of major immune cell populations in dogs and acts as a resource for comparative immuno-oncology research.
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Affiliation(s)
- Dylan T Ammons
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
| | - R Adam Harris
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lyndah Chow
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Steven Dow
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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McDonald E, Kehoe E, Deines D, McCarthy M, Wright B, Huse S. High-parameter immunophenotyping reveals distinct immune cell profiles in pruritic dogs and cats. Front Vet Sci 2025; 11:1498964. [PMID: 39911485 PMCID: PMC11795398 DOI: 10.3389/fvets.2024.1498964] [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: 09/19/2024] [Accepted: 12/10/2024] [Indexed: 02/07/2025] Open
Abstract
Introduction Immunophenotyping is a powerful tool for grading disease severity, aiding in diagnosis, predicting clinical response, and guiding the development of novel therapeutics. Methods This pilot study employs high parameter immunophenotyping panels (15 markers for dog, 12 for cat) and leverages unsupervised clustering to identify immune cell populations. Our analysis uses machine learning and statistical algorithms to perform unsupervised clustering, multiple visualizations, and statistical analysis of high parameter flow cytometry data. This method reduces user bias and precisely identifies cell populations, demonstrating its potential to detect variations and differentiate populations effectively. To enhance our understanding of cat and dog biology and test the unsupervised clustering approach on real-world samples, we performed in-depth profiling of immune cell populations in blood collected from client-owned and laboratory animals [dogs (n = 55) and cats (n = 68)]. These animals were categorized based on pruritic behavior or routine check-ups (non-pruritic controls). Results Unsupervised clustering revealed various immune cell populations, including T-cell subsets distinguished by CD62L expression and distinct monocyte subsets. Notably, there were significant differences in monocyte subsets between pruritic and non-pruritic animals. Pruritic dogs and cats showed significant shifts in CD62LHi T-cell subsets compared to non-pruritic controls, with opposite trends observed between pruritic cats and dogs. Discussion These findings underscore the importance of advancing veterinary immunophenotyping, expanding our knowledge about marker expression on circulating immune cells and driving progress in understanding veterinary-specific biology and uncovering new insights into various conditions and diseases.
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Affiliation(s)
- Erin McDonald
- Veterinary Medicine Research and Development (VMRD), Zoetis Inc, Fort Collins, CO, United States
| | - Eric Kehoe
- Veterinary Medicine Research and Development (VMRD), Zoetis Inc, Fort Collins, CO, United States
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Zhou T, Pu SY, Zhang SJ, Zhou QJ, Zeng M, Lu JS, Lu X, Wang YN, Wang GD. Dog10K: an integrated Dog10K database summarizing canine multi-omics. Nucleic Acids Res 2025; 53:D939-D947. [PMID: 39436034 PMCID: PMC11701641 DOI: 10.1093/nar/gkae928] [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: 08/13/2024] [Revised: 09/14/2024] [Accepted: 10/04/2024] [Indexed: 10/23/2024] Open
Abstract
The diversity observed in canine breed phenotypes, together with their risk for heritabily disorders of relevance to dogs and humans, makes the species an ideal subject for studies aimed at understanding the genetic basis of complex traits and human biomedical models. Dog10K is an ongoing international collaboration that aims to uncover the genetic basis of phenotypic diversity, disease, behavior, and domestication history of dogs. To best present and make the extensive data accessible and user friendly, we have established the Dog10K (http://dog10k.kiz.ac.cn/) database, a comprehensive-omics resource summarizing multiple types of data. This database integrates single nucleotide variants (SNVs) from 1987 canine genomes, de-novo mutations (DNMs) from 43 dog breeds with >40× sequence, RNA-seq data of 105057 single nuclei from hippocampus, 74067 single cells from leukocytes and 30 blood samples from published canid studies. We provide clear visualization, statistics, browse, searching, and downloading functions for all data. We have integrated three analysis tools, Selscan, LiftOver and AgeConversion, to aid researchers in custom exploration of the comprehensive-omics data. The Dog10K database will serve as a foundational platform for analyzing, presenting and utilizing canine multi-omics data.
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Affiliation(s)
- Tong Zhou
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shao-Yan Pu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Biodiversity Data Center of Kunming Institute of Zoology, Chinese Academy of sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Shao-Jie Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Qi-Jun Zhou
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Min Zeng
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Sheng Lu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Biodiversity Data Center of Kunming Institute of Zoology, Chinese Academy of sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Xuemei Lu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Biodiversity Data Center of Kunming Institute of Zoology, Chinese Academy of sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ya-Nan Wang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Biodiversity Data Center of Kunming Institute of Zoology, Chinese Academy of sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Dong Wang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Chokeshaiusaha K, Sananmuang T, Puthier D, Kedkovid R. Development of a deep learning-based 1D convolutional neural network model for cross-species natural killer T cell identification using peripheral blood mononuclear cell single-cell RNA sequencing data. Vet World 2024; 17:2846-2857. [PMID: 39897371 PMCID: PMC11784060 DOI: 10.14202/vetworld.2024.2846-2857] [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: 09/11/2024] [Accepted: 11/13/2024] [Indexed: 02/04/2025] Open
Abstract
Background and Aim Natural killer T (NKT) cells exhibit the traits of both T and NK cells. Although their roles have been well studied in humans and mice, limited knowledge is available regarding their roles in dogs and pigs, which serve as models for human immunology. Single-cell RNA sequencing (scRNA-Seq) can elucidate NKT cell functions. However, identifying cells in mixed populations, like peripheral blood mononuclear cells (PBMCs) is challenging using this technique. This study presented the application of one-dimensional convolutional neural network (1DCNN) for the identification of NKT cells within scRNA-seq data derived from PBMCs. Materials and Methods We used human scRNA-Seq data to train a 1DCNN model for cross-species identification of NKT cells in canine and porcine PBMC datasets. K-means clustering was used to isolate human NKT cells for training the 1DCNN model. The trained model predicted NKT cell subpopulations in PBMCs from all species. We performed Differential gene expression and Gene Ontology (GO) enrichment analyses to assess shared gene functions across species. Results We successfully trained the 1DCNN model on human scRNA-Seq data, achieving 99.3% accuracy, and successfully identified NKT cell candidates in human, canine, and porcine PBMC datasets using the model. Across species, these NKT cells shared 344 genes with significantly elevated expression (FDR ≤ 0.001). GO term enrichment analyses confirmed the association of these genes with the immunoactivity of NKT cells. Conclusion This study developed a 1DCNN model for cross-species NKT cell identification and identified conserved immune function genes. The approach has broad implications for identifying other cell types in comparative immunology, and future studies are needed to validate these findings.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology, Tawan-OK, Chon Buri, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology, Tawan-OK, Chon Buri, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Roongtham Kedkovid
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Eto S, Kato D, Saeki K, Iguchi T, Shiyu Q, Kamoto S, Yoshitake R, Shinada M, Ikeda N, Tsuboi M, Chambers J, Uchida K, Nishimura R, Nakagawa T. Comprehensive Analysis of the Tumour Immune Microenvironment in Canine Urothelial Carcinoma Reveals Immunosuppressive Mechanisms Induced by the COX-Prostanoid Cascade. Vet Comp Oncol 2024; 22:500-512. [PMID: 39179510 DOI: 10.1111/vco.12999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/04/2024] [Accepted: 07/13/2024] [Indexed: 08/26/2024]
Abstract
A comprehensive understanding of the tumour immune microenvironment (TIME) is essential for advancing precision medicine and identifying potential therapeutic targets. This study focused on canine urothelial carcinoma (cUC) recognised for its high sensitivity to cyclooxygenase (COX) inhibitors. Using immunohistochemical techniques, we quantified the infiltration of seven immune cell populations within cUC tumour tissue to identify clinicopathological features that characterise the TIME in cUC. Our results revealed several notable factors, including the significantly higher levels of CD3+ T cells and CD8+ T cells within tumour cell nests in cases treated with preoperative COX inhibitors compared to untreated cases. Based on the immunohistochemistry data, we further performed a comparative analysis using publicly available RNA-seq data from untreated cUC tissues (n = 29) and normal bladder tissues (n = 4) to explore the link between COX-prostanoid pathways and the immune response to tumours. We observed increased expression of COX-2, microsomal prostaglandin E2 synthase-1 (mPGES-1) and mPGES-2 in cUC tissues. However, only mPGES-2 showed a negative correlation with the cytotoxic T-cell (CTL)-related genes CD8A and granzyme B (GZMB). In addition, a broader analysis of solid tumours using The Cancer Genome Atlas (TCGA) database revealed similar patterns in several human tumours, suggesting a common mechanism in dogs and humans. Our results suggest that the COX-2/mPGES-2 pathway may act as a cross-species tumour-intrinsic factor that weakens anti-tumour immunity, and that COX inhibitors may convert TIME from a 'cold tumour' to a 'hot tumour' state by counteracting COX/mPGES-2-mediated immunosuppression.
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Affiliation(s)
- Shotaro Eto
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Daiki Kato
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kohei Saeki
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, Japan
| | - Takaaki Iguchi
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Qin Shiyu
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Satoshi Kamoto
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Yoshitake
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Shinada
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Namiko Ikeda
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaya Tsuboi
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - James Chambers
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuyuki Uchida
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Nishimura
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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10
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Song C, Tong T, Dai B, Zhu Y, Chen E, Zhang M, Zhang W. Osteoimmunology in bone malignancies: a symphony with evil. JOURNAL OF THE NATIONAL CANCER CENTER 2024; 4:354-368. [PMID: 39735445 PMCID: PMC11674455 DOI: 10.1016/j.jncc.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 12/31/2024] Open
Abstract
Bone marrow is pivotal for normal hematopoiesis and immune responses, yet it is often compromised by malignancies. The bone microenvironment (BME), composed of bone and immune cells, maintains skeletal integrity and blood production. The emergence of primary or metastatic tumors in the skeletal system results in severe complications and contributes significantly to cancer-related mortality. These tumors set off a series of interactions among cancer, bone, and immune cells, and disrupt the BME locally or distantly. However, the drivers, participants, and underlying molecules of these interactions are not fully understood. This review explores the crosstalk between bone metabolism and immune responses, synthesizing current knowledge on the intersection of cancer and osteoimmune biology. It outlines how bone marrow immune cells can either facilitate or hinder tumor progression by interacting with bone cells and pinpoints the molecules responsible for immunosuppression within bone tumors. Moreover, it discusses how primary tumors remotely alter the BME, leading to systemic immune suppression in cancer patients. This knowledge provides critical rationales for emerging immunotherapies in the treatment of bone-related tumors. Taken together, by summarizing the intricate relationship between tumor cells and the BME, this review aims to deepen the understanding of the diversity, complexity, and dynamics at play during bone tumor progression. Ultimately, it highlights the potential of targeting bone-tumor interactions to correct aberrant immune functions, thereby inhibiting tumor growth and metastasis.
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Affiliation(s)
- Churui Song
- Department of Breast Surgery and Oncology, Cancer Institute, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tie Tong
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Biqi Dai
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yue Zhu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Elina Chen
- College of Natural Sciences, University of Texas at Austin, 110 Inner Campus Drive, Austin, USA
| | - Min Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weijie Zhang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, and Department of Orthopaedic Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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11
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Ramarapu R, Wulcan JM, Chang H, Moore PF, Vernau W, Keller SM. Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes. Front Immunol 2024; 15:1438004. [PMID: 39620216 PMCID: PMC11604454 DOI: 10.3389/fimmu.2024.1438004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/23/2024] [Indexed: 12/11/2024] Open
Abstract
Introduction The domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. Methods Peripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, αβ T cell receptor transcripts and γδ T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Results Unsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and γδ T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis identified a subset of CD8+ cytotoxic T cells with skewed TRA and TRB gene usage, conserved TRA and TRB junctional motifs, restricted TRA/TRB pairing and reduced diversity in TRG junctional length. We also identified a public γδ T cell subset with invariant TRD and TRG chains and a CD4+ TEM-like phenotype. Among monocytic cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. Discussion Our study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.
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MESH Headings
- Animals
- Cats
- Single-Cell Analysis
- Transcriptome
- Species Specificity
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Dogs
- Sequence Analysis, RNA
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- RNA-Seq
- V(D)J Recombination/genetics
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Affiliation(s)
- Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Judit M. Wulcan
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
| | - Peter F. Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Stefan M. Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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12
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Bryan JN, Maitz CA. Translational History and Hope of Immunotherapy of Canine Tumors. Clin Cancer Res 2024; 30:4272-4285. [PMID: 39042399 PMCID: PMC11444889 DOI: 10.1158/1078-0432.ccr-23-2266] [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: 02/29/2024] [Revised: 05/13/2024] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
Companion dogs have served an important role in cancer immunotherapy research. Sharing similar environments and diets with humans, dogs naturally develop many of the same cancers. These shared exposures, coupled with dogs' diverse genetic makeup, make them ideal subjects for studying cancer therapies. Tumors like osteosarcoma, hemangiosarcoma, soft-tissue sarcoma, and non-Hodgkin lymphoma occur with greater frequency than their counterpart disease in humans. Canine brain tumors allow the study of therapy strategies with imaging, surgery, and radiotherapy equipment in veterinary patients with near-human geometry. Nonspecific immunostimulants, autologous and allogeneic vaccines, immune checkpoint inhibitors, and cellular therapies used in treating canine cancers have been tested in veterinary clinical trials. These treatments have not only improved outcomes for dogs but have also provided valuable insights for human cancer treatment. Advancements in radiation technology and the development of tools to characterize canine immune responses have further facilitated the ability to translate veterinary clinical trial results to human applications. Advancements in immunotherapy of canine tumors have directly supported translation to human clinical trials leading to approved therapies for patients with cancer around the world. The study of immunotherapy in dogs has been and will continue to be a promising avenue for advancing human cancer treatment.
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Affiliation(s)
- Jeffrey N. Bryan
- Comparative Oncology, Radiobiology, and Epigenetics Laboratory, Department of Veterinary Medicine and Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO
| | - Charles A. Maitz
- Comparative Oncology, Radiobiology, and Epigenetics Laboratory, Department of Veterinary Medicine and Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO
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13
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Kim MC, Borcherding N, Song WJ, Kolb R, Zhang W. Leveraging single-cell transcriptomic data to uncover immune suppressive cancer cell subsets in triple-negative canine breast cancers. Front Vet Sci 2024; 11:1434617. [PMID: 39376916 PMCID: PMC11457229 DOI: 10.3389/fvets.2024.1434617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 08/28/2024] [Indexed: 10/09/2024] Open
Abstract
Introduction Single-cell RNA sequencing (scRNA-seq) has become an essential tool for uncovering the complexities of various physiological and immunopathological conditions in veterinary medicine. However, there is currently limited information on immune-suppressive cancer subsets in canine breast cancers. In this study, we aimed to identify and characterize immune-suppressive subsets of triple-negative canine breast cancer (TNBC) by utilizing integrated scRNA-seq data from published datasets. Methods Published scRNA-seq datasets, including data from six groups of 30 dogs, were subjected to integrated bioinformatic analysis. Results Immune modulatory TNBC subsets were identified through functional enrichment analysis using immune-suppressive gene sets, including those associated with anti-inflammatory and M2-like macrophages. Key immune-suppressive signaling, such as viral infection, angiogenesis, and leukocyte chemotaxis, was found to play a role in enabling TNBC to evade immune surveillance. In addition, interactome analysis revealed significant interactions between distinct subsets of cancer cells and effector T cells, suggesting potential T-cell suppression. Discussion The present study demonstrates a versatile and scalable approach to integrating and analyzing scRNA-seq data, which successfully identified immune-modulatory subsets of canine TNBC. It also revealed potential mechanisms through which TNBC promotes immune evasion in dogs. These findings are crucial for advancing the understanding of the immune pathogenesis of canine TNBC and may aid in the development of new immune-based therapeutic strategies.
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Affiliation(s)
- Myung-Chul Kim
- Veterinary Laboratory Medicine, Clinical Pathology, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Woo-Jin Song
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Laboratory of Veterinary Internal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Ryan Kolb
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL, United States
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14
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Yoshimoto S, Kudo A, Rotolo A, Foos K, Olenick L, Takagi S, Mason NJ. Validation of a PD-1/CD28 chimeric switch receptor to augment CAR-T function in dogs with spontaneous B cell lymphoma. iScience 2024; 27:110863. [PMID: 39314237 PMCID: PMC11418608 DOI: 10.1016/j.isci.2024.110863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 07/07/2024] [Accepted: 08/29/2024] [Indexed: 09/25/2024] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy has achieved unprecedented clinical outcomes in patients with relapsed/refractory B cell leukemias; however, response rates in patients with large B cell lymphoma (LBCL) are less impressive. Expression of PD-1 on activated T cells and PD-L1 on malignant, stromal, and immune cells within the tumor microenvironment (TME) contribute to CAR-T exhaustion, hypofunction, and treatment failures. Here, a comparative approach is taken to develop a chimeric switch receptor (CSR) with potential to augment CAR-T persistence, function, and clinical efficacy in immune competent, pet dogs with spontaneous B cell lymphoma (BCL). We show that similar to human CAR-T cells, expression of a PD-1/CD28 CSR in canine CAR-T cells results in enhanced function against PD-L1+ targets and preserves central memory phenotype. We also demonstrate that these effects depend upon active CSR signaling. This work paves the way for in vivo studies in canine BCL patients to inform human trial design.
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Affiliation(s)
- Sho Yoshimoto
- Laboratory of Small Animal Surgery, Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Ayano Kudo
- Laboratory of Small Animal Surgery, Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Antonia Rotolo
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kay Foos
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren Olenick
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Satoshi Takagi
- Laboratory of Small Animal Surgery, Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Nicola J. Mason
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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15
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Lang HP, Osum KC, Friedenberg SG. A review of CD4 + T cell differentiation and diversity in dogs. Vet Immunol Immunopathol 2024; 275:110816. [PMID: 39173398 PMCID: PMC11421293 DOI: 10.1016/j.vetimm.2024.110816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024]
Abstract
CD4+ T cells are an integral component of the adaptive immune response, carrying out many functions to combat a diverse range of pathogenic challenges. These cells exhibit remarkable plasticity, differentiating into specialized subsets such as T helper type 1 (TH1), TH2, TH9, TH17, TH22, regulatory T cells (Tregs), and follicular T helper (TFH) cells. Each subset is capable of addressing a distinct immunological need ranging from pathogen eradication to regulation of immune homeostasis. As the immune response subsides, CD4+ T cells rest down into long-lived memory phenotypes-including central memory (TCM), effector memory (TEM), resident memory (TRM), and terminally differentiated effector memory cells (TEMRA) that are localized to facilitate a swift and potent response upon antigen re-encounter. This capacity for long-term immunological memory and rapid reactivation upon secondary exposure highlights the role CD4+ T cells play in sustaining both adaptive defense mechanisms and maintenance. Decades of mouse, human, and to a lesser extent, pig T cell research has provided the framework for understanding the role of CD4+ T cells in immune responses, but these model systems do not always mimic each other. Although our understanding of pig immunology is not as extensive as mouse or human research, we have gained valuable insight by studying this model. More akin to pigs, our understanding of CD4+ T cells in dogs is much less complete. This disparity exists in part because canine immunologists depend on paradigms from mouse and human studies to characterize CD4+ T cells in dogs, with a fraction of available lineage-defining antibody markers. Despite this, every major CD4+ T cell subset has been described to some extent in dogs. These subsets have been studied in various contexts, including in vitro stimulation, homeostatic conditions, and across a range of disease states. Canine CD4+ T cells have been categorized according to lineage-defining characteristics, trafficking patterns, and what cytokines they produce upon stimulation. This review addresses our current understanding of canine CD4+ T cells from a comparative perspective by highlighting both the similarities and differences from mouse, human, and pig CD4+ T cell biology. We also discuss knowledge gaps in our current understanding of CD4+ T cells in dogs that could provide direction for future studies in the field.
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Affiliation(s)
- Haeree P Lang
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Kevin C Osum
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA.
| | - Steven G Friedenberg
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
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16
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Wang Z, Chow L, Das S, Impastato R, Manchester AC, Dow S. Host-microbe interactions in the nasal cavity of dogs with chronic idiopathic rhinitis. Front Vet Sci 2024; 11:1385471. [PMID: 39188898 PMCID: PMC11345268 DOI: 10.3389/fvets.2024.1385471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
Chronic rhinitis (CR) is a frustrating clinical syndrome in dogs and our understanding of the disease pathogenesis in is limited. Increasingly, host-microbe interactions are considered key drives of clinical disease in sites of persistent mucosal inflammation such as the nasal and oral cavities. Therefore, we applied next generation sequencing tools to interrogate abnormalities present in the nose of dogs with CR and compared immune and microbiome profiles to those of healthy dogs. Host nasal cell transcriptomes were evaluated by RNA sequencing, while microbial communities were assessed by 16S rRNA sequencing. Correlation analysis was then used to identify significant interactions between nasal cell transcriptomes and the nasal microbiome and how these interactions were altered in animals with CR. Notably, we observed significant downregulation of multiple genes associated with ciliary function in dogs with CR, suggesting a previously undetected role for ciliary dysfunction in this syndrome. We also found significant upregulation of immune genes related to the TNF-α and interferon pathways. The nasal microbiome was also significantly altered in CR dogs, with overrepresentation of several potential pathobionts. Interactome analysis revealed significant correlations between bacteria in the genus Porphyromonas and the upregulated host inflammatory responses in dogs with CR, as well as defective ciliary function which was correlated with Streptococcus abundance. These findings provide new insights into host-microbe interactions in a canine model of CR and indicate the presence of potentially causal relationships between nasal pathobionts and the development of nasal inflammation and ciliary dysfunction.
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Affiliation(s)
| | | | | | | | | | - Steven Dow
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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17
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Manchester AC, Ammons DT, Lappin MR, Dow S. Single cell transcriptomic analysis of the canine duodenum in chronic inflammatory enteropathy and health. Front Immunol 2024; 15:1397590. [PMID: 38933260 PMCID: PMC11199541 DOI: 10.3389/fimmu.2024.1397590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic inflammatory enteropathy (CIE) is a common condition in dogs causing recurrent or persistent gastrointestinal clinical signs. Pathogenesis is thought to involve intestinal mucosal inflammatory infiltrates, but histopathological evaluation of intestinal biopsies from dogs with CIE fails to guide treatment, inform prognosis, or correlate with clinical remission. We employed single-cell RNA sequencing to catalog and compare the diversity of cells present in duodenal mucosal endoscopic biopsies from 3 healthy dogs and 4 dogs with CIE. Through characterization of 35,668 cells, we identified 31 transcriptomically distinct cell populations, including T cells, epithelial cells, and myeloid cells. Both healthy and CIE samples contributed to each cell population. T cells were broadly subdivided into GZMAhigh (putatively annotated as tissue resident) and IL7Rhigh (putatively annotated as non-resident) T cell categories, with evidence of a skewed proportion favoring an increase in the relative proportion of IL7Rhigh T cells in CIE dogs. Among the myeloid cells, neutrophils from CIE samples exhibited inflammatory (SOD2 and IL1A) gene expression signatures. Numerous differentially expressed genes were identified in epithelial cells, with gene set enrichment analysis suggesting enterocytes from CIE dogs may be undergoing stress responses and have altered metabolic properties. Overall, this work reveals the previously unappreciated cellular heterogeneity in canine duodenal mucosa and provides new insights into molecular mechanisms which may contribute to intestinal dysfunction in CIE. The cell type gene signatures developed through this study may also be used to better understand the subtleties of canine intestinal physiology in health and disease.
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Affiliation(s)
- Alison C. Manchester
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Dylan T. Ammons
- Colorado State University, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Michael R. Lappin
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
| | - Steven Dow
- Colorado State University, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
- Colorado State University, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, United States
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18
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Ramarapu R, Wulcan JM, Chang H, Moore PF, Vernau W, Keller SM. Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595010. [PMID: 38826195 PMCID: PMC11142102 DOI: 10.1101/2024.05.21.595010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Introduction The domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. Methods Peripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, alpha/beta T cell receptor transcripts and gamma/delta T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Results Unsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and gamma/delta T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis demonstrated a skewed T-cell receptor alpha gene usage and a restricted T-cell receptor gamma junctional length in CD8+ cytotoxic T cells compared to other alpha/beta T cell subsets. Among myeloid cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. Discussion Our study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.
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Affiliation(s)
- Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Judit M Wulcan
- 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
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
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19
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Bryan JN. Updates in Osteosarcoma. Vet Clin North Am Small Anim Pract 2024; 54:523-539. [PMID: 38158305 DOI: 10.1016/j.cvsm.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Clinical care of osteosarcoma (OSA) in dogs has seen little change during the past 2 decades, relying on amputation and platinum-based chemotherapy for pain control and survival. Recent advancements offer hope for improved outcomes. Genomic research reveals shared genetic abnormalities between canine and human OSA. Multidimensional imaging provides valuable staging and prognostic information. Limb-sparing approaches including stereotactic body radiation therapy are routine. Ablative therapies such as microwave ablation and histotripsy show promise. Immunotherapy including cell therapy and immune checkpoint inhibition are available. Radiopharmaceuticals are tuned to target OSA cells directly. These innovations may enhance treatment and prognosis for dogs with OSA.
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Affiliation(s)
- Jeffrey N Bryan
- Comparative Oncology Radiobiology and Epigenetics Laboratory, University of Missouri Columbia, Ellis Fischel Cancer Center, 900 East Campus Drive, Columbia, MO 65211, USA.
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20
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Ammons DT, Hopkins LS, Cronise KE, Kurihara J, Regan DP, Dow S. Single-cell RNA sequencing reveals the cellular and molecular heterogeneity of treatment-naïve primary osteosarcoma in dogs. Commun Biol 2024; 7:496. [PMID: 38658617 PMCID: PMC11043452 DOI: 10.1038/s42003-024-06182-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: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Osteosarcoma (OS) is a heterogeneous, aggressive malignancy of the bone that disproportionally affects children and adolescents. Therapeutic interventions for OS are limited, which is in part due to the complex tumor microenvironment (TME). As such, we used single-cell RNA sequencing (scRNA-seq) to describe the cellular and molecular composition of the TME in 6 treatment-naïve dogs with spontaneously occurring primary OS. Through analysis of 35,310 cells, we identified 41 transcriptomically distinct cell types including the characterization of follicular helper T cells, mature regulatory dendritic cells (mregDCs), and 8 tumor-associated macrophage (TAM) populations. Cell-cell interaction analysis predicted that mregDCs and TAMs play key roles in modulating T cell mediated immunity. Furthermore, we completed cross-species cell type gene signature homology analysis and found a high degree of similarity between human and canine OS. The data presented here act as a roadmap of canine OS which can be applied to advance translational immuno-oncology research.
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Affiliation(s)
- Dylan T Ammons
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Leone S Hopkins
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kathryn E Cronise
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jade Kurihara
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Daniel P Regan
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven Dow
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
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21
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Han P, Guo Y, Zhang W, Wang D, Wu Y, Li X, Zhu M. Single-Cell RNA-Sequencing Reveals Heterogeneity and Transcriptional Dynamics in Porcine Circulating CD8 + T Cells. Cells 2024; 13:692. [PMID: 38667307 PMCID: PMC11049515 DOI: 10.3390/cells13080692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Pigs are the most important source of meat and valuable biomedical models. However, the porcine immune system, especially the heterogeneity of CD8 T cell subtypes, has not been fully characterized. Here, using single-cell RNA sequencing, we identified 14 major cell types from peripheral blood circulating cells of pigs and observed remarkable heterogeneity among CD8 T cell types. Upon re-clustering of CD8+ T cells, we defined four CD8 T cell subtypes and revealed their potential differentiation trajectories and transcriptomic differences among them. Additionally, we identified transcription factors with potential regulatory roles in maintaining CD8 T cell differentiation. The cell-cell communication analysis inferred an extensive interaction between CD8 T cells and other immune cells. Finally, cross-species analysis further identified species-specific and conserved cell types across different species. Overall, our study provides the first insight into the extensive functional heterogeneity and state transitions among porcine CD8 T cell subtypes in pig peripheral blood, complements the knowledge of porcine immunity, and enhances its potential as a biomedical model.
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Affiliation(s)
- Pingping Han
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
| | - Yaping Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
| | - Yalan Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (P.H.); (Y.G.); (W.Z.); (D.W.); (Y.W.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
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22
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Kehl A, Aupperle-Lellbach H, de Brot S, van der Weyden L. Review of Molecular Technologies for Investigating Canine Cancer. Animals (Basel) 2024; 14:769. [PMID: 38473154 PMCID: PMC10930838 DOI: 10.3390/ani14050769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Genetic molecular testing is starting to gain traction as part of standard clinical practice for dogs with cancer due to its multi-faceted benefits, such as potentially being able to provide diagnostic, prognostic and/or therapeutic information. However, the benefits and ultimate success of genomic analysis in the clinical setting are reliant on the robustness of the tools used to generate the results, which continually expand as new technologies are developed. To this end, we review the different materials from which tumour cells, DNA, RNA and the relevant proteins can be isolated and what methods are available for interrogating their molecular profile, including analysis of the genetic alterations (both somatic and germline), transcriptional changes and epigenetic modifications (including DNA methylation/acetylation and microRNAs). We also look to the future and the tools that are currently being developed, such as using artificial intelligence (AI) to identify genetic mutations from histomorphological criteria. In summary, we find that the molecular genetic characterisation of canine neoplasms has made a promising start. As we understand more of the genetics underlying these tumours and more targeted therapies become available, it will no doubt become a mainstay in the delivery of precision veterinary care to dogs with cancer.
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Affiliation(s)
- Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (A.K.); (H.A.-L.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Heike Aupperle-Lellbach
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (A.K.); (H.A.-L.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland;
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23
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Han P, Zhang W, Wang D, Wu Y, Li X, Zhao S, Zhu M. Comparative transcriptome analysis of T lymphocyte subpopulations and identification of critical regulators defining porcine thymocyte identity. Front Immunol 2024; 15:1339787. [PMID: 38384475 PMCID: PMC10879363 DOI: 10.3389/fimmu.2024.1339787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. Method Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. Results The comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. Discussion Our findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.
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Affiliation(s)
- Pingping Han
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yalan Wu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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24
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Nance RL, Wang X, Sandey M, Matz BM, Thomas A, Smith BF. Single-Nuclei Multiome (ATAC + Gene Expression) Sequencing of a Primary Canine Osteosarcoma Elucidates Intra-Tumoral Heterogeneity and Characterizes the Tumor Microenvironment. Int J Mol Sci 2023; 24:16365. [PMID: 38003552 PMCID: PMC10671194 DOI: 10.3390/ijms242216365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Osteosarcoma (OSA) is a highly aggressive bone tumor primarily affecting pediatric or adolescent humans and large-breed dogs. Canine OSA shares striking similarities with its human counterpart, making it an invaluable translational model for uncovering the disease's complexities and developing novel therapeutic strategies. Tumor heterogeneity, a hallmark of OSA, poses significant challenges to effective treatment due to the evolution of diverse cell populations that influence tumor growth, metastasis, and resistance to therapies. In this study, we apply single-nuclei multiome sequencing, encompassing ATAC (Assay for Transposase-Accessible Chromatin) and GEX (Gene Expression, or RNA) sequencing, to a treatment-naïve primary canine osteosarcoma. This comprehensive approach reveals the complexity of the tumor microenvironment by simultaneously capturing the transcriptomic and epigenomic profiles within the same nucleus. Furthermore, these results are analyzed in conjunction with bulk RNA sequencing and differential analysis of the same tumor and patient-matched normal bone. By delving into the intricacies of OSA at this unprecedented level of detail, we aim to unravel the underlying mechanisms driving intra-tumoral heterogeneity, opening new avenues for therapeutic interventions in both human and canine patients. This study pioneers an approach that is broadly applicable, while demonstrating significant heterogeneity in the context of a single individual's tumor.
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Affiliation(s)
- Rebecca L. Nance
- Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA; (R.L.N.); (X.W.)
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA;
| | - Xu Wang
- Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA; (R.L.N.); (X.W.)
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA;
| | - Maninder Sandey
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA;
| | - Brad M. Matz
- Department of Clinical Sciences, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA;
| | - AriAnna Thomas
- Department of Nursing, Tuskegee University, Tuskegee, AL 36088, USA;
| | - Bruce F. Smith
- Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA; (R.L.N.); (X.W.)
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, USA;
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25
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Nirala BK, Yamamichi T, Petrescu DI, Shafin TN, Yustein JT. Decoding the Impact of Tumor Microenvironment in Osteosarcoma Progression and Metastasis. Cancers (Basel) 2023; 15:5108. [PMID: 37894474 PMCID: PMC10605493 DOI: 10.3390/cancers15205108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma (OS) is a heterogeneous, highly metastatic bone malignancy in children and adolescents. Despite advancements in multimodal treatment strategies, the prognosis for patients with metastatic or recurrent disease has not improved significantly in the last four decades. OS is a highly heterogeneous tumor; its genetic background and the mechanism of oncogenesis are not well defined. Unfortunately, no effective molecular targeted therapy is currently available for this disease. Understanding osteosarcoma's tumor microenvironment (TME) has recently gained much interest among scientists hoping to provide valuable insights into tumor heterogeneity, progression, metastasis, and the identification of novel therapeutic avenues. Here, we review the current understanding of the TME of OS, including different cellular and noncellular components, their crosstalk with OS tumor cells, and their involvement in tumor progression and metastasis. We also highlight past/current clinical trials targeting the TME of OS for effective therapies and potential future therapeutic strategies with negligible adverse effects.
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Affiliation(s)
| | | | | | | | - Jason T. Yustein
- Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA; (B.K.N.); (T.Y.); (D.I.P.); (T.N.S.)
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26
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Ammons D, Hopkins L, Cronise K, Kurihara J, Regan D, Dow S. Single-cell RNA sequencing reveals the cellular and molecular heterogeneity of treatment-naïve primary osteosarcoma in dogs. RESEARCH SQUARE 2023:rs.3.rs-3232360. [PMID: 37609233 PMCID: PMC10441479 DOI: 10.21203/rs.3.rs-3232360/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Osteosarcoma (OS) is a heterogeneous, aggressive malignancy of the bone that disproportionally affects children and adolescents. Therapeutic interventions for OS are limited, which is in part due to the complex tumor microenvironment (TME) that has proven to be refractory to immunotherapies. Thus, there is a need to better define the complexity of the OS TME. To address this need, we used single-cell RNA sequencing (scRNA-seq) to describe the cellular and molecular composition of the TME in 6 treatment-naïve dogs with spontaneously occurring primary OS. Through analysis of 35,310 cells, we identified 30 distinct immune cell types, 9 unique tumor populations, 1 cluster of fibroblasts, and 1 cluster of endothelial cells. Independent reclustering of major cell types revealed the presence of follicular helper T cells, mature regulatory dendritic cells (mregDCs), and 8 transcriptomically distinct macrophage/monocyte populations. Cell-cell interaction inference analysis predicted that mregDCs and tumor-associated macrophages (TAMs) play key roles in modulating T cell mediate immunity. Furthermore, we used publicly available human OS scRNA-seq data to complete a cross-species cell type gene signature homology analysis. The analysis revealed a high degree of cell type gene signature homology between species, suggesting the cellular composition of OS is largely conserved between humans and dogs. Our findings provide key new insights into the biology of canine OS and highlight the conserved features of OS across species. Generally, the data presented here acts as a cellular and molecular roadmap of canine OS which can be applied to advance the translational immuno-oncology research field.
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