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Secombes CJ. Cytokines - Early vertebrate genes and evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 160:105239. [PMID: 39117166 DOI: 10.1016/j.dci.2024.105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/12/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
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Yan Y, Zhu S, Jia M, Chen X, Qi W, Gu F, Valencak TG, Liu JX, Sun HZ. Advances in single-cell transcriptomics in animal research. J Anim Sci Biotechnol 2024; 15:102. [PMID: 39090689 PMCID: PMC11295521 DOI: 10.1186/s40104-024-01063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024] Open
Abstract
Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand for high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of animal research, offering an effective method to study the gene expression of high-throughput single cells of different tissues/organs in animals. In an unprecedented manner, researchers have identified cell types/subtypes and their marker genes, inferred cellular fate trajectories, and revealed cell‒cell interactions in animals using single-cell transcriptomics. In this paper, we introduce the development of single-cell technology and review the processes, advancements, and applications of single-cell transcriptomics in animal research. We summarize recent efforts using single-cell transcriptomics to obtain a more profound understanding of animal nutrition and health, reproductive performance, genetics, and disease models in different livestock species. Moreover, the practical experience accumulated based on a large number of cases is highlighted to provide a reference for determining key factors (e.g., sample size, cell clustering, and cell type annotation) in single-cell transcriptomics analysis. We also discuss the limitations and outlook of single-cell transcriptomics in the current stage. This paper describes the comprehensive progress of single-cell transcriptomics in animal research, offering novel insights and sustainable advancements in agricultural productivity and animal health.
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Affiliation(s)
- Yunan Yan
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Senlin Zhu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Jia
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi Chen
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenlingli Qi
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengfei Gu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Teresa G Valencak
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Agency for Health and Food Safety Austria, 1220, Vienna, Austria
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
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Dubovik T, Lukačišin M, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G'Sell M, Shen-Orr SS. Interactions between immune cell types facilitate the evolution of immune traits. Nature 2024; 632:350-356. [PMID: 38866051 PMCID: PMC11306095 DOI: 10.1038/s41586-024-07661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.
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Affiliation(s)
- Tania Dubovik
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Martin Lukačišin
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Elina Starosvetsky
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Benjamin LeRoy
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Nike, Beaverton, OR, USA
| | - Rachelly Normand
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Massachusetts General Hospital, Boston, MA, USA
| | - Yasmin Admon
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Yishai Ofran
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Haematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
- Haematology and Bone Marrow Transplantation Department and the Eisenberg R&D Authority, Shaare Zedek Medical Centre, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Max G'Sell
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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Kan H, Chen Y. Revealing endogenous conditions for Peto's paradox via an ordinary differential equation model. J Math Biol 2024; 89:27. [PMID: 38970664 PMCID: PMC11227477 DOI: 10.1007/s00285-024-02123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Cancer, a disease intimately linked to cellular mutations, is commonly believed to exhibit a positive association with the cell count and lifespan of a species. Despite this assumption, the observed uniformity in cancer rates across species, referred to as the Peto's paradox, presents a conundrum. Recognizing that tumour progression is not solely dependent on cancer cells but involves intricate interactions among various cell types, this study employed a Lotka-Volterra (LV) ordinary differential equation model to analyze the evolution of cancerous cells and the cancer incidence in an immune environment. As a result, this study uncovered the sufficient conditions underlying the absence of correlation in Peto's paradox and provide insights into the reasons for the equitable distribution of cancer incidence across diverse species by applying nondimensionalization and drawing an analogy between the characteristic time interval for the variation of cell populations in the ODE model and that of cell cycles of a species.
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Affiliation(s)
- Haichun Kan
- SCS Laboratory, Department of Human and Engineered Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yu Chen
- SCS Laboratory, Department of Human and Engineered Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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Lyons A, Brown J, Davenport KM. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Curr Issues Mol Biol 2024; 46:5291-5306. [PMID: 38920988 PMCID: PMC11202421 DOI: 10.3390/cimb46060316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/27/2024] Open
Abstract
Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.
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Ramarapu R, Wulcan JM, Chang H, Moore PF, Vernau W, Keller SM. Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595010. [PMID: 38826195 PMCID: PMC11142102 DOI: 10.1101/2024.05.21.595010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Introduction The domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. Methods Peripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, alpha/beta T cell receptor transcripts and gamma/delta T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Results Unsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and gamma/delta T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis demonstrated a skewed T-cell receptor alpha gene usage and a restricted T-cell receptor gamma junctional length in CD8+ cytotoxic T cells compared to other alpha/beta T cell subsets. Among myeloid cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. Discussion Our study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.
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Affiliation(s)
- Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Judit M Wulcan
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
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Guito JC, Kirejczyk SGM, Schuh AJ, Amman BR, Sealy TK, Graziano J, Spengler JR, Harmon JR, Wozniak DM, Prescott JB, Towner JS. Coordinated inflammatory responses dictate Marburg virus control by reservoir bats. Nat Commun 2024; 15:1826. [PMID: 38418477 PMCID: PMC10902335 DOI: 10.1038/s41467-024-46226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Bats are increasingly recognized as reservoirs of emerging zoonotic pathogens. Egyptian rousette bats (ERBs) are the known reservoir of Marburg virus (MARV), a filovirus that causes deadly Marburg virus disease (MVD) in humans. However, ERBs harbor MARV asymptomatically, likely due to a coadapted and specific host immunity-pathogen relationship. Recently, we measured transcriptional responses in MARV-infected ERB whole tissues, showing that these bats possess a disease tolerant strategy that limits pro-inflammatory gene induction, presumably averting MVD-linked immunopathology. However, the host resistant strategy by which ERBs actively limit MARV burden remains elusive, which we hypothesize requires localized inflammatory responses unresolvable at bulk-tissue scale. Here, we use dexamethasone to attenuate ERB pro-inflammatory responses and assess MARV replication, shedding and disease. We show that MARV-infected ERBs naturally mount coordinated pro-inflammatory responses at liver foci of infection, comprised of recruited mononuclear phagocytes and T cells, the latter of which proliferate with likely MARV-specificity. When pro-inflammatory responses are diminished, ERBs display heightened MARV replication, oral/rectal shedding and severe MVD-like liver pathology, demonstrating that ERBs balance immunoprotective tolerance with discreet MARV-resistant pro-inflammatory responses. These data further suggest that natural ERB immunomodulatory stressors like food scarcity and habitat disruption may potentiate viral shedding, transmission and therefore outbreak risk.
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Affiliation(s)
- Jonathan C Guito
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Shannon G M Kirejczyk
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- StageBio, Mount Jackson, VA, 22842, USA
| | - Amy J Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Brian R Amman
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Tara K Sealy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - James Graziano
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jessica R Harmon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - David M Wozniak
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany
- Virology Department, Bernhard-Nocht-Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Joseph B Prescott
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany.
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
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Islam M, Behura SK. Single-Cell Transcriptional Response of the Placenta to the Ablation of Caveolin-1: Insights into the Adaptive Regulation of Brain-Placental Axis in Mice. Cells 2024; 13:215. [PMID: 38334607 PMCID: PMC10854826 DOI: 10.3390/cells13030215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Caveolin-1 (Cav1) is a major plasma membrane protein that plays important functions in cellular metabolism, proliferation, and senescence. Mice lacking Cav1 show abnormal gene expression in the fetal brain. Though evidence for placental influence on brain development is emerging, whether the ablation of Cav1 affects the regulation of the brain-placental axis remains unexamined. The current study tests the hypothesis that gene expression changes in specific cells of the placenta and the fetal brain are linked to the deregulation of the brain-placental axis in Cav1-null mice. By performing single-nuclei RNA sequencing (snRNA-seq) analyses, we show that the abundance of the extravillious trophoblast (EVT) and stromal cells, but not the cytotrophoblast (CTB) or syncytiotrophoblast (STB), are significantly impacted due to Cav1 ablation in mice. Interestingly, specific genes related to brain development and neurogenesis were significantly differentially expressed in trophoblast cells due to Cav1 deletion. Comparison of single-cell gene expression between the placenta and the fetal brain further showed that specific genes such as plexin A1 (Plxna1), phosphatase and actin regulator 1 (Phactr1) and amyloid precursor-like protein 2 (Aplp2) were differentially expressed between the EVT and STB cells of the placenta, and also, between the radial glia and ependymal cells of the fetal brain. Bulk RNA-seq analysis of the whole placenta and the fetal brain further identified genes differentially expressed in a similar manner between the placenta and the fetal brain due to the absence of Cav1. The deconvolution of reference cell types from the bulk RNA-seq data further showed that the loss of Cav1 impacted the abundance of EVT cells relative to the stromal cells in the placenta, and that of the glia cells relative to the neuronal cells in the fetal brain. Together, the results of this study suggest that the ablation of Cav1 causes deregulated gene expression in specific cell types of the placenta and the fetal brain in mice.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. BIOLOGY 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
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Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
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Quan F, Liang X, Cheng M, Yang H, Liu K, He S, Sun S, Deng M, He Y, Liu W, Wang S, Zhao S, Deng L, Hou X, Zhang X, Xiao Y. Annotation of cell types (ACT): a convenient web server for cell type annotation. Genome Med 2023; 15:91. [PMID: 37924118 PMCID: PMC10623726 DOI: 10.1186/s13073-023-01249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge. METHODS To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods. RESULTS By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT ( http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/ ), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified. CONCLUSIONS We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.
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Affiliation(s)
- Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Mingjiang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Huan Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Kun Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shengyuan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shangqin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Menglan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yanzhen He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuai Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuxiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Lantian Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xiaobo Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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11
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Yaparla A, Stern DB, Hossainey MRH, Crandall KA, Grayfer L. Amphibian myelopoiesis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 146:104701. [PMID: 37196852 DOI: 10.1016/j.dci.2023.104701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Macrophage-lineage cells are indispensable to immunity and physiology of all vertebrates. Amongst these, amphibians represent a key stage in vertebrate evolution and are facing decimating population declines and extinctions, in large part due to emerging infectious agents. While recent studies indicate that macrophages and related innate immune cells are critically involved during these infections, much remains unknown regarding the ontogeny and functional differentiation of these cell types in amphibians. Accordingly, in this review we coalesce what has been established to date about amphibian blood cell development (hematopoiesis), the development of key amphibian innate immune cells (myelopoiesis) and the differentiation of amphibian macrophage subsets (monopoiesis). We explore the current understanding of designated sites of larval and adult hematopoiesis across distinct amphibian species and consider what mechanisms may lend to these species-specific adaptations. We discern the identified molecular mechanisms governing the functional differentiation of disparate amphibian (chiefly Xenopus laevis) macrophage subsets and describe what is known about the roles of these subsets during amphibian infections with intracellular pathogens. Macrophage lineage cells are at the heart of so many vertebrate physiological processes. Thus, garnering greater understanding of the mechanisms responsible for the ontogeny and functionality of these cells in amphibians will lend to a more comprehensive view of vertebrate evolution.
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Affiliation(s)
- Amulya Yaparla
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
| | - David B Stern
- Milken Institute School of Public Health, Computational Biology Institute, George Washington University, Washington, DC, 20052, USA
| | | | - Keith A Crandall
- Milken Institute School of Public Health, Computational Biology Institute, George Washington University, Washington, DC, 20052, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA.
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