Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

Jiao, Anjun; Zhang, Cangang; Wang, Xin; Sun, Lina; Liu, Haiyan; Su, Yanhong; Lei, Lei; Li, Wenhua; Ding, Renyi; Ding, Chenguang; Dou, Meng; Tian, Peng; Sun, Chenming; Yang, Xiaofeng; Zhang, Lianjun; Zhang, Baojun

doi:10.1016/j.jare.2023.02.017

Cited by 19 publications

(15 citation statements)

References 86 publications

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“…We reasoned that experimentally driving the immune status of ERBs toward an overly immune tolerant, anti-inflammatory state in which pro-inflammatory responses are suppressed would abrogate this viral control, leading to altered cell tropism, enhanced replication and shedding, and potentially MVD-like pathology 28 , 29 , 31 , 32 . Through a novel use of the glucocorticoid (GC) drug dexamethasone (Dex) 28 , 29 , 31 in bats and state-of-the-art molecular pathology tools to target key representative, highly-conserved immune markers 33 – 35 , we show that discreet pro-inflammatory responses control MARV during ERB infection, and that these findings support the idea that immunomodulatory ecological stressor conditions could ostensibly undermine this control in wild bat populations 3 .…”

Section: Introductionmentioning

confidence: 76%

“…Second, the extent of our analysis is constrained by a lack of resources including ERB-specific reagents and availability of juvenile bats, necessitating careful selection of representative time points, tissues and immune targets known to be critical to both immune control and filovirus disease progression. And third, although the annotated cellular and molecular targets we selected for our study (e.g., CD14) are functionally conserved across many mammalian, vertebrate and even invertebrate species (e.g., evidence of active TNF and related superfamily members identified in coral, jellyfish and mollusks) [33][34][35] , with any differences in ERBs likely ascribed to their transcriptional regulation or nuanced activities rather than core response role, nascent understanding of bat immunology means caution should nevertheless be taken when drawing conclusions about putative functional similarities between ERB targets and their counterparts in longer-studied mammalian animal models.…”

Section: Discussionmentioning

confidence: 99%

“…Previous histopathological inspection of ERB tissues was limited to hematoxylin/eosin (H&E) staining and immunohistochemical (IHC) detection of MARV antigen due to a lack of ERB-compatible reagents 10,11 . To investigate ERB inflammatory responses convincingly, we examined viral tropism along with multiple relevant immune cell populations via cross-reactive antibodies or species-specific RNA probes following experimental MARV inoculation, with molecular targets selected that are functionally integral to each immune cell type and highly evolutionarily conserved across mammals and/or vertebrates [33][34][35] . To evaluate MARV-mediated immunologic and pathologic changes, ERBs were euthanized 6 days post-inoculation (DPI) at peak MARV loads typically observed in these bats, or 12DPI when MARV is largely resolved, time points established by previous ERB infection studies [9][10][11][12] .…”

Section: Erb Cellular Responses and Pathology Upon Marv Infectionmentioning

confidence: 99%

“…Given the cytokine dysregulation characteristic of MVD in filovirus spillover hosts such as humans 6,13,14,39 and the known immunomodulatory effects by GCs on cytokine signaling pathways 28,29,31 , we sought to correlate spatial expression of classical representative pro-inflammatory (tumor necrosis factor, TNF and interleukin-6, IL6) and anti-inflammatory (IL10) cytokine markers in ERB livers and spleens to suppression of pro-inflammatory responses by Dex.Indeed, these cytokines have been shown to be highly involved in dictating both inflammatory signaling and MVD onset/severity, as well as to be functionally conserved across the animal kingdom, with origins dating as far back as the Precambrian era 6,[33][34][35]39 . In uninfected IM (Dex) bats, there was a general reduction in RNA for all three cytokines compared to naïve control (Neg) bats, with TNF in particular showing reduced expression, the exception being a modest increase in IL10 in the liver (Fig.…”

Section: Cytokine Responses In Normal and Im Bat Infectionmentioning

confidence: 99%

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Coordinated inflammatory responses dictate Marburg virus control by reservoir bats

Guito,

Kirejczyk,

Schuh

et al. 2024

Nat Commun

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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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Section: Introductionmentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Erb Cellular Responses and Pathology Upon Marv Infectionmentioning

confidence: 99%

Section: Cytokine Responses In Normal and Im Bat Infectionmentioning

confidence: 99%

See 2 more Smart Citations

Coordinated inflammatory responses dictate Marburg virus control by reservoir bats

Guito,

Kirejczyk,

Schuh

et al. 2024

Nat Commun

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“…Consequently, there has been a bloom in single cell RNA-sequencing studies of the peripheral leukocytes in a variety of mammalian species including the dog, cow, horse, and pig (18)(19)(20)(21)(22). Additionally, single cell data facilitates the study of cross species variations in immune cell type and evolution of these cells (12).…”

Section: Introductionmentioning

confidence: 99%

Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes

Ramarapu,

Wulcan,

Chang

et al. 2024

Preprint

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Introduction: The domestic cat (Felis catus) is a valued companion animal and the second most popular pet (over 46.5 million US households). They are also an important model system for virally-induced cancers (feline leukemia virus) and virally-mediated immunodeficiency (feline immunodeficiency virus). However, species specific research limitations such as a lack of reagents and immune cell markers limit our ability to utilize these models to their full capacity. The goal of this study is to characterize the transcriptomic landscape of circulating feline T cells and other captured leukocytes utilizing CD5 (only available selective feline T cell marker) flow cytometry enriched single cell RNA-sequencing and V(D)J repertoire analysis in clinically healthy domestic shorthair cats between the ages of 6 months and 9 years as well as contextualize them with the leukocytes of other species. Methods: 5 mL of peripheral whole blood was collected from 4 healthy cats (6 months, 1 year, 4 years, 9 years) and were housed at the UC Davis Nutrition and Pet Care Center. Samples were enriched for T cells by flow cytometry using a mouse anti-feline CD5 monoclonal antibody. The GEX library was constructed using the Chromium Next GEM Single Cell 5′ Kit v2 (10x Genomics). The V(D)J library for all 4 T cell receptor loci was prepared using the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Sequencing was done via Illumina NovaSeq S4 and pre-processed using the Cell Ranger for alignment to the feline genome (felis_catus_9.0). Processing and downstream analyses were conducted via Seurat v5. Additional annotated datasets for cross species T cell integration were acquired from peer-reviewed literature. Results: Unsupervised clustering of GEX data revealed 7 major populations- T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved different populations of naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and γδ T cells for the first time. Cross species analysis revealed relatively high conservation of T cell subtypes 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 marked differences in CD8+ cytotoxic T cells from other alpha/beta T cell subsets including productive TRG transcript expression. Among the myeloid cells, we resolved 3 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 the subtypes of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. Additionally, we also characterize subtypes in the myeloid cells expanding our understanding of the feline immune system. We have also demonstrated species immune cell relatedness which can provide an important foundation for further translational immunology, pathogenesis, translational treatments, and species-tropism of pathogens in veterinary medicine and research.

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Recent Developments in Transcriptomic Technologies: Applications to Immunological Systems and Diseases

Andrew,

Zulcinski,

Emmett

et al. 2024

RNA Technologies

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Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

Cited by 19 publications

References 86 publications

Coordinated inflammatory responses dictate Marburg virus control by reservoir bats

Coordinated inflammatory responses dictate Marburg virus control by reservoir bats

Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes

Recent Developments in Transcriptomic Technologies: Applications to Immunological Systems and Diseases

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