Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
J Adv Res
2023 Jan 04;55:73-87. doi: 10.1016/j.jare.2023.02.017.
Show Gene links
Show Anatomy links
Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species.
Jiao A
,
Zhang C
,
Wang X
,
Sun L
,
Liu H
,
Su Y
,
Lei L
,
Li W
,
Ding R
,
Ding C
,
Dou M
,
Tian P
,
Sun C
,
Yang X
,
Zhang L
,
Zhang B
.
???displayArticle.abstract???
INTRODUCTION: Both innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates.
OBJECTIVES: Here, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species.
METHODS: Single-cell RNA sequencing (scRNA-seq).
RESULTS: We uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human.
CONCLUSIONS: Therefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.
Abesadze,
[Role of the spleen in regulating thrombocytopoiesis].
1978, Pubmed
Abesadze,
[Role of the spleen in regulating thrombocytopoiesis].
1978,
Pubmed
Agematsu,
Memory B cells and CD27.
2000,
Pubmed
Akira,
Pathogen recognition and innate immunity.
2006,
Pubmed
Allan,
CD1d and CD1c expression in human B cells is regulated by activation and retinoic acid receptor signaling.
2011,
Pubmed
Allard,
The ectonucleotidases CD39 and CD73: Novel checkpoint inhibitor targets.
2017,
Pubmed
Anderson,
Evolutionary origins of lymphocytes: ensembles of T cell and B cell transcriptional regulators in a cartilaginous fish.
2004,
Pubmed
Andrews,
Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity.
2022,
Pubmed
Barata,
Flip the coin: IL-7 and IL-7R in health and disease.
2019,
Pubmed
Barral,
The location of splenic NKT cells favours their rapid activation by blood-borne antigen.
2012,
Pubmed
Bixel,
Mouse CD99 participates in T-cell recruitment into inflamed skin.
2004,
Pubmed
Boehm,
Evolution of lymphoid tissues.
2012,
Pubmed
Brendolan,
Development and function of the mammalian spleen.
2007,
Pubmed
Buchmann,
Evolution of Innate Immunity: Clues from Invertebrates via Fish to Mammals.
2014,
Pubmed
Busslinger,
Transcriptional control of early B cell development.
2004,
Pubmed
Butler,
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
2018,
Pubmed
Cai,
Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig.
2023,
Pubmed
Casson,
Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens.
2015,
Pubmed
Chang,
Siglecs at the Host-Pathogen Interface.
2020,
Pubmed
Chimpanzee Sequencing and Analysis Consortium,
Initial sequence of the chimpanzee genome and comparison with the human genome.
2005,
Pubmed
Cook,
Transcription Factor Bhlhe40 in Immunity and Autoimmunity.
2020,
Pubmed
Cooper,
The evolution of adaptive immune systems.
2006,
Pubmed
Crotty,
A brief history of T cell help to B cells.
2015,
Pubmed
Flajnik,
A cold-blooded view of adaptive immunity.
2018,
Pubmed
Gao,
Novel functions of murine B1 cells: active phagocytic and microbicidal abilities.
2012,
Pubmed
Gaud,
Regulatory mechanisms in T cell receptor signalling.
2018,
Pubmed
Goitsuka,
MIST functions through distinct domains in immunoreceptor signaling in the presence and absence of LAT.
2001,
Pubmed
Gu,
Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
2016,
Pubmed
Gui,
MCL1 enhances the survival of CD8+ memory T Cells after viral infection.
2015,
Pubmed
Guilliams,
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
2022,
Pubmed
He,
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs.
2020,
Pubmed
He,
IRF-7 Is a Critical Regulator of Type 2 Innate Lymphoid Cells in Allergic Airway Inflammation.
2019,
Pubmed
Hernández,
Single-cell transcriptional analysis reveals ILC-like cells in zebrafish.
2018,
Pubmed
Hernández-Caselles,
CD33 (Siglec-3) Inhibitory Function: Role in the NKG2D/DAP10 Activating Pathway.
2019,
Pubmed
Hou,
Research progress on CD169-positive macrophages in tumors.
2021,
Pubmed
Ionescu,
Memory B Cells and Long-lived Plasma Cells.
2019,
Pubmed
Iwasaki,
Regulation of adaptive immunity by the innate immune system.
2010,
Pubmed
Jackson,
FcR-like 2 Inhibition of B cell receptor-mediated activation of B cells.
2010,
Pubmed
Johnson,
NCBI BLAST: a better web interface.
2008,
Pubmed
Kach,
A finer tuning of G-protein signaling through regulated control of RGS proteins.
2012,
Pubmed
Kang,
Efficient and precise single-cell reference atlas mapping with Symphony.
2021,
Pubmed
Kim,
CXCL16 positively correlated with M2-macrophage infiltration, enhanced angiogenesis, and poor prognosis in thyroid cancer.
2019,
Pubmed
Klein,
Sex differences in immune responses.
2016,
Pubmed
Kremlitzka,
Complement receptor type 1 (CR1, CD35) is a potent inhibitor of B-cell functions in rheumatoid arthritis patients.
2013,
Pubmed
Kumar,
Mfuzz: a software package for soft clustering of microarray data.
2007,
Pubmed
Laing,
Fish T cells: recent advances through genomics.
2011,
Pubmed
Lee,
The transcription factor KLF2 restrains CD4⁺ T follicular helper cell differentiation.
2015,
Pubmed
Lewis,
Structure and function of the immune system in the spleen.
2019,
Pubmed
Lewis Marffy,
Leukocyte Immunoglobulin-Like Receptors (LILRs) on Human Neutrophils: Modulators of Infection and Immunity.
2020,
Pubmed
Li,
The apolipoprotein multigene family: biosynthesis, structure, structure-function relationships, and evolution.
1988,
Pubmed
Li,
FCRL3 promotes TLR9-induced B-cell activation and suppresses plasma cell differentiation.
2013,
Pubmed
Li,
B lymphocytes from early vertebrates have potent phagocytic and microbicidal abilities.
2006,
Pubmed
,
Xenbase
Lugar,
Molecular characterization of circulating plasma cells in patients with active systemic lupus erythematosus.
2012,
Pubmed
Madissoon,
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
2019,
Pubmed
Marie,
A whole-genome RNAi screen uncovers a novel role for human potassium channels in cell killing by the parasite Entamoeba histolytica.
2015,
Pubmed
Masuda,
Defining the immunological phenotype of Fc receptor-like B (FCRLB) deficient mice: Confounding role of the inhibitory FcγRIIb.
2010,
Pubmed
Mebius,
Structure and function of the spleen.
2005,
Pubmed
Morelli,
Internalization of circulating apoptotic cells by splenic marginal zone dendritic cells: dependence on complement receptors and effect on cytokine production.
2003,
Pubmed
Nagashima,
Arachidonate 5-lipoxygenase establishes adaptive humoral immunity by controlling primary B cells and their cognate T-cell help.
2011,
Pubmed
Nechanitzky,
Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells.
2013,
Pubmed
Norsworthy,
Murine CD93 (C1qRp) contributes to the removal of apoptotic cells in vivo but is not required for C1q-mediated enhancement of phagocytosis.
2004,
Pubmed
Øverland,
Phagocytosis by B-cells and neutrophils in Atlantic salmon (Salmo salar L.) and Atlantic cod (Gadus morhua L.).
2010,
Pubmed
Pancer,
The evolution of adaptive immunity.
2006,
Pubmed
Parra,
Pivotal advance: peritoneal cavity B-1 B cells have phagocytic and microbicidal capacities and present phagocytosed antigen to CD4+ T cells.
2012,
Pubmed
Poholek,
IL-21 Controls ILC3 Cytokine Production and Promotes a Protective Phenotype in a Mouse Model of Colitis.
2019,
Pubmed
Polte,
Critical role for syndecan-4 in dendritic cell migration during development of allergic airway inflammation.
2015,
Pubmed
Rauta,
Immune system and immune responses in fish and their role in comparative immunity study: a model for higher organisms.
2012,
Pubmed
Rőszer,
Understanding the Mysterious M2 Macrophage through Activation Markers and Effector Mechanisms.
2015,
Pubmed
Sánchez-Martín,
The chemokine CXCL12 regulates monocyte-macrophage differentiation and RUNX3 expression.
2011,
Pubmed
Savage,
Regulatory T Cell Development.
2020,
Pubmed
Shannon,
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
2003,
Pubmed
Slyper,
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
2020,
Pubmed
Stuart,
Comprehensive Integration of Single-Cell Data.
2019,
Pubmed
Tabula Muris Consortium,
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.
2018,
Pubmed
Tang,
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.
2017,
Pubmed
Toda,
Conservation of characteristics and functions of CD4 positive lymphocytes in a teleost fish.
2011,
Pubmed
Viola,
The Metabolic Signature of Macrophage Responses.
2019,
Pubmed
von Mering,
STRING: a database of predicted functional associations between proteins.
2003,
Pubmed
Walker,
Regulatory T cells: Folate receptor 4: a new handle on regulation and memory?
2007,
Pubmed
Wang,
Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection.
2021,
Pubmed
Wentzel,
Transcriptome sequencing supports a conservation of macrophage polarization in fish.
2020,
Pubmed
Wiegertjes,
Polarization of immune responses in fish: The 'macrophages first' point of view.
2016,
Pubmed
Wu,
Recent Advances on Phagocytic B Cells in Teleost Fish.
2020,
Pubmed
Xiao,
Metabolic landscape of the tumor microenvironment at single cell resolution.
2019,
Pubmed
Yu,
clusterProfiler: an R package for comparing biological themes among gene clusters.
2012,
Pubmed
Yue,
A comparative encyclopedia of DNA elements in the mouse genome.
2014,
Pubmed
Zhang,
Chemokine CXCL16 regulates neutrophil and macrophage infiltration into injured muscle, promoting muscle regeneration.
2009,
Pubmed
Zhu,
B cells in teleost fish act as pivotal initiating APCs in priming adaptive immunity: an evolutionary perspective on the origin of the B-1 cell subset and B7 molecules.
2014,
Pubmed
Zimmerman,
Phagocytic B cells in a reptile.
2010,
Pubmed
