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Heydari AA, Sindi SS. Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing. BIOPHYSICS REVIEWS 2023; 4:011306. [PMID: 38505815 PMCID: PMC10903438 DOI: 10.1063/5.0091135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 12/19/2022] [Indexed: 03/21/2024]
Abstract
Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single-cell resolution while maintaining cellular compositions within a tissue. Having both expression profiles and tissue organization enables researchers to better understand cellular interactions and heterogeneity, providing insight into complex biological processes that would not be possible with traditional sequencing technologies. Data generated by ST technologies are inherently noisy, high-dimensional, sparse, and multi-modal (including histological images, count matrices, etc.), thus requiring specialized computational tools for accurate and robust analysis. However, many ST studies currently utilize traditional scRNAseq tools, which are inadequate for analyzing complex ST datasets. On the other hand, many of the existing ST-specific methods are built upon traditional statistical or machine learning frameworks, which have shown to be sub-optimal in many applications due to the scale, multi-modality, and limitations of spatially resolved data (such as spatial resolution, sensitivity, and gene coverage). Given these intricacies, researchers have developed deep learning (DL)-based models to alleviate ST-specific challenges. These methods include new state-of-the-art models in alignment, spatial reconstruction, and spatial clustering, among others. However, DL models for ST analysis are nascent and remain largely underexplored. In this review, we provide an overview of existing state-of-the-art tools for analyzing spatially resolved transcriptomics while delving deeper into the DL-based approaches. We discuss the new frontiers and the open questions in this field and highlight domains in which we anticipate transformational DL applications.
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52
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Loos P, Baiwir J, Maquet C, Javaux J, Sandor R, Lallemand F, Marichal T, Machiels B, Gillet L. Dampening type 2 properties of group 2 innate lymphoid cells by a gammaherpesvirus infection reprograms alveolar macrophages. Sci Immunol 2023; 8:eabl9041. [PMID: 36827420 DOI: 10.1126/sciimmunol.abl9041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Immunological dysregulation in asthma is associated with changes in exposure to microorganisms early in life. Gammaherpesviruses (γHVs), such as Epstein-Barr virus, are widespread human viruses that establish lifelong infection and profoundly shape host immunity. Using murid herpesvirus 4 (MuHV-4), a mouse γHV, we show that after infection, lung-resident and recruited group 2 innate lymphoid cells (ILC2s) exhibit a reduced ability to expand and produce type 2 cytokines in response to house dust mites, thereby contributing to protection against asthma. In contrast, MuHV-4 infection triggers GM-CSF production by those lung ILC2s, which orders the differentiation of monocytes (Mos) into alveolar macrophages (AMs) without promoting their type 2 functions. In the context of γHV infection, ILC2s are therefore essential cells within the pulmonary niche that imprint the tissue-specific identity of Mo-derived AMs and shape their function well beyond the initial acute infection.
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Affiliation(s)
- Pauline Loos
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - Jérôme Baiwir
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - Céline Maquet
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - Justine Javaux
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - Rémy Sandor
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - François Lallemand
- Centre Hospitalier Universitaire de Liège, Département de Physique Médicale, Service médical de radiothérapie, Liège 4000, Belgium
| | - Thomas Marichal
- Laboratory of Immunophysiology, GIGA-Research and Faculty of Veterinary Medicine, ULiège, Liège 4000, Belgium
| | - Bénédicte Machiels
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
| | - Laurent Gillet
- Laboratory of Immunology and Vaccinology, Faculty of Veterinary Medicine, FARAH, ULiège, Liège 4000, Belgium
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Han H, Cummings S, Shade KTC, Johnson J, Qian G, Gans J, Shankara S, Escobedo J, Zarazinski E, Bodinizzo R, Bangari D, Bryce P, Hicks A. Cellular mechanisms and effects of IL-4 receptor blockade in experimental conjunctivitis evoked by skin inflammation. JCI Insight 2023; 8:163495. [PMID: 36626228 PMCID: PMC9977427 DOI: 10.1172/jci.insight.163495] [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: 07/11/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Ocular surface diseases, including conjunctivitis, are recognized as common comorbidities in atopic dermatitis (AD) and occur at an increased frequency in patients with AD treated with biologics targeting IL-4 receptor α (IL-4Rα) or IL-13. However, the inflammatory mechanisms underlying this pathology are unknown. Here, we developed a potentially novel mouse model of skin inflammation-evoked conjunctivitis and showed that it is dependent on CD4+ T cells and basophils. Blockade of IL-4Rα partially attenuated conjunctivitis development, downregulated basophil activation, and led to a reduction in expression of genes related to type 2 cytokine responses. Together, these data suggest that an IL-4Rα/basophil axis plays a role in the development of murine allergic conjunctivitis. Interestingly, we found a significant augmentation of a number of genes that encode tear proteins and enzymes in anti-IL-4Rα-treated mice, and it may underlie the partial efficacy in this model and may represent candidate mediators of the increased frequency of conjunctivitis following dupilumab in patients with AD.
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Affiliation(s)
- Hongwei Han
- Sanofi, Immunology and Inflammation Research Therapeutic Area, Cambridge, Massachusetts, USA
| | - Sheila Cummings
- Sanofi, Global Discovery Pathology, Translational In-vivo Models Platform, Cambridge, Massachusetts, USA
| | - Kai-Ting C. Shade
- Sanofi, Immunology and Inflammation Research Therapeutic Area, Cambridge, Massachusetts, USA
| | - Jennifer Johnson
- Sanofi, Global Discovery Pathology, Translational In-vivo Models Platform, Cambridge, Massachusetts, USA
| | - George Qian
- Sanofi, Immunology and Inflammation Research Therapeutic Area, Cambridge, Massachusetts, USA
| | - Joseph Gans
- Sanofi, Translational Science Single Cell & Functional Genomics, Cambridge, Massachusetts, USA
| | - Srinivas Shankara
- Sanofi, Translational Science Single Cell & Functional Genomics, Cambridge, Massachusetts, USA
| | - Javier Escobedo
- Sanofi, Translational Science Single Cell & Functional Genomics, Cambridge, Massachusetts, USA
| | - Erik Zarazinski
- Sanofi, In-vivo Research Center, Translational In-vivo Models Platform, Cambridge, Massachusetts, USA
| | - Renee Bodinizzo
- Sanofi, In-vivo Research Center, Translational In-vivo Models Platform, Cambridge, Massachusetts, USA
| | - Dinesh Bangari
- Sanofi, Global Discovery Pathology, Translational In-vivo Models Platform, Cambridge, Massachusetts, USA
| | - Paul Bryce
- Sanofi, Immunology and Inflammation Research Therapeutic Area, Cambridge, Massachusetts, USA
| | - Alexandra Hicks
- Sanofi, Immunology and Inflammation Research Therapeutic Area, Cambridge, Massachusetts, USA
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54
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Pernet E, Sun S, Sarden N, Gona S, Nguyen A, Khan N, Mawhinney M, Tran KA, Chronopoulos J, Amberkar D, Sadeghi M, Grant A, Wali S, Prevel R, Ding J, Martin JG, Thanabalasuriar A, Yipp BG, Barreiro LB, Divangahi M. Neonatal imprinting of alveolar macrophages via neutrophil-derived 12-HETE. Nature 2023; 614:530-538. [PMID: 36599368 PMCID: PMC9945843 DOI: 10.1038/s41586-022-05660-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/14/2022] [Indexed: 01/06/2023]
Abstract
Resident-tissue macrophages (RTMs) arise from embryonic precursors1,2, yet the developmental signals that shape their longevity remain largely unknown. Here we demonstrate in mice genetically deficient in 12-lipoxygenase and 15-lipoxygenase (Alox15-/- mice) that neonatal neutrophil-derived 12-HETE is required for self-renewal and maintenance of alveolar macrophages (AMs) during lung development. Although the seeding and differentiation of AM progenitors remained intact, the absence of 12-HETE led to a significant reduction in AMs in adult lungs and enhanced senescence owing to increased prostaglandin E2 production. A compromised AM compartment resulted in increased susceptibility to acute lung injury induced by lipopolysaccharide and to pulmonary infections with influenza A virus or SARS-CoV-2. Our results highlight the complexity of prenatal RTM programming and reveal their dependency on in trans eicosanoid production by neutrophils for lifelong self-renewal.
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Affiliation(s)
- Erwan Pernet
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada.
| | - Sarah Sun
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Nicole Sarden
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Saideep Gona
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Angela Nguyen
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nargis Khan
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Martin Mawhinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Kim A Tran
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Julia Chronopoulos
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Dnyandeo Amberkar
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Mina Sadeghi
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Alexandre Grant
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Shradha Wali
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Renaud Prevel
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Jun Ding
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - James G Martin
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Ajitha Thanabalasuriar
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Bryan G Yipp
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases and Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Luis B Barreiro
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Maziar Divangahi
- McGill University Health Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
- Department of Pathology, McGill University, Montreal, Quebec, Canada.
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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55
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Jardine L, Schim van der Loeff I, Haq IJ, Sproat TDR. Gestational Development of the Human Immune System. Immunol Allergy Clin North Am 2023; 43:1-15. [PMID: 36410996 DOI: 10.1016/j.iac.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Building an immune system is a monumental task critical to the survival of the fetus and newborn. A functional fetal immune system must complement the maternal immune system in handling in utero infection; abstain from damaging non-self-reactions that would compromise the materno-fetal interface; mobilize in response to infection and equip mucosal tissues for pathogen exposure at birth. There is growing appreciation that immune cells also have noncanonical roles in development and specifically may contribute to tissue morphogenesis. In this review we detail how hematopoietic and lymphoid organs jointly establish cellular constituents of the immune system; how these constituents are organized in 2 mucosal sites-gut and lung-where early life immune function has long-term consequences for health; and how exemplar diseases of prematurity and inborn errors of immunity reveal dominant pathways in prenatal immunity.
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Affiliation(s)
- Laura Jardine
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom; Haematology Department, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom.
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Iram J Haq
- Translational and Clinical Research Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom; Department of Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Thomas D R Sproat
- Neonatal Unit, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Richardson Road, Newcastle Upon Tyne NE1 4LP, United Kingdom
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56
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Chen Y, Zhang X, Peng X, Jin Y, Ding P, Xiao J, Li C, Wang F, Chang A, Yue Q, Pu M, Chen P, Shen J, Li M, Jia T, Wang H, Huang L, Guo G, Zhang W, Liu H, Wang X, Chen D. SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases. Nucleic Acids Res 2023; 51:D1150-D1159. [PMID: 36305818 PMCID: PMC9825432 DOI: 10.1093/nar/gkac930] [Citation(s) in RCA: 2] [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: 08/14/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 01/30/2023] Open
Abstract
It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.
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Affiliation(s)
- Yangfeng Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Xingliang Zhang
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, China
- Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Xi Peng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yicheng Jin
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Peiwen Ding
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Jiedan Xiao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Changxiao Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Fei Wang
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Ashley Chang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Qizhen Yue
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Mingyi Pu
- Department of Medicine, Sun Yat-sen University, Shenzhen 518106, China
| | - Peixin Chen
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Mengrou Li
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Tengfei Jia
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- The Future Laboratory, Tsinghua University, Beijing 100084, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai 200032, China
| | - Dongsheng Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
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57
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Cantu A, Gutierrez MC, Dong X, Leek C, Sajti E, Lingappan K. Remarkable sex-specific differences at single-cell resolution in neonatal hyperoxic lung injury. Am J Physiol Lung Cell Mol Physiol 2023; 324:L5-L31. [PMID: 36283964 PMCID: PMC9799156 DOI: 10.1152/ajplung.00269.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 01/12/2023] Open
Abstract
Exposure to supraphysiological concentrations of oxygen (hyperoxia) predisposes to bronchopulmonary dysplasia (BPD), which is characterized by abnormal alveolarization and pulmonary vascular development, in preterm neonates. Neonatal hyperoxia exposure is used to recapitulate the phenotype of human BPD in murine models. Male sex is considered an independent predictor for the development of BPD, but the main mechanisms underlying sexually dimorphic outcomes are unknown. Our objective was to investigate sex-specific and cell-type specific transcriptional changes that drive injury in the neonatal lung exposed to hyperoxia at single-cell resolution and delineate the changes in cell-cell communication networks in the developing lung. We used single-cell RNA sequencing (scRNAseq) to generate transcriptional profiles of >35,000 cells isolated from the lungs of neonatal male and female C57BL/6 mice exposed to 95% [Formula: see text] between PND1-5 (saccular stage of lung development) or normoxia and euthanized at PND7 (alveolar stage of lung development). ScRNAseq identified 22 cell clusters with distinct populations of endothelial, epithelial, mesenchymal, and immune cells. Our data identified that the distal lung vascular endothelium (composed of aerocytes and general capillary endothelial cells) is exquisitely sensitive to hyperoxia exposure with the emergence of an intermediate capillary endothelial population with both general capillaries (gCap) and aerocytes or alveolar capillaries (aCap) markers. We also identified a myeloid-derived suppressor cell population from the lung neutrophils. Sex-specific differences were evident in all lung cell subpopulations but were striking among the lung immune cells. Finally, we identified that the specific intercellular communication networks and the ligand-receptor pairs that are impacted by neonatal hyperoxia exposure.
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Affiliation(s)
- Abiud Cantu
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Manuel C Gutierrez
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xiaoyu Dong
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Connor Leek
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eniko Sajti
- Department of Pediatrics, University of California, La Jolla, California
| | - Krithika Lingappan
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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58
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Gong X, Zhang Y, Ai J, Li K. Application of Single-Cell RNA Sequencing in Ovarian Development. Biomolecules 2022; 13:47. [PMID: 36671432 PMCID: PMC9855652 DOI: 10.3390/biom13010047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
The ovary is a female reproductive organ that plays a key role in fertility and the maintenance of endocrine homeostasis, which is of great importance to women's health. It is characterized by a high heterogeneity, with different cellular subpopulations primarily containing oocytes, granulosa cells, stromal cells, endothelial cells, vascular smooth muscle cells, and diverse immune cell types. Each has unique and important functions. From the fetal period to old age, the ovary experiences continuous structural and functional changes, with the gene expression of each cell type undergoing dramatic changes. In addition, ovarian development strongly relies on the communication between germ and somatic cells. Compared to traditional bulk RNA sequencing techniques, the single-cell RNA sequencing (scRNA-seq) approach has substantial advantages in analyzing individual cells within an ever-changing and complicated tissue, classifying them into cell types, characterizing single cells, delineating the cellular developmental trajectory, and studying cell-to-cell interactions. In this review, we present single-cell transcriptome mapping of the ovary, summarize the characteristics of the important constituent cells of the ovary and the critical cellular developmental processes, and describe key signaling pathways for cell-to-cell communication in the ovary, as revealed by scRNA-seq. This review will undoubtedly improve our understanding of the characteristics of ovarian cells and development, thus enabling the identification of novel therapeutic targets for ovarian-related diseases.
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Affiliation(s)
| | | | - Jihui Ai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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59
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Shibuya R, Kim BS. Skin-homing basophils and beyond. Front Immunol 2022; 13:1059098. [PMID: 36618424 PMCID: PMC9815541 DOI: 10.3389/fimmu.2022.1059098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Basophils have been implicated in type 2 inflammation and numerous disorders in the skin such as helminth infection, atopic dermatitis, and urticaria. Although similar in form and function to tissue-resident mast cells, classical studies on basophils have centered on those from the hematopoietic compartment. However, increasing studies in tissues like the skin demonstrate that basophils may take on particular characteristics by responding to unique developmental, chemotactic, and activation cues. Herein, we highlight how recent studies in barrier immunology suggest the presence of skin-homing basophils that harbor a unique identity in terms of phenotype, function, and motility. These concepts may uniquely inform how basophils contribute to diseases at multiple epithelial surfaces and our ability to therapeutically target the innate immune system in disease.
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Affiliation(s)
- Rintaro Shibuya
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Brian S. Kim
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, United States,*Correspondence: Brian S. Kim,
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60
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Pohl ST, Prada ML, Espinet E, Jurkowska R. Practical Considerations for Complex Tissue Dissociation for Single-Cell Transcriptomics. Methods Mol Biol 2022; 2584:371-387. [PMID: 36495461 DOI: 10.1007/978-1-0716-2756-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell and single-nucleus RNA sequencing have revolutionized biomedical research, allowing analysis of complex tissues, identification of novel cell types, and mapping of development as well as disease states. Successful application of this technology critically relies on the dissociation of solid organs and tissues into high-quality single-cell (or nuclei) suspensions.In this chapter, we examine several key aspects of the tissue handling workflow that need to be considered when establishing an efficient tissue processing protocol for single-cell RNA sequencing (scRNA-seq). These include tissue collection, transport, and storage, as well as the choice of the dissociation conditions. We emphasize the importance of the tissue quality check and discuss the advantages (and potential limitations) of tissue cryopreservation. We provide practical tips and considerations on each of the steps of the processing workflow, and comment on how to maximize cell viability and integrity, which are critical for obtaining high-quality single-cell transcriptomic data.
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Affiliation(s)
- Stephanie T Pohl
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | - Maria Llamazares Prada
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) and Translational Lung Research Center, Heidelberg, Germany
| | - Elisa Espinet
- Anatomy Unit, Department of Pathology and Experimental Therapy, School of Medicine, University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain
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Poto R, Gambardella AR, Marone G, Schroeder JT, Mattei F, Schiavoni G, Varricchi G. Basophils from allergy to cancer. Front Immunol 2022; 13:1056838. [PMID: 36578500 PMCID: PMC9791102 DOI: 10.3389/fimmu.2022.1056838] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Human basophils, first identified over 140 years ago, account for just 0.5-1% of circulating leukocytes. While this scarcity long hampered basophil studies, innovations during the past 30 years, beginning with their isolation and more recently in the development of mouse models, have markedly advanced our understanding of these cells. Although dissimilarities between human and mouse basophils persist, the overall findings highlight the growing importance of these cells in health and disease. Indeed, studies continue to support basophils as key participants in IgE-mediated reactions, where they infiltrate inflammatory lesions, release pro-inflammatory mediators (histamine, leukotriene C4: LTC4) and regulatory cytokines (IL-4, IL-13) central to the pathogenesis of allergic diseases. Studies now report basophils infiltrating various human cancers where they play diverse roles, either promoting or hampering tumorigenesis. Likewise, this activity bears remarkable similarity to the mounting evidence that basophils facilitate wound healing. In fact, both activities appear linked to the capacity of basophils to secrete IL-4/IL-13, with these cytokines polarizing macrophages toward the M2 phenotype. Basophils also secrete several angiogenic factors (vascular endothelial growth factor: VEGF-A, amphiregulin) consistent with these activities. In this review, we feature these newfound properties with the goal of unraveling the increasing importance of basophils in these diverse pathobiological processes.
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Affiliation(s)
- Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy,Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy,World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
| | - Adriana Rosa Gambardella
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy,Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy,World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy,Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), Naples, Italy
| | - John T. Schroeder
- Department of Medicine, Division of Allergy and Clinical Immunology, Johns Hopkins Asthma and Allergy Center, Johns Hopkins University, Baltimore, MD, United States
| | - Fabrizio Mattei
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanna Schiavoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy,*Correspondence: Gilda Varricchi, ; Giovanna Schiavoni,
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy,World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy,Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), Naples, Italy,*Correspondence: Gilda Varricchi, ; Giovanna Schiavoni,
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62
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Intestinal microbe-derived metabolites instruct macrophages in the lungs. Nat Immunol 2022; 23:1662-1664. [PMID: 36456738 DOI: 10.1038/s41590-022-01358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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63
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Allergen immunotherapy, cancer, and immune disorders. Curr Opin Allergy Clin Immunol 2022; 22:428-434. [PMID: 36165426 DOI: 10.1097/aci.0000000000000858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an update on the intriguing relationships between allergies, allergen immunotherapy, cancer, and immune disorders. Allergic diseases and cancer are increasing in incidence and prevalence and a potential relationship, or not, between these diseases have been suggested for many years. RECENT FINDINGS Recent findings suggest that there may be some causative effects between certain types of cancer and allergic diseases, as described in the text. Some types of cancer may be more linked to the presence of an allergic disease, than others. However, epigenetic factors, such as tobacco smoke alcohol and toxic substances should also be taken into consideration. SUMMARY The association between allergy and cancer is complex and depends on the specific allergy and the specific organ under consideration. Regarding pancreatic cancer, colorectal cancer (CRC), and glioma, all types of allergies were shown to be a protective factor. Conversely, asthma is a risk factor for lung cancer as is atopic dermatitis for skin cancer. Despite extensive research, no definite relationship has been determined, and no clear relationship, either positive or negative, to allergies can be observed. These results should be corroborated with large epidemiological well designed prospective studies due to some weaknesses in the previous investigations.
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64
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Alveolar macrophage metabolic programming via a C-type lectin receptor protects against lipo-toxicity and cell death. Nat Commun 2022; 13:7272. [PMID: 36433992 PMCID: PMC9700784 DOI: 10.1038/s41467-022-34935-w] [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: 09/22/2021] [Accepted: 11/12/2022] [Indexed: 11/27/2022] Open
Abstract
Alveolar macrophages (AM) hold lung homeostasis intact. In addition to the defense against inhaled pathogens and deleterious inflammation, AM also maintain pulmonary surfactant homeostasis, a vital lung function that prevents pulmonary alveolar proteinosis. Signals transmitted between AM and pneumocytes of the pulmonary niche coordinate these specialized functions. However, the mechanisms that guide the metabolic homeostasis of AM remain largely elusive. We show that the NK cell-associated receptor, NKR-P1B, is expressed by AM and is essential for metabolic programming. Nkrp1b-/- mice are vulnerable to pneumococcal infection due to an age-dependent collapse in the number of AM and the formation of lipid-laden AM. The AM of Nkrp1b-/- mice show increased uptake but defective metabolism of surfactant lipids. We identify a physical relay between AM and alveolar type-II pneumocytes that is dependent on pneumocyte Clr-g expression. These findings implicate the NKR-P1B:Clr-g signaling axis in AM-pneumocyte communication as being important for maintaining metabolism in AM.
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65
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Poto R, Criscuolo G, Marone G, Brightling CE, Varricchi G. Human Lung Mast Cells: Therapeutic Implications in Asthma. Int J Mol Sci 2022; 23:14466. [PMID: 36430941 PMCID: PMC9693207 DOI: 10.3390/ijms232214466] [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: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Mast cells are strategically located in different compartments of the lung in asthmatic patients. These cells are widely recognized as central effectors and immunomodulators in different asthma phenotypes. Mast cell mediators activate a wide spectrum of cells of the innate and adaptive immune system during airway inflammation. Moreover, these cells modulate the activities of several structural cells (i.e., fibroblasts, airway smooth muscle cells, bronchial epithelial and goblet cells, and endothelial cells) in the human lung. These findings indicate that lung mast cells and their mediators significantly contribute to the immune induction of airway remodeling in severe asthma. Therapies targeting mast cell mediators and/or their receptors, including monoclonal antibodies targeting IgE, IL-4/IL-13, IL-5/IL-5Rα, IL-4Rα, TSLP, and IL-33, have been found safe and effective in the treatment of different phenotypes of asthma. Moreover, agonists of inhibitory receptors expressed by human mast cells (Siglec-8, Siglec-6) are under investigation for asthma treatment. Increasing evidence suggests that different approaches to depleting mast cells show promising results in severe asthma treatment. Novel treatments targeting mast cells can presumably change the course of the disease and induce drug-free remission in bronchial asthma. Here, we provide an overview of current and promising treatments for asthma that directly or indirectly target lung mast cells.
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Affiliation(s)
- Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy
| | - Gjada Criscuolo
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), 80131 Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), 80131 Naples, Italy
| | - Chris E. Brightling
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester LE1 7RH, UK
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), 80131 Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), 80131 Naples, Italy
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66
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Brownfield DG, de Arce AD, Ghelfi E, Gillich A, Desai TJ, Krasnow MA. Alveolar cell fate selection and lifelong maintenance of AT2 cells by FGF signaling. Nat Commun 2022; 13:7137. [PMID: 36414616 PMCID: PMC9681748 DOI: 10.1038/s41467-022-34059-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
The lung's gas exchange surface is comprised of alveolar AT1 and AT2 cells that are corrupted in several common and deadly diseases. They arise from a bipotent progenitor whose differentiation is thought to be dictated by differential mechanical forces. Here we show the critical determinant is FGF signaling. Fgfr2 is expressed in the developing progenitors in mouse then restricts to nascent AT2 cells and remains on throughout life. Its ligands are expressed in surrounding mesenchyme and can, in the absence of exogenous mechanical cues, induce progenitors to form alveolospheres with intermingled AT2 and AT1 cells. FGF signaling directly and cell autonomously specifies AT2 fate; progenitors lacking Fgfr2 in vitro and in vivo exclusively acquire AT1 fate. Fgfr2 loss in AT2 cells perinatally results in reprogramming to AT1 identity, whereas loss or inhibition later in life triggers AT2 apoptosis and compensatory regeneration. We propose that Fgfr2 signaling selects AT2 fate during development, induces a cell non-autonomous AT1 differentiation signal, then continuously maintains AT2 identity and survival throughout life.
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Affiliation(s)
- Douglas G Brownfield
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA.
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Departments of Physiology and Biomedical Engineering and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
| | - Alex Diaz de Arce
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Astrid Gillich
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA
| | - Tushar J Desai
- Department of Internal Medicine and Stem Cell Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA.
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Matsumura T, Totani H, Gunji Y, Fukuda M, Yokomori R, Deng J, Rethnam M, Yang C, Tan TK, Karasawa T, Kario K, Takahashi M, Osato M, Sanda T, Suda T. A Myb enhancer-guided analysis of basophil and mast cell differentiation. Nat Commun 2022; 13:7064. [PMID: 36400777 PMCID: PMC9674656 DOI: 10.1038/s41467-022-34906-1] [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: 03/03/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb -68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb -68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
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Affiliation(s)
- Takayoshi Matsumura
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan ,grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Haruhito Totani
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yoshitaka Gunji
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Masahiro Fukuda
- grid.428397.30000 0004 0385 0924Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rui Yokomori
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianwen Deng
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Malini Rethnam
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tze King Tan
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tadayoshi Karasawa
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Kazuomi Kario
- grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Masafumi Takahashi
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Motomi Osato
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toshio Suda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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68
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Multiple Death Pathways of Neutrophils Regulate Alveolar Macrophage Proliferation. Cells 2022; 11:cells11223633. [PMID: 36429062 PMCID: PMC9688429 DOI: 10.3390/cells11223633] [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: 10/10/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
Abstract
Alveolar macrophage (AM) proliferation and self-renewal play an important role in the lung tissue microenvironment. However, the impact of immune cells, especially the neutrophils, on AM homeostasis or function is not well characterized. In this study, we induced in vivo migration of neutrophils into bronchoalveolar lavage (BAL) fluid and lung using CXCL1, and then co-cultured these with AMs in vitro. Neutrophils in the BAL (BAL-neutrophils), rather than neutrophils of bone marrow (BM-neutrophils), were found to inhibit AM proliferation. Analysis of publicly available data showed high heterogeneity of lung neutrophils with distinct molecular signatures of BM- and blood-neutrophils. Unexpectedly, BAL-neutrophils from influenza virus PR8-infected mice (PR8-neutrophils) did not inhibit the proliferation of AMs. Bulk RNA sequencing further revealed that co-culture of AMs with PR8-neutrophils induced IFN-α and -γ responses and inflammatory response, and AMs co-cultured with BAL-neutrophils showed higher expression of metabolism- and ROS-associated genes; in addition, BAL-neutrophils from PR8-infected mice modulated AM polarization and phagocytosis. BAL-neutrophil-mediated suppression of AM proliferation was abrogated by a combination of inhibitors of different neutrophil death pathways. Collectively, our findings suggest that multiple cell death pathways of neutrophils regulate the proliferation of AMs. Targeting neutrophil death may represent a potential therapeutic strategy for improving AM homeostasis during respiratory diseases.
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69
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Park MD, Silvin A, Ginhoux F, Merad M. Macrophages in health and disease. Cell 2022; 185:4259-4279. [PMID: 36368305 PMCID: PMC9908006 DOI: 10.1016/j.cell.2022.10.007] [Citation(s) in RCA: 165] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022]
Abstract
The heterogeneity of tissue macrophages, in health and in disease, has become increasingly transparent over the last decade. But with the plethora of data comes a natural need for organization and the design of a conceptual framework for how we can better understand the origins and functions of different macrophages. We propose that the ontogeny of a macrophage-beyond its fundamental derivation as either embryonically or bone marrow-derived, but rather inclusive of the course of its differentiation, amidst steady-state cues, disease-associated signals, and time-constitutes a critical piece of information about its contribution to homeostasis or the progression of disease.
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Affiliation(s)
- Matthew D Park
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aymeric Silvin
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France; Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research (A(∗)STAR), Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore.
| | - Miriam Merad
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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70
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Eenjes E, Tibboel D, Wijnen RMH, Schnater JM, Rottier RJ. SOX2 and SOX21 in Lung Epithelial Differentiation and Repair. Int J Mol Sci 2022; 23:13064. [PMID: 36361852 PMCID: PMC9657681 DOI: 10.3390/ijms232113064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
The lung originates from the ventral foregut and develops into an intricate branched structure of airways, alveoli, vessels and support tissue. As the lung develops, cells become specified and differentiate into the various cell lineages. This process is controlled by specific transcription factors, such as the SRY-related HMG-box genes SOX2 and SOX21, that are activated or repressed through intrinsic and extrinsic signals. Disturbances in any of these processes during the development of the lung may lead to various pediatric lung disorders, such as Congenital Diaphragmatic Hernia (CDH), Congenital Pulmonary Airway Malformation (CPAM) and Broncho-Pulmonary Dysplasia (BPD). Changes in the composition of the airways and the alveoli may result in reduced respiratory function and eventually lead to chronic lung disorders. In this concise review, we describe different intrinsic and extrinsic cellular processes required for proper differentiation of the epithelium during development and regeneration, and the influence of the microenvironment on this process with special focus on SOX2 and SOX21.
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Affiliation(s)
- Evelien Eenjes
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Johannes Marco Schnater
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robbert J. Rottier
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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71
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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72
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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73
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Xu Z, Wang X, Fan L, Wang F, Lin B, Wang J, Trevejo-Nuñez G, Chen W, Chen K. Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization. iScience 2022; 25:104900. [PMID: 36039299 PMCID: PMC9418911 DOI: 10.1016/j.isci.2022.104900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/14/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding lung immunity requires an unbiased profiling of tissue-resident T cells at their precise anatomical locations within the lung, but such information has not been characterized in the immunized mouse model. In this pilot study, using 10x Genomics Chromium and Visium platform, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after immunization using a well-established Klebsiella pneumoniae infection model. We built an optimized deconvolution pipeline to accurately decipher specific cell-type compositions by anatomic location. We discovered that combining scATAC-seq and scRNA-seq data may provide more robust cell-type identification, especially for lineage-specific T helper cells. Combining all three modalities, we observed a dynamic change in the location of T helper cells as well as their corresponding chemokines. In summary, our proof-of-principle study demonstrated the power and potential of single-cell multi-omics analysis to uncover spatial- and cell-type-dependent mechanisms of lung immunity.
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Affiliation(s)
- Zhongli Xu
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Xinjun Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Li Fan
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fujing Wang
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Becky Lin
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Wei Chen
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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74
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Dörr D, Obermayer B, Weiner JM, Zimmermann K, Anania C, Wagner LK, Lyras EM, Sapozhnikova V, Lara-Astiaso D, Prósper F, Lang R, Lupiáñez DG, Beule D, Höpken UE, Leutz A, Mildner A. C/EBPβ regulates lipid metabolism and
Pparg
isoform 2 expression in alveolar macrophages. Sci Immunol 2022; 7:eabj0140. [DOI: 10.1126/sciimmunol.abj0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pulmonary alveolar proteinosis (PAP) is a syndrome characterized by accumulation of surfactant lipoproteins within the lung alveoli. Alveolar macrophages (AMs) are crucial for surfactant clearance, and their differentiation depends on colony-stimulating factor 2 (CSF2), which regulates the establishment of an AM-characteristic gene regulatory network. Here, we report that the transcription factor CCAAT/enhancer binding protein β (C/EBPβ) is essential for the development of the AM identity, as demonstrated by transcriptome and chromatin accessibility analysis. Furthermore, C/EBPβ-deficient AMs showed severe defects in proliferation, phagocytosis, and lipid metabolism, collectively resulting in a PAP-like syndrome. Mechanistically, the long C/EBPβ protein variants LAP* and LAP together with CSF2 signaling induced the expression of
Pparg
isoform 2 but not
Pparg
isoform 1, a molecular regulatory mechanism that was also observed in other CSF2-primed macrophages. These results uncover C/EBPβ as a key regulator of AM cell fate and shed light on the molecular networks controlling lipid metabolism in macrophages.
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Affiliation(s)
- Dorothea Dörr
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - January Mikolaj Weiner
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karin Zimmermann
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Chiara Anania
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetics and Sex Development Group, Berlin, Germany
| | - Lisa Katharina Wagner
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Ekaterini Maria Lyras
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Valeriia Sapozhnikova
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - David Lara-Astiaso
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Roland Lang
- Institute of Clinical Microbiology, Immunology, and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Darío G. Lupiáñez
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetics and Sex Development Group, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Uta E. Höpken
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Achim Leutz
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Alexander Mildner
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biomedicine, Medicity University of Turku, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
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75
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Wu C, Qiu Y, Zhang R, Li X, Liang H, Wang M, Li F, Zhu M, Ye G, Liu H, Li G, Zhao L. Association of peripheral basophils with tumor M2 macrophage infiltration and outcomes of the anti-PD-1 inhibitor plus chemotherapy combination in advanced gastric cancer. J Transl Med 2022; 20:386. [PMID: 36058929 PMCID: PMC9441040 DOI: 10.1186/s12967-022-03598-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the anti-programmed death-1 (PD-1) inhibitor plus chemotherapy combination has been approved as the standard first-line treatment for advanced gastric cancer, a proportion of patients do not significantly benefit from this therapy. Who would respond poorly to this treatment and the underlying mechanisms of treatment failure are far from clear. METHODS We retrospectively analyzed the associations between the peripheral basophils at baseline and clinical outcomes in 63 advanced gastric cancer patients treated with anti-PD-1 plus chemotherapy and 54 patients treated with chemotherapy alone. Immunohistochemistry and immunofluorescence staining in gastric cancer samples were utilized to investigate the basophil-related immunophenotype. RESULTS The optimal cutoff of basophil count to distinguish responders to anti-PD-1 plus chemotherapy from non-responders was 20.0/μL. Compared with the low basophil group (≤ 20.0/μL, n = 40), the high basophil group (> 20.0/μL, n = 23) had a significantly lower objective response rate (ORR 17.4% vs. 67.5%, p = 0.0001), worse progression-free survival (median PFS 4.0 vs. 15.0 months, p = 0.0003), and worse overall survival (median OS not reached, p = 0.027). Multivariate analyses identified a basophil count of > 20.0/μL as an independent risk factor for a worse ORR (OR 0.040, 95% CI 0.007-0.241, p = 0.0004), worse PFS (HR 3.720, 95% CI 1.823-7.594, p = 0.0003) and worse OS (HR 3.427, 95% CI 1.698-6.917, p = 0.001). In contrast, there was no significant association between peripheral basophil counts and tumor response or survival in the chemotherapy-alone group (p > 0.05). In primary gastric cancer samples, we observed a correlation between higher peripheral basophil counts and the accumulation of tumor-infiltrating basophils (r = 0.6833, p = 0.005). Tumor-infiltrating basophils were found to be spatially proximate to M2 macrophages within TME and positively correlated with tumor M2 macrophage infiltration (r = 0.7234, p = 0.0023). The peripheral basophil counts also had a significant positive correlation with tumor-infiltrating M2 macrophage counts (r = 0.6584, p = 0.003). Further validation in tumor samples treated with the neoadjuvant anti-PD-1 inhibitor plus chemotherapy combination suggests that the peripheral basophils, tumor infiltration of basophils, and M2 macrophages were significantly more abundant in non-responders than in responders (p = 0.0333, p = 0.0007, and p = 0.0066, respectively). CONCLUSIONS The peripheral basophil count was observed to be a potential biomarker of anti-PD-1 efficacy for advanced gastric cancer. Moreover, basophils may induce an immune-evasive tumor microenvironment by increasing M2 macrophage infiltration, which could be a potential immunotherapeutic target for advanced gastric cancer.
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Affiliation(s)
- Chaorui Wu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yaopeng Qiu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Renyi Zhang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Xiaoqing Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Huayuan Liang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Minghao Wang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Fengping Li
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Mansheng Zhu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Gengtai Ye
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Hao Liu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Guoxin Li
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Liying Zhao
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
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76
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Bergmann C, Poli A, Agache I, Bianchini R, Bax HJ, Castells M, Crescioli S, Dombrowicz D, Ferastraoaru D, Fiebiger E, Gould HJ, Hartmann K, Izquierdo E, Jordakieva G, Josephs DH, Jutel M, Levi‐Schaffer F, de las Vecillas L, Lotze MT, Osborn G, Pascal M, Redegeld F, Rosenstreich D, Roth‐Walter F, Schmidt‐Weber C, Shamji M, Steveling EH, Turner MC, Untersmayr E, Jensen‐Jarolim E, Karagiannis SN. AllergoOncology: Danger signals in allergology and oncology: A European Academy of Allergy and Clinical Immunology (EAACI) Position Paper. Allergy 2022; 77:2594-2617. [PMID: 35152450 PMCID: PMC9545837 DOI: 10.1111/all.15255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023]
Abstract
The immune system interacts with many nominal 'danger' signals, endogenous danger-associated (DAMP), exogenous pathogen (PAMP) and allergen (AAMP)-associated molecular patterns. The immune context under which these are received can promote or prevent immune activating or inflammatory mechanisms and may orchestrate diverse immune responses in allergy and cancer. Each can act either by favouring a respective pathology or by supporting the immune response to confer protective effects, depending on acuity or chronicity. In this Position Paper under the collective term danger signals or DAMPs, PAMPs and AAMPs, we consider their diverse roles in allergy and cancer and the connection between these in AllergoOncology. We focus on their interactions with different immune cells of the innate and adaptive immune system and how these promote immune responses with juxtaposing clinical outcomes in allergy and cancer. While danger signals present potential targets to overcome inflammatory responses in allergy, these may be reconsidered in relation to a history of allergy, chronic inflammation and autoimmunity linked to the risk of developing cancer, and with regard to clinical responses to anti-cancer immune and targeted therapies. Cross-disciplinary insights in AllergoOncology derived from dissecting clinical phenotypes of common danger signal pathways may improve allergy and cancer clinical outcomes.
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Affiliation(s)
- Christoph Bergmann
- Department of OtorhinolaryngologyRKM740 Interdisciplinary ClinicsDüsseldorfGermany
| | - Aurélie Poli
- Neuro‐Immunology GroupDepartment of OncologyLuxembourg Institute of HealthLuxembourgLuxembourg
| | - Ioana Agache
- Faculty of MedicineTransylania University BrasovBrasovRomania
| | - Rodolfo Bianchini
- Comparative MedicineThe Interuniversity Messerli Research InstituteUniversity of Veterinary Medicine ViennaMedical University of ViennaUniversity of ViennaViennaAustria
| | - Heather J. Bax
- St. John's Institute of DermatologySchool of Basic & Medical BiosciencesGuy's Hospital, King's College LondonLondonUnited Kindgom,School of Cancer and Pharmaceutical SciencesGuy's Hospital, King's College LondonLondonUnited Kingdom
| | - Mariana Castells
- Division of Allergy and Clinical Immunology, Department of MedicineBrigham and Women's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Silvia Crescioli
- St. John's Institute of DermatologySchool of Basic & Medical BiosciencesGuy's Hospital, King's College LondonLondonUnited Kindgom
| | - David Dombrowicz
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1011‐EGIDLilleFrance
| | - Denisa Ferastraoaru
- Department of Internal Medicine/Allergy and Immunology, Montefiore Medical CenterAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Edda Fiebiger
- Division of Gastroenterology, Hepatology and Nutrition Research, Department of Medicine ResearchChildren's University Hospital BostonBostonMassachusettsUSA
| | - Hannah J. Gould
- Randall Centre for Cell and Molecular Biophysics, School of Basic & Medical BiosciencesKing's College London, New Hunt's HouseLondonUnited Kingdom,Medical Research Council & Asthma UK Centre in Allergic Mechanisms of AsthmaLondonUnited Kingdom
| | - Karin Hartmann
- Department of DermatologyUniversity of BaselBaselSwitzerland
| | - Elena Izquierdo
- IMMA, School of Medicine, Institute of Applied Molecular MedicineCEU San Pablo UniversityMadridSpain
| | - Galateja Jordakieva
- Department of Physical Medicine, Rehabilitation and Occupational MedicineMedical University of ViennaViennaAustria
| | - Debra H. Josephs
- St. John's Institute of DermatologySchool of Basic & Medical BiosciencesGuy's Hospital, King's College LondonLondonUnited Kindgom,School of Cancer and Pharmaceutical SciencesGuy's Hospital, King's College LondonLondonUnited Kingdom
| | - Marek Jutel
- Department of Clinical ImmunologyWroclaw Medical UniversityWroclawPoland,ALL‐MED Medical Research InstituteWroclawPoland
| | - Francesca Levi‐Schaffer
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Faculty of MedicineThe Institute for Drug Research, The Hebrew University of JerusalemJerusalemIsrael
| | | | - Michael T. Lotze
- G.27A Hillman Cancer CenterUniversity of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Gabriel Osborn
- St. John's Institute of DermatologySchool of Basic & Medical BiosciencesGuy's Hospital, King's College LondonLondonUnited Kindgom
| | - Mariona Pascal
- Department of Immunology, CDB, Hospital Clinic de BarcelonaInstitut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de BarcelonaBarcelonaSpain
| | - Frank Redegeld
- Division of Pharmacology, Faculty of ScienceUtrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtThe Netherlands
| | - David Rosenstreich
- Department of Internal Medicine/Allergy and Immunology, Montefiore Medical CenterAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Franziska Roth‐Walter
- Comparative MedicineThe Interuniversity Messerli Research InstituteUniversity of Veterinary Medicine ViennaMedical University of ViennaUniversity of ViennaViennaAustria,Center of Pathophysiology, Infectiology and ImmunologyInstitute of Pathophysiology and Allergy Research, Medical University ViennaViennaAustria
| | - Carsten Schmidt‐Weber
- Center of Allergy & Environment (ZAUM)Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental HealthMunichGermany,German Center for Lung Research (DZL)MunichGermany
| | - Mohamed Shamji
- Immunomodulation and Tolerance Group, Imperial College London, and Allergy and Clinical ImmunologyImperial College LondonLondonUnited Kingdom
| | | | | | - Eva Untersmayr
- Center of Pathophysiology, Infectiology and ImmunologyInstitute of Pathophysiology and Allergy Research, Medical University ViennaViennaAustria
| | - Erika Jensen‐Jarolim
- Comparative MedicineThe Interuniversity Messerli Research InstituteUniversity of Veterinary Medicine ViennaMedical University of ViennaUniversity of ViennaViennaAustria,Center of Pathophysiology, Infectiology and ImmunologyInstitute of Pathophysiology and Allergy Research, Medical University ViennaViennaAustria
| | - Sophia N. Karagiannis
- St. John's Institute of DermatologySchool of Basic & Medical BiosciencesGuy's Hospital, King's College LondonLondonUnited Kindgom,Breast Cancer Now Research UnitSchool of Cancer and Pharmaceutical Sciences, King's College London, Guy's Hospital,LondonSE1 9RTUnited Kindgom
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77
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Song Z, Wang T, Wu Y, Fan M, Wu H. dsCellNet: A new computational tool to infer cell-cell communication networks in the developing and aging brain. Comput Struct Biotechnol J 2022; 20:4072-4081. [PMID: 35983234 PMCID: PMC9364093 DOI: 10.1016/j.csbj.2022.07.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022] Open
Abstract
Cell-cell interactions mediated by ligand-receptor complexes are critical to coordinating organismal development and functions. Majority of studies focus on the key time point, the mediator cell types or the critical genes during organismal development or diseases. However, most existing methods are specifically designed for stationary paired samples, there hasn't been a repository to deal with inferring cell-cell communications in developmental series RNA-seq data, which usually contains multiple developmental stages. Here we present a cell-cell interaction networks inference method and its application for developmental series RNA-seq data (termed dsCellNet) from the developing and aging brain. dsCellNet is implemented as an open-access R package on GitHub. It identifies interactions according to protein localizations and reinforces them via dynamic time warping within each time point and between adjacent time points, respectively. Then, fuzzy clustering of those interactions helps us refine key time points and connections. Compared to other published methods, our methods display high accuracy and high tolerance based on both simulated data and real data. Moreover, our methods can help identify the most active cell type and genes, which may provide a powerful tool to uncover the mechanisms underlying the organismal development and disease.
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Affiliation(s)
- Zhihong Song
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Ting Wang
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Yan Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Ming Fan
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China.,School of Information Science & Engineering, Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Haitao Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China.,Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu Province, China.,Chinese Institute for Brain Research, 102206 Beijing, China
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78
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Yi L, Yang L. Stem-like T cells and niches: Implications in human health and disease. Front Immunol 2022; 13:907172. [PMID: 36059484 PMCID: PMC9428355 DOI: 10.3389/fimmu.2022.907172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, accumulating evidence has elucidated the important role of T cells with stem-like characteristics in long-term maintenance of T cell responses and better patient outcomes after immunotherapy. The fate of TSL cells has been correlated with many physiological and pathological human processes. In this review, we described present advances demonstrating that stem-like T (TSL) cells are central players in human health and disease. We interpreted the evolutionary characteristics, mechanism and functions of TSL cells. Moreover, we discuss the import role of distinct niches and how they affect the stemness of TSL cells. Furthermore, we also outlined currently available strategies to generate TSL cells and associated affecting factors. Moreover, we summarized implication of TSL cells in therapies in two areas: stemness enhancement for vaccines, ICB, and adoptive T cell therapies, and stemness disruption for autoimmune disorders.
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79
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Hu X, Zhou X. Impact of single-cell RNA sequencing on understanding immune regulation. J Cell Mol Med 2022; 26:4645-4657. [PMID: 35906816 PMCID: PMC9443940 DOI: 10.1111/jcmm.17493] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 02/05/2023] Open
Abstract
Single‐cell RNA sequencing (scRNA‐seq), one of the most powerful technologies, can describe the transcriptomic heterogeneity of single cells and reveal previously unreported cell types or states in complex tissues. With the rapid development of scRNA‐seq, it has renewed our view of cellular heterogeneity and its significance for deeply understanding cell development and function. There are a large number of studies applying scRNA‐seq to investigate the heterogeneity of immune cells and disease pathogenesis, focusing on differences among every individual cell, which have provided novel inspiration for disease therapy and biological processes. In this review, we describe the development of scRNA‐seq and its application in immune‐related physiological states, regulatory mechanisms and diseases. In addition, we further discuss the opportunities and challenges of scRNA‐seq in immune regulation.
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Affiliation(s)
- Xueli Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Chengdu, China
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80
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Ma L, Ye Y, Lu H, Xing Y, Zhao Z, Quan C, Jia Z, Lu Y, Li Y, Zhou G. A Study on the Radiosensitivity of Radiation-Induced Lung Injury at the Acute Phase Based on Single-Cell Transcriptomics. Front Immunol 2022; 13:941976. [PMID: 35967301 PMCID: PMC9364823 DOI: 10.3389/fimmu.2022.941976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background and Aims Radiation-induced lung injury (RILI) is the most common complication associated with chest tumors, such as lung and breast cancers, after radiotherapy; however, the pathogenic mechanisms are unclear. Single-cell RNA sequencing has laid the foundation for studying RILI at the cellular microenvironmental level. This study focused on changes during the acute pneumonitis stage of RILI at the cellular microenvironmental level and investigated the interactions between different cell types. Methods An acute RILI model in mice and a single-cell transcriptional library were established. Intercellular communication networks were constructed to study the heterogeneity and intercellular interactions among different cell types. Results A single-cell transcriptome map was established in a mouse model of acute lung injury. In total, 18,500 single-cell transcripts were generated, and 10 major cell types were identified. The heterogeneity and radiosensitivity of each cell type or subtype in the lung tissues during the acute stage were revealed. It was found that immune cells had higher radiosensitivity than stromal cells. Immune cells were highly heterogeneous in terms of radiosensitivity, while some immune cells had the characteristics of radiation resistance. Two groups of radiation-induced Cd8+Mki67+ T cells and Cd4+Cxcr6+ helper T cells were identified. The presence of these cells was verified using immunofluorescence. The ligand-receptor interactions were analyzed by constructing intercellular communication networks. These explained the origins of the cells and revealed that they had been recruited from endothelial cells to the inflammatory site. Conclusions This study revealed the heterogeneity of in vivo radiosensitivity of different cell types in the lung at the initial stage post irradiation
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Affiliation(s)
- Luyu Ma
- Beijing Institute of Radiation Medicine, Beijing, China
- Department of Rehabilitation Medicine, Eighth Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Yumeng Ye
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Hao Lu
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuan Xing
- The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Zhen Zhao
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Cheng Quan
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Zhaoqian Jia
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Yiming Lu
- Beijing Institute of Radiation Medicine, Beijing, China
- *Correspondence: Gangqiao Zhou, ; Yang Li, ; Yiming Lu,
| | - Yang Li
- Beijing Institute of Radiation Medicine, Beijing, China
- Department of Pharmacy, Academy of Life Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Gangqiao Zhou, ; Yang Li, ; Yiming Lu,
| | - Gangqiao Zhou
- Beijing Institute of Radiation Medicine, Beijing, China
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Gangqiao Zhou, ; Yang Li, ; Yiming Lu,
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81
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Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.04.479209. [PMID: 35169794 PMCID: PMC8845414 DOI: 10.1101/2022.02.04.479209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Inference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin â€" a flexible and scalable framework for comparative analysis of CCC at single-cell resolution. We leverage multiple published datasets to show that Scriabin recovers expected CCC edges and use spatial transcriptomic data, genetic perturbation screens, and direct experimental manipulation of receptor-ligand interactions to validate that the recovered edges are biologically meaningful. We then apply Scriabin to uncover co-expressed programs of CCC from atlas-scale datasets, validating known communication pathways required for maintaining the intestinal stem cell niche and revealing species-specific communication pathways. Finally, we utilize single-cell communication networks calculated using Scriabin to follow communication pathways that operate between timepoints in longitudinal datasets, highlighting bystander cells as important initiators of inflammatory reactions in acute SARS-CoV-2 infection. Our approach represents a broadly applicable strategy to leverage single-cell resolution data maximally toward uncovering CCC circuitry and rich niche-phenotype relationships in health and disease.
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82
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Furlong-Silva J, Cook PC. Fungal-mediated lung allergic airway disease: The critical role of macrophages and dendritic cells. PLoS Pathog 2022; 18:e1010608. [PMID: 35834490 PMCID: PMC9282651 DOI: 10.1371/journal.ppat.1010608] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Fungi are abundant in the environment, causing our lungs to be constantly exposed to a diverse range of species. While the majority of these are cleared effectively in healthy individuals, constant exposure to spores (especially Aspergillus spp.) can lead to the development of allergic inflammation that underpins and worsen diseases such as asthma. Despite this, the precise mechanisms that underpin the development of fungal allergic disease are poorly understood. Innate immune cells, such as macrophages (MΦs) and dendritic cells (DCs), have been shown to be critical for mediating allergic inflammation to a range of different allergens. This review will focus on the crucial role of MΦ and DCs in mediating antifungal immunity, evaluating how these immune cells mediate allergic inflammation within the context of the lung environment. Ultimately, we aim to highlight important future research questions that will lead to novel therapeutic strategies for fungal allergic diseases.
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Affiliation(s)
- Julio Furlong-Silva
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Peter Charles Cook
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- * E-mail:
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83
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Zhu J, Yan M, Yan H, Xu L, Jiang Z, Liao G, Zhou Y, Liu W, Liang X, Li X, Xiao Y, Zhang Y. Single-Cell Transcriptomic Analysis Reveals the Crosstalk Propensity Between the Tumor Intermediate State and the CD8+ T Exhausted State to be Associated with Clinical Benefits in Melanoma. Front Immunol 2022; 13:766852. [PMID: 35903095 PMCID: PMC9314667 DOI: 10.3389/fimmu.2022.766852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous crosstalk between tumor cells and CD8+ T cells leads to substantial variation in clinical benefits from immunotherapy in melanoma. Due to spatial distribution and functional state heterogeneity, it is still unknown whether there is a crosstalk propensity between tumor cells and CD8+ T cells in melanoma, and how this crosstalk propensity affects the clinical outcome of patients. Using public single-cell transcriptome data, extensive heterogeneous functional states and ligand–receptor interactions of tumor cells and CD8+ T cells were revealed in melanoma. Furthermore, based on the association between cell–cell communication intensity and cell state activity in a single cell, we identified a crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state. This crosstalk propensity was further verified by pseudo-spatial proximity, spatial co-location, and the intra/intercellular signal transduction network. At the sample level, the tumor intermediate state and the CD8+ T exhausted state synergistically indicated better prognosis and both reduced in immunotherapy-resistant samples. The risk groups defined based on these two cell states could comprehensively reflect tumor genomic mutations and anti-tumor immunity information. The low-risk group had a higher BRAF mutation fraction as well as stronger antitumor immune response. Our findings highlighted the crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state, which may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for new therapeutic strategies.
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Affiliation(s)
- Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
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84
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Peng G, Fadeel B. Understanding the bidirectional interactions between two-dimensional materials, microorganisms, and the immune system. Adv Drug Deliv Rev 2022; 188:114422. [PMID: 35810883 DOI: 10.1016/j.addr.2022.114422] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 07/04/2022] [Indexed: 12/11/2022]
Abstract
Two-dimensional (2D) materials such as the graphene-based materials, transition metal dichalcogenides, transition metal carbides and nitrides (MXenes), black phosphorus, hexagonal boron nitride, and others have attracted considerable attention due to their unique physicochemical properties. This is true not least in the field of medicine. Understanding the interactions between 2D materials and the immune system is therefore of paramount importance. Furthermore, emerging evidence suggests that 2D materials may interact with microorganisms - pathogens as well as commensal bacteria that dwell in and on our body. We discuss the interplay between 2D materials, the immune system, and the microbial world in order to bring a systems perspective to bear on the biological interactions of 2D materials. The use of 2D materials as vectors for drug delivery and as immune adjuvants in tumor vaccines, and 2D materials to counteract inflammation and promote tissue regeneration, are explored. The bio-corona formation on and biodegradation of 2D materials, and the reciprocal interactions between 2D materials and microorganisms, are also highlighted. Finally, we consider the future challenges pertaining to the biomedical applications of various classes of 2D materials.
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Affiliation(s)
- Guotao Peng
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Bengt Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
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85
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Shichino S, Ueha S, Hashimoto S, Ogawa T, Aoki H, Wu B, Chen CY, Kitabatake M, Ouji-Sageshima N, Sawabata N, Kawaguchi T, Okayama T, Sugihara E, Hontsu S, Ito T, Iwata Y, Wada T, Ikeo K, Sato TA, Matsushima K. TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq. Commun Biol 2022; 5:602. [PMID: 35760847 PMCID: PMC9245575 DOI: 10.1038/s42003-022-03536-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/27/2022] [Indexed: 12/22/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data. However, droplet- and plate-based scRNA-seq techniques have cell sampling bias that could affect the cell composition of scRNA-seq datasets. Here we developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform. TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell-cell interactions and expression of growth factors/interleukins in cell subsets than 10X Chromium v2 and Smart-seq2. Expanding TAS-Seq application will improve understanding and atlas construction of lung biology at the single-cell level.
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Affiliation(s)
- Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shinichi Hashimoto
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Tatsuro Ogawa
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Hiroyasu Aoki
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Bin Wu
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Chang-Yu Chen
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | | | | | - Noriyoshi Sawabata
- Department of Thoracic and Cardio-Vascular Surgery, Nara Medical University, Nara, Japan
| | - Takeshi Kawaguchi
- Department of Thoracic and Cardio-Vascular Surgery, Nara Medical University, Nara, Japan
| | | | - Eiji Sugihara
- Research and Development Center for Precision Medicine, University of Tsukuba, Ibaragi, Japan
- Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University, Aichi, Japan
| | - Shigeto Hontsu
- Department of Respiratory Medicine, Nara Medical University, Nara, Japan
| | - Toshihiro Ito
- Department of Immunology, Nara Medical University, Nara, Japan
| | - Yasunori Iwata
- Division of Infection Control, Kanazawa University Hospital, Department of Nephrology and Laboratory Medicine, Kanazawa University, Ishikawa, Japan
| | - Takashi Wada
- Division of Infection Control, Kanazawa University Hospital, Department of Nephrology and Laboratory Medicine, Kanazawa University, Ishikawa, Japan
| | - Kazuho Ikeo
- National Institute of Genetics, Shizuoka, Japan
| | - Taka-Aki Sato
- Research and Development Center for Precision Medicine, University of Tsukuba, Ibaragi, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan.
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86
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Zhang R, Chen S, Chen L, Ye L, Jiang Y, Peng H, Guo Z, Li M, Jiang X, Guo P, Yu D, Zhang R, Niu Y, Zhuang Y, Aschner M, Zheng Y, Li D, Chen W. Single-cell transcriptomics reveals immune dysregulation mediated by IL-17A in initiation of chronic lung injuries upon real-ambient particulate matter exposure. Part Fibre Toxicol 2022; 19:42. [PMID: 35739565 PMCID: PMC9219231 DOI: 10.1186/s12989-022-00483-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background Long-term exposure to fine particulate matter (PM2.5) increases susceptibility to chronic respiratory diseases, including inflammation and interstitial fibrosis. However, the regulatory mechanisms by which the immune response mediates the initiation of pulmonary fibrosis has yet to be fully characterized. This study aimed to illustrate the interplay between different cell clusters and key pathways in triggering chronic lung injuries in mice following PM exposure. Results Six-week-old C57BL/6J male mice were exposed to PM or filtered air for 16 weeks in a real-ambient PM exposure system in Shijiazhuang, China. The transcriptional profiles of whole lung cells following sub-chronic PM exposure were characterized by analysis of single-cell transcriptomics. The IL-17A knockout (IL-17A−/−) mouse model was utilized to determine whether the IL-17 signaling pathway mediated immune dysregulation in PM-induced chronic lung injuries. After 16-week PM exposure, chronic lung injuries with excessive collagen deposition and increased fibroblasts, neutrophils, and monocytes were noted concurrent with a decreased number of major classes of immune cells. Single-cell analysis showed that activation of the IL-17 signaling pathway was involved in the progression of pulmonary fibrosis upon sub-chronic PM exposure. Depletion of IL-17A led to significant decline in chronic lung injuries, which was mainly triggered by reduced recruitment of myeloid-derived suppressor cells (MDSCs) and downregulation of TGF-β. Conclusion These novel findings demonstrate that immunosuppression via the IL-17A pathway plays a critical role in the initiation of chronic lung injuries upon sub-chronic PM exposure. Supplementary Information The online version contains supplementary material available at 10.1186/s12989-022-00483-w.
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Affiliation(s)
- Rui Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lizhu Ye
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yue Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hui Peng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zhanyu Guo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Miao Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinhang Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ping Guo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Dianke Yu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, 266021, China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yujie Niu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yuan Zhuang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Yuxin Zheng
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, 266021, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China.
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87
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Poto R, Quinti I, Marone G, Taglialatela M, de Paulis A, Casolaro V, Varricchi G. IgG Autoantibodies Against IgE from Atopic Dermatitis Can Induce the Release of Cytokines and Proinflammatory Mediators from Basophils and Mast Cells. Front Immunol 2022; 13:880412. [PMID: 35711458 PMCID: PMC9192953 DOI: 10.3389/fimmu.2022.880412] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/27/2022] [Indexed: 12/18/2022] Open
Abstract
IgE-mediated release of proinflammatory mediators and cytokines from basophils and mast cells is a central event in allergic disorders. Several groups of investigators have demonstrated the presence of autoantibodies against IgE and/or FcεRI in patients with chronic spontaneous urticaria. By contrast, the prevalence and functional activity of anti-IgE autoantibodies in atopic dermatitis (AD) are largely unknown. We evaluated the ability of IgG anti-IgE from patients with AD to induce the in vitro IgE-dependent activation of human basophils and skin and lung mast cells. Different preparations of IgG anti-IgE purified from patients with AD and rabbit IgG anti-IgE were compared for their triggering effects on the in vitro release of histamine and type 2 cytokines (IL-4, IL-13) from basophils and of histamine and lipid mediators (prostaglandin D2 and cysteinyl leukotriene C4) from human skin and lung mast cells. One preparation of human IgG anti-IgE out of six patients with AD induced histamine release from basophils, skin and lung mast cells. This preparation of human IgG anti-IgE induced the secretion of cytokines and eicosanoids from basophils and mast cells, respectively. Human monoclonal IgE was a competitive antagonist of both human and rabbit IgG anti-IgE. Human anti-IgE was more potent than rabbit anti-IgE for IL-4 and IL-13 production by basophils and histamine, prostaglandin D2 and leukotriene C4 release from mast cells. Functional anti-IgE autoantibodies rarely occur in patients with AD. When present, they induce the release of proinflammatory mediators and cytokines from basophils and mast cells, thereby possibly contributing to sustained IgE-dependent inflammation in at least a subset of patients with this disorder.
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Affiliation(s)
- Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,World Allergy Organization (WAO) Center of Excellence, Naples, Italy
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,World Allergy Organization (WAO) Center of Excellence, Naples, Italy.,Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples, Italy
| | | | - Amato de Paulis
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,World Allergy Organization (WAO) Center of Excellence, Naples, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,World Allergy Organization (WAO) Center of Excellence, Naples, Italy.,Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples, Italy
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88
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DJ-1 governs airway progenitor cell/eosinophil interactions to promote allergic inflammation. J Allergy Clin Immunol 2022; 150:1178-1193.e13. [PMID: 35724763 DOI: 10.1016/j.jaci.2022.03.036] [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: 09/29/2021] [Revised: 03/09/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND DJ-1 is an antioxidant protein known to regulate mast cell mediated allergic response, but its role in airway eosinophilic interactions and allergic inflammation is not known. OBJECTIVE The aim of this study was to investigate the role of DJ-1 in airway eosinophilic inflammation in vitro and in vivo. METHODS Ovalbumin-induced airway allergic inflammation was established in mice. ELISA was adopted to analyze DJ-1 and cytokine levels in mouse bronchoalveolar lavage fluid. Transcriptional profiling of mouse lung tissues was conducted by single-cell RNA sequencing technology. The role of DJ-1 in the differentiation of airway progenitor cells into goblet cells was examined by organoid cultures, immunofluorescence staining, quantitative PCR, and cell transplantation in normal, DJ-1 knockout (KO), or conditional DJ-1 KO mice. RESULTS We observed that DJ-1 was increased in the lung tissues of ovalbumin-sensitized and challenged mice. DJ-1 KO mice exhibited reduced airway eosinophil infiltration and goblet cell differentiation. Mechanistically, we discovered that eosinophil-club cell interactions are reduced in the absence of DJ-1. Organoid cultures indicated that eosinophils impair the proliferative potential of club cells. Intratracheal transplantation of DJ-1-deficient eosinophils suppresses airway goblet cell differentiation. Loss of DJ-1 inhibits the metabolism of arachidonic acid into cysteinyl leukotrienes in eosinophils while these secreted metabolites promote airway goblet cell fate in organoid cultures and in vivo. CONCLUSION DJ-1-mediated interactions between airway epithelial progenitor cells and immune cells are essential in controlling airway goblet cell metaplasia and eosinophilia. Blockade of the DJ-1 pathway is protective against airway allergic inflammation.
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89
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Doke T, Abedini A, Aldridge DL, Yang YW, Park J, Hernandez CM, Balzer MS, Shrestra R, Coppock G, Rico JMI, Han SY, Kim J, Xin S, Piliponsky AM, Angelozzi M, Lefebvre V, Siracusa MC, Hunter CA, Susztak K. Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nat Immunol 2022; 23:947-959. [PMID: 35552540 DOI: 10.1038/s41590-022-01200-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/01/2022] [Indexed: 02/06/2023]
Abstract
Inflammation is an important component of fibrosis but immune processes that orchestrate kidney fibrosis are not well understood. Here we apply single-cell sequencing to a mouse model of kidney fibrosis. We identify a subset of kidney tubule cells with a profibrotic-inflammatory phenotype characterized by the expression of cytokines and chemokines associated with immune cell recruitment. Receptor-ligand interaction analysis and experimental validation indicate that CXCL1 secreted by profibrotic tubules recruits CXCR2+ basophils. In mice, these basophils are an important source of interleukin-6 and recruitment of the TH17 subset of helper T cells. Genetic deletion or antibody-based depletion of basophils results in reduced renal fibrosis. Human kidney single-cell, bulk gene expression and immunostaining validate a function for basophils in patients with kidney fibrosis. Collectively, these studies identify basophils as contributors to the development of renal fibrosis and suggest that targeting these cells might be a useful clinical strategy to manage chronic kidney disease.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel L Aldridge
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Ya-Wen Yang
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Jihwan Park
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hernandez
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Michael S Balzer
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Rojesh Shrestra
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Gaia Coppock
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Juan M Inclan Rico
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Seung Yub Han
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sheng Xin
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Adrian M Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Marco Angelozzi
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Veronique Lefebvre
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark C Siracusa
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
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90
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Gambardella AR, Poto R, Tirelli V, Schroeder JT, Marone G, Mattei F, Varricchi G, Schiavoni G. Differential Effects of Alarmins on Human and Mouse Basophils. Front Immunol 2022; 13:894163. [PMID: 35693823 PMCID: PMC9177950 DOI: 10.3389/fimmu.2022.894163] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epithelial-derived alarmins (IL-33, TSLP, and IL-25) play an upstream role in the pathogenesis of asthma. Basophil-derived cytokines are a pivotal component of allergic inflammation. We evaluated the in vitro effects of IL-33, TSLP, and IL-25, alone and in combination with IL-3 on purified peripheral blood human basophils (hBaso) and bone marrow-derived mouse basophils (mBaso) in modulating the production of IL-4, IL-13, CXCL8 or the mouse CXCL8 equivalents CXCL1 and CXCL2. IL-3 and IL-33, but not TSLP and IL-25, concentration-dependently induced IL-4, IL-13, and CXCL8 release from hBaso. IL-3 synergistically potentiated the release of cytokines induced by IL-33 from hBaso. In mBaso, IL-3 and IL-33 rapidly induced IL-4 and IL-13 mRNA expression and protein release. IL-33, but not IL-3, induced CXCL2 and CXCL1 from mBaso. Differently from hBaso, TSLP induced IL-4, IL-13, CXCL1 and CXCL2 mRNA expression and protein release from mBaso. IL-25 had no effect on IL-4, IL-13, and CXCL1/CXCL2 mRNA expression and protein release even in the presence of IL-3. No synergism was observed between IL-3 and either IL-25 or TSLP. IL-3 inhibited both TSLP- and IL-33-induced CXCL1 and CXCL2 release from mBaso. Our results highlight some similarities and marked differences between the effects of IL-3 and alarmins on the release of cytokines from human and mouse basophils.
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Affiliation(s)
- Adriana R. Gambardella
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (ISS), Rome, Italy
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Remo Poto
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (ISS), Rome, Italy
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO) Center of Excellence, Naples, Italy
| | | | - John T. Schroeder
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO) Center of Excellence, Naples, Italy
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Fabrizio Mattei
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO) Center of Excellence, Naples, Italy
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
- *Correspondence: Gilda Varricchi, ; Giovanna Schiavoni,
| | - Giovanna Schiavoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (ISS), Rome, Italy
- *Correspondence: Gilda Varricchi, ; Giovanna Schiavoni,
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91
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA. .,Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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92
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Mamtimin M, Pinarci A, Han C, Braun A, Anders HJ, Gudermann T, Mammadova-Bach E. Extracellular DNA Traps: Origin, Function and Implications for Anti-Cancer Therapies. Front Oncol 2022; 12:869706. [PMID: 35574410 PMCID: PMC9092261 DOI: 10.3389/fonc.2022.869706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 12/16/2022] Open
Abstract
Extracellular DNA may serve as marker in liquid biopsies to determine individual diagnosis and prognosis in cancer patients. Cell death or active release from various cell types, including immune cells can result in the release of DNA into the extracellular milieu. Neutrophils are important components of the innate immune system, controlling pathogens through phagocytosis and/or the release of neutrophil extracellular traps (NETs). NETs also promote tumor progression and metastasis, by modulating angiogenesis, anti-tumor immunity, blood clotting and inflammation and providing a supportive niche for metastasizing cancer cells. Besides neutrophils, other immune cells such as eosinophils, dendritic cells, monocytes/macrophages, mast cells, basophils and lymphocytes can also form extracellular traps (ETs) during cancer progression, indicating possible multiple origins of extracellular DNA in cancer. In this review, we summarize the pathomechanisms of ET formation generated by different cell types, and analyze these processes in the context of cancer. We also critically discuss potential ET-inhibiting agents, which may open new therapeutic strategies for cancer prevention and treatment.
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Affiliation(s)
- Medina Mamtimin
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Akif Pinarci
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Chao Han
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Attila Braun
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Joachim Anders
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Thomas Gudermann
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,German Center for Lung Research, Munich, Germany
| | - Elmina Mammadova-Bach
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
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93
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Castaño N, Kim S, Martin AM, Galli SJ, Nadeau KC, Tang SKY. Exponential magnetophoretic gradient for the direct isolation of basophils from whole blood in a microfluidic system. LAB ON A CHIP 2022; 22:1690-1701. [PMID: 35438713 PMCID: PMC9080715 DOI: 10.1039/d2lc00154c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite their rarity in peripheral blood, basophils play important roles in allergic disorders and other diseases including sepsis and COVID-19. Existing basophil isolation methods require many manual steps and suffer from significant variability in purity and recovery. We report an integrated basophil isolation device (i-BID) in microfluidics for negative immunomagnetic selection of basophils directly from 100 μL of whole blood within 10 minutes. We use a simulation-driven pipeline to design a magnetic separation module to apply an exponentially increasing magnetic force to capture magnetically tagged non-basophils flowing through a microtubing sandwiched between magnetic flux concentrators sweeping across a Halbach array. The exponential profile captures non-basophils effectively while preventing their excessive initial buildup causing clogging. The i-BID isolates basophils with a mean purity of 93.9% ± 3.6% and recovery of 95.6% ± 3.4% without causing basophil degradation or unintentional activation. Our i-BID has the potential to enable basophil-based point-of-care diagnostics such as rapid allergy assessment.
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Affiliation(s)
- Nicolas Castaño
- Department of Mechanical Engineering, Stanford University, USA.
| | - Sungu Kim
- Department of Mechanical Engineering, Stanford University, USA.
| | - Adrian M Martin
- Department of Mechanical Engineering, Stanford University, USA.
| | - Stephen J Galli
- Department of Pathology, Stanford University, USA.
- Department of Microbiology and Immunology, Stanford University, USA
| | - Kari C Nadeau
- Department of Medicine and Pediatrics, with courtesy in Otolaryngology and in Population Science and Epidemiology, Stanford University, USA.
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, USA
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, USA.
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94
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Gur C, Wang SY, Sheban F, Zada M, Li B, Kharouf F, Peleg H, Aamar S, Yalin A, Kirschenbaum D, Braun-Moscovici Y, Jaitin DA, Meir-Salame T, Hagai E, Kragesteen BK, Avni B, Grisariu S, Bornstein C, Shlomi-Loubaton S, David E, Shreberk-Hassidim R, Molho-Pessach V, Amar D, Tzur T, Kuint R, Gross M, Barboy O, Moshe A, Fellus-Alyagor L, Hirsch D, Addadi Y, Erenfeld S, Biton M, Tzemach T, Elazary A, Naparstek Y, Tzemach R, Weiner A, Giladi A, Balbir-Gurman A, Amit I. LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma. Cell 2022; 185:1373-1388.e20. [PMID: 35381199 PMCID: PMC7612792 DOI: 10.1016/j.cell.2022.03.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/26/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Systemic sclerosis (scleroderma, SSc) is an incurable autoimmune disease with high morbidity and mortality rates. Here, we conducted a population-scale single-cell genomic analysis of skin and blood samples of 56 healthy controls and 97 SSc patients at different stages of the disease. We found immune compartment dysfunction only in a specific subtype of diffuse SSc patients but global dysregulation of the stromal compartment, particularly in a previously undefined subset of LGR5+-scleroderma-associated fibroblasts (ScAFs). ScAFs are perturbed morphologically and molecularly in SSc patients. Single-cell multiome profiling of stromal cells revealed ScAF-specific markers, pathways, regulatory elements, and transcription factors underlining disease development. Systematic analysis of these molecular features with clinical metadata associates specific ScAF targets with disease pathogenesis and SSc clinical traits. Our high-resolution atlas of the sclerodermatous skin spectrum will enable a paradigm shift in the understanding of SSc disease and facilitate the development of biomarkers and therapeutic strategies.
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Affiliation(s)
- Chamutal Gur
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel; Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Shuang-Yin Wang
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel.
| | - Fadi Sheban
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Mor Zada
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Fadi Kharouf
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Hagit Peleg
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Suhail Aamar
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Adam Yalin
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | | | - Yolanda Braun-Moscovici
- Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion-Israeli Institute of Technology, Haifa, Israel
| | | | - Tomer Meir-Salame
- Flow Cytometry Unit, Department of Biological Services, Weizmann Institute, Rehovot, Israel
| | - Efrat Hagai
- Flow Cytometry Unit, Department of Biological Services, Weizmann Institute, Rehovot, Israel
| | | | - Batia Avni
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Sigal Grisariu
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | | | | | - Eyal David
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Rony Shreberk-Hassidim
- Dermatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Vered Molho-Pessach
- Dermatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Dalit Amar
- Plastic Surgery Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Tomer Tzur
- Plastic Surgery Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Rottem Kuint
- Institue of Pulmonology Medicine, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Moshe Gross
- Orthopedic Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Oren Barboy
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Adi Moshe
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | | | - Dana Hirsch
- The Department of Veterinary Resources, Weizmann Institute, Rehovot, Israel
| | - Yoseph Addadi
- Life Sciences Core Facilities, Weizmann Institute, Rehovot, Israel
| | - Shlomit Erenfeld
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Moshe Biton
- Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Tehila Tzemach
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Anat Elazary
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yaakov Naparstek
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Reut Tzemach
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel; Rheumatology Institute at the Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Assaf Weiner
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Amir Giladi
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Alexandra Balbir-Gurman
- Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion-Israeli Institute of Technology, Haifa, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel.
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95
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Lao JC, Bui CB, Pang MA, Cho SX, Rudloff I, Elgass K, Schröder J, Maksimenko A, Mangan NE, Starkey MR, Skuza EM, Sun YBY, Beker F, Collins CL, Kamlin OF, König K, Malhotra A, Tan K, Theda C, Young MJ, McLean CA, Wilson NJ, Sehgal A, Hansbro PM, Pearson JT, Polo JM, Veldman A, Berger PJ, Nold-Petry CA, Nold MF. Type 2 immune polarization is associated with cardiopulmonary disease in preterm infants. Sci Transl Med 2022; 14:eaaz8454. [PMID: 35385341 DOI: 10.1126/scitranslmed.aaz8454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Postnatal maturation of the immune system is poorly understood, as is its impact on illnesses afflicting term or preterm infants, such as bronchopulmonary dysplasia (BPD) and BPD-associated pulmonary hypertension. These are both cardiopulmonary inflammatory diseases that cause substantial mortality and morbidity with high treatment costs. Here, we characterized blood samples collected from 51 preterm infants longitudinally at five time points, 20 healthy term infants at birth and age 3 to 16 weeks, and 5 healthy adults. We observed strong associations between type 2 immune polarization in circulating CD3+CD4+ T cells and cardiopulmonary illness, with odds ratios up to 24. Maternal magnesium sulfate therapy, delayed hepatitis B vaccination, and increasing fetal, but not maternal, chorioamnionitis severity were associated with attenuated type 2 polarization. Blocking type 2 mediators such as interleukin-4 (IL-4), IL-5, IL-13, or signal transducer and activator of transcription 6 (STAT6) in murine neonatal cardiopulmonary disease in vivo prevented changes in cell type composition, increases in IL-1β and IL-13, and losses of pulmonary capillaries, but not gains in larger vessels. Thereby, type 2 blockade ameliorated lung inflammation, protected alveolar and vascular integrity, and confirmed the pathological impact of type 2 cytokines and STAT6. In-depth flow cytometry and single-cell transcriptomics of mouse lungs further revealed complex associations between immune polarization and cardiopulmonary disease. Thus, this work advances knowledge on developmental immunology and its impact on early life disease and identifies multiple therapeutic approaches that may relieve inflammation-driven suffering in the youngest patients.
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Affiliation(s)
- Jason C Lao
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Christine B Bui
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Merrin A Pang
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Steven X Cho
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Ina Rudloff
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Kirstin Elgass
- Monash Micro Imaging, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Jan Schröder
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Anton Maksimenko
- Imaging and Medical Beamline, Australian Synchrotron, Melbourne, Victoria 3168, Australia
| | - Niamh E Mangan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Victoria 3168, Australia
| | - Malcolm R Starkey
- Priority Research Centres for Healthy Lungs and GrowUpWell, Hunter Medical Research Institute and University of Newcastle, Newcastle, New South Wales 2308, Australia.,Department of Immunology and Pathology, Monash University, Melbourne, Victoria 3004, Australia
| | - Elisabeth M Skuza
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Yu B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Friederike Beker
- Mater Research Institute, University of Queensland, Brisbane, Queensland 4101, Australia.,Neonatal Services, Mercy Hospital for Women, Melbourne, Victoria 3084, Australia
| | - Clare L Collins
- Neonatal Services, Mercy Hospital for Women, Melbourne, Victoria 3084, Australia
| | - Omar F Kamlin
- Department of Newborn Research, Royal Women's Hospital, Melbourne, Victoria 3052, Australia.,University of Melbourne, Melbourne, Victoria 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia
| | - Kai König
- Department of Paediatrics, Medicum Wesemlin, Lucerne 6006, Switzerland
| | - Atul Malhotra
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria 3168, Australia
| | - Kenneth Tan
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria 3168, Australia
| | - Christiane Theda
- Department of Newborn Research, Royal Women's Hospital, Melbourne, Victoria 3052, Australia.,University of Melbourne, Melbourne, Victoria 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia
| | - Morag J Young
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Catriona A McLean
- Department of Anatomical Pathology, Alfred Health, Melbourne, Victoria 3004, Australia.,Department of Medicine, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Nicholas J Wilson
- CSL Limited, Bio21 Institute, Parkville, Melbourne, Victoria 3052, Australia
| | - Arvind Sehgal
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria 3168, Australia
| | - Philip M Hansbro
- Priority Research Centres for Healthy Lungs and GrowUpWell, Hunter Medical Research Institute and University of Newcastle, Newcastle, New South Wales 2308, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Ultimo, Sydney, New South Wales 2007, Australia
| | - James T Pearson
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute and Department of Physiology, Monash University, Melbourne, Victoria 3800, Australia.,Department of Cardiac Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan.,Victorian Heart Institute, Melbourne, Victoria 3168, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, South Australia 5005, Australia.,South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alex Veldman
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Department of Pediatrics, Helios HSK, Wiesbaden 65199, Germany.,Department of Pediatric Cardiology, J. Liebig University, Gießen 35392, Germany
| | - Philip J Berger
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Claudia A Nold-Petry
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Marcel F Nold
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria 3168, Australia
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96
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Wang K, Zhao Q, Yan T, Guo D, Liu J, Wang G, Du J. The Prognostic Value of Multiple Systemic Inflammatory Biomarkers in Preoperative Patients With Non-small Cell Lung Cancer. Front Surg 2022; 9:830642. [PMID: 35445073 PMCID: PMC9013845 DOI: 10.3389/fsurg.2022.830642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
Introduction The preoperative inflammatory and nutrient status of the patient are closely correlated to the outcome of surgery-based treatment for non-small cell lung cancer (NSCLC). We aimed to investigate the prognostic value of inflammation and nutrient biomarkers in preoperative patients with non-small cell lung cancer (NSCLC) by constructing a prognostic predictive model. Methods We retrospectively studied 995 patients with NSCLC who underwent surgery in the Shandong Provincial Hospital and randomly allocated them into the training and validation group with a ratio of 7:3. We then compared their prognostic performance and conducted univariate Cox analyses with several clinicopathological variables. Based on the performance of the receiver operating characteristic (ROC) curves and decision curves analysis (DCA), the prognostic model was optimized and validated. Result The median overall overall survival (OS) of patients was 74 months. Univariate Cox analysis indicated that fifteen inflammatory biomarkers were significantly correlated with OS (p < 0.100). Multivariate Cox analysis revealed that the model incorporating grade, age, stage, basophil-to-lymphocyte ratio (BLR, ≥0.00675 vs. < 0.00675) and albumin-to-globulin ratio (AGR, ≥1.40 vs. <1.40) showed the maximum area under the curve (AUC, 0.744). The C-index in the training and validation group was 0.690 and 0.683, respectively. The 3-year integrated discrimination improvement (IDI) compared to TNM (Tumor Node Metastasis) stage was 0.035 vs. 0.011 in the training and validation group, respectively. Conclusions Lower AGR, ANRI, and higher BLR were associated with a worse outcome for patients with NSCLC. We constructed a prognostic nomogram with risk stratification based on inflammatory and nutrient biomarkers. The discrimination and calibration abilities of the model were evaluated to confirm its validity, indicating the potential utility of this prognostic model for clinical guidance.
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Affiliation(s)
- Kai Wang
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Healthcare Respiratory Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qidi Zhao
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Yan
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Deyu Guo
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jichang Liu
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guanghui Wang
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Jiajun Du
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97
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Pancheva A, Wheadon H, Rogers S, Otto TD. Using topic modeling to detect cellular crosstalk in scRNA-seq. PLoS Comput Biol 2022; 18:e1009975. [PMID: 35395014 PMCID: PMC9064087 DOI: 10.1371/journal.pcbi.1009975] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 05/03/2022] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-cell interactions are vital for numerous biological processes including development, differentiation, and response to inflammation. Currently, most methods for studying interactions on scRNA-seq level are based on curated databases of ligands and receptors. While those methods are useful, they are limited to our current biological knowledge. Recent advances in single cell protocols have allowed for physically interacting cells to be captured, and as such we have the potential to study interactions in a complemantary way without relying on prior knowledge. We introduce a new method based on Latent Dirichlet Allocation (LDA) for detecting genes that change as a result of interaction. We apply our method to synthetic datasets to demonstrate its ability to detect genes that change in an interacting population compared to a reference population. Next, we apply our approach to two datasets of physically interacting cells to identify the genes that change as a result of interaction, examples include adhesion and co-stimulatory molecules which confirm physical interaction between cells. For each dataset we produce a ranking of genes that are changing in subpopulations of the interacting cells. In addition to the genes discussed in the original publications, we highlight further candidates for interaction in the top 100 and 300 ranked genes. Lastly, we apply our method to a dataset generated by a standard droplet-based protocol not designed to capture interacting cells, and discuss its suitability for analysing interactions. We present a method that streamlines detection of interactions and does not require prior clustering and generation of synthetic reference profiles to detect changes in expression.
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Affiliation(s)
- Alexandrina Pancheva
- Institute for Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Helen Wheadon
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Thomas D. Otto
- Institute for Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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98
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Abstract
In the past decade, substantial advances have been made in understanding the biology of tumour-associated macrophages (TAMs), and their clinical relevance is emerging. A particular aspect that is becoming increasingly clear is that the interaction of TAMs with cancer cells and stromal cells in the tumour microenvironment enables and sustains most of the hallmarks of cancer. Therefore, manipulation of TAMs could enable improved disease control in a substantial fraction of patients across a large number of cancer types. In this Review, we examine the diversity of TAMs in various cancer indications and how this heterogeneity is being revisited with the advent of single-cell technologies, and then explore the current knowledge on the functional roles of different TAM states and the prognostic and predictive value of TAM-related signatures. We also review agents targeting TAMs that are currently being or will soon be tested in clinical trials, and how manipulations of TAMs can improve existing anticancer treatments. Finally, we discuss how TAM-targeting approaches could be further integrated into routine clinical practice, considering a precision oncology approach and viewing TAMs as a dynamic population that can evolve under treatment pressure.
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99
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Correia C, Weiskittel TM, Ung CY, Villasboas Bisneto JC, Billadeau DD, Kaufmann SH, Li H. Uncovering Pharmacological Opportunities for Cancer Stem Cells-A Systems Biology View. Front Cell Dev Biol 2022; 10:752326. [PMID: 35359437 PMCID: PMC8962639 DOI: 10.3389/fcell.2022.752326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer stem cells (CSCs) represent a small fraction of the total cancer cell population, yet they are thought to drive disease propagation, therapy resistance and relapse. Like healthy stem cells, CSCs possess the ability to self-renew and differentiate. These stemness phenotypes of CSCs rely on multiple molecular cues, including signaling pathways (for example, WNT, Notch and Hedgehog), cell surface molecules that interact with cellular niche components, and microenvironmental interactions with immune cells. Despite the importance of understanding CSC biology, our knowledge of how neighboring immune and tumor cell populations collectively shape CSC stemness is incomplete. Here, we provide a systems biology perspective on the crucial roles of cellular population identification and dissection of cell regulatory states. By reviewing state-of-the-art single-cell technologies, we show how innovative systems-based analysis enables a deeper understanding of the stemness of the tumor niche and the influence of intratumoral cancer cell and immune cell compositions. We also summarize strategies for refining CSC systems biology, and the potential role of this approach in the development of improved anticancer treatments. Because CSCs are amenable to cellular transitions, we envision how systems pharmacology can become a major engine for discovery of novel targets and drug candidates that can modulate state transitions for tumor cell reprogramming. Our aim is to provide deeper insights into cancer stemness from a systems perspective. We believe this approach has great potential to guide the development of more effective personalized cancer therapies that can prevent CSC-mediated relapse.
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Affiliation(s)
- Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Taylor M Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | | | - Daniel D Billadeau
- Department of Immunology, Mayo Clinic, Rochester, MN, United States,Division of Oncology Research, Mayo Clinic, Rochester, MN, United States
| | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, United States,Division of Oncology Research, Mayo Clinic, Rochester, MN, United States
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,*Correspondence: Hu Li,
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100
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Choi S, Choi J, Cheon S, Song J, Kim SY, Kim JE, Nam DH, Manzar G, Kim SM, Kang HS, Kim KK, Jeong SH, Lee JH, Park EK, Lee M, Lee HA, Kim KS, Park HJ, Oh WK, Park C, Lee CH, Kim EM. Pulmonary fibrosis model using micro-CT analyzable human PSC-derived alveolar organoids containing alveolar macrophage-like cells. Cell Biol Toxicol 2022; 38:557-575. [PMID: 35267148 PMCID: PMC8907399 DOI: 10.1007/s10565-022-09698-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/26/2022] [Indexed: 12/14/2022]
Abstract
Human lung organoids (hLOs) are useful for disease modelling and drug screening. However, a lack of immune cells in hLOs limits the recapitulation of in vivo cellular physiology. Here, we generated hLOs containing alveolar macrophage (AMφ)–like cells derived from pluripotent stem cells (PSC). To bridge hLOs with advanced human lung high-resolution X-ray computed tomography (CT), we acquired quantitative micro-CT images. Three hLO types were observed during differentiation. Among them, alveolar hLOs highly expressed not only lung epithelial cell markers but also AMφ-specific markers. Furthermore, CD68+ AMφ-like cells were spatially organized on the luminal epithelial surface of alveolar hLOs. Bleomycin-treated alveolar hLOs showed upregulated expression of fibrosis-related markers and extracellular matrix deposits in the alveolar sacs. Alveolar hLOs also showed structural alterations such as excessive tissue fraction under bleomycin treatment. Therefore, we suggest that micro-CT analyzable PSC-derived alveolar hLOs are a promising in vitro model to predict lung toxicity manifestations, including fibrosis.
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Affiliation(s)
- Seri Choi
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.,Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jiwoong Choi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, School of Medicine, University of Kansas, Kansas City, KS, 66160, USA
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jihong Song
- Department of Internal Medicine, Santa Clara Valley Medical Center, San Jose, CA, 95128, USA
| | - Seung-Yeon Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.,Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ji-Eun Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Dae-Hwan Nam
- Immune Research Institute, Seegene Medical Foundation, Seoul, 04805, Republic of Korea
| | - Gohar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77025, USA
| | - Su-Man Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyung-Sik Kang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang Hoon Jeong
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, 123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi, 15355, Republic of Korea
| | - Ju-Han Lee
- Department of Pathology, Ansan Hospital, Korea University College of Medicine, 123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi, 15355, Republic of Korea
| | - Eun-Kee Park
- Department of Medical Humanities and Social Medicine, College of Medicine, Kosin University, Busan, 49267, Republic of Korea
| | - Minseob Lee
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Hyang-Ae Lee
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Ki-Suk Kim
- R&D Center for Advanced Pharmaceuticals and Evaluation, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Han-Jin Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Won Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Chang Hyun Lee
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
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