Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Jiang, Mengmeng; Xiao, Yanyu; Weigao, E; Ma, Lifeng; Wang, Jingjing; Chen, Haide; Gao, Ce; Yuan, Ling; Guo, Qile; Peng, Jinrong; Han, Xiaoping; Guo, Guoji

doi:10.3389/fcell.2021.743421

Cited by 60 publications

(63 citation statements)

References 63 publications

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“…Our input of 5,000 cells per sample was well within the 10x Genomics guidelines of 500 to 10,000. Given the previously published proportion of overall somatic cells in zebrafish testes of ∼1.4% ( 39 ), there would likely be less than 30 somatic cells in our sample, which borders the cluster threshold of 30 cells; this number diminishes for specific somatic cell types such as immune cells. Additionally, we have shown scRNA-seq underdetects immune cell gene expression as compared to bulk RNA-seq, all other factors held constant ( 60 ).…”

Section: Resultsmentioning

confidence: 92%

“…The 13 datasets span five species (five human datasets ( 29–33 ); five mouse ( 32 , 34–37 ); one sheep ( 38 ); one macaque ( 33 ); one zebrafish ( 39 )), and vary widely among and between species. The relative contribution of each cell type population to the total dataset is seldom explicitly reported in the main text (of the identified studies, 23%).…”

Section: Resultsmentioning

confidence: 99%

“…Cell type-specific transcriptome dynamics in heterogeneous tissue can be undetected with methods that require analyses of pooled, presumably uniform cells. Previous scRNA-seq studies have investigated the neonatal ( 29 ) and adult ( 30–38 ) testes in mammalian species, and one other adult zebrafish testes dataset exists as part of a scRNA-seq atlas ( 39 ). We examined the adult zebrafish testes in detail from an exploratory and toxicological standpoint to characterize the baseline testicular landscape in this emerging model organism, and to understand the long-term effects of early-life exposure to an environmental contaminant.…”

Section: Introductionmentioning

confidence: 99%

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Insight into 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced disruption of zebrafish spermatogenesis via single cell RNA-seq

et al. 2022

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2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent and environmentally persistent endocrine disrupting chemical. Our previous work demonstrated the latent reproductive maladies of early-life TCDD exposure in zebrafish. Zebrafish acutely exposed to low, environmentally relevant levels of TCDD (50 pg/mL) during two windows of sexual differentiation in development (1 hour of exposure at 3 and 7 weeks postfertilization) were later infertile, showed a reduction in sperm, and exhibited gene expression consistent with an altered microenvironment, even months after exposure. Due to the highly heterogeneous cell- type and -stage landscape of the testes, we hypothesized various cell types contribute markedly different profiles toward the pathology of TCDD exposure. To investigate the contributions of the diverse cell types in the adult zebrafish testes to TCDD-induced pathology, we utilized single-cell RNA-seq and the 10x Genomics platform. The method successfully captured every stage of testicular germ cell development. Testes of adult fish exposed during sexual differentiation to TCDD contained sharply decreased populations of late spermatocytes, spermatids, and spermatozoa. Spermatogonia and early spermatocyte populations were, in contrast, enriched following exposure. Pathway analysis of differentially expressed genes supported previous findings that TCDD exposure resulted in male infertility, and suggested this outcome is due to apoptosis of spermatids and spermatozoa, even years after exposure cessation. Increased germ cell apoptosis was confirmed histologically. These results provide support for an environmental exposure explanation of idiopathic male infertility.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Insight into 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced disruption of zebrafish spermatogenesis via single cell RNA-seq

et al. 2022

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“…Most of the teleost SCTs published to date were derived from zebrafish and are of high value for comparative immunology. Some studies are of remarkable complexity and cover the spectrum of hematopoietic cells (including various populations of innate and adaptive immune cells) in diverse tissue types of both embryonic and adult zebrafish ( 126 , 127 ). More specific scRNA-seq approaches focused on zebrafish B cells that express the macrophage-characteristic marker gene MPEG1.1 ( 117 ) or zebrafish macrophages associated with the central nervous system (CNS) that promote neurogenesis ( 128 ) and share conserved expression profiles with their counterparts in mammals ( 129 ).…”

Section: Technological Advances and Its Translation To Fish Immunologymentioning

confidence: 99%

RNA-Seq of Single Fish Cells – Seeking Out the Leukocytes Mediating Immunity in Teleost Fishes

et al. 2022

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The immune system is a complex and sophisticated biological system, spanning multiple levels of complexity, from the molecular level to that of tissue. Our current understanding of its function and complexity, of the heterogeneity of leukocytes, is a result of decades of concentrated efforts to delineate cellular markers using conventional methods of antibody screening and antigen identification. In mammalian models, this led to in-depth understanding of individual leukocyte subsets, their phenotypes, and their roles in health and disease. The field was further propelled forward by the development of single-cell (sc) RNA-seq technologies, offering an even broader and more integrated view of how cells work together to generate a particular response. Consequently, the adoption of scRNA-seq revealed the unexpected plasticity and heterogeneity of leukocyte populations and shifted several long-standing paradigms of immunology. This review article highlights the unprecedented opportunities offered by scRNA-seq technology to unveil the individual contributions of leukocyte subsets and their crosstalk in generating the overall immune responses in bony fishes. Single-cell transcriptomics allow identifying unseen relationships, and formulating novel hypotheses tailored for teleost species, without the need to rely on the limited number of fish-specific antibodies and pre-selected markers. Several recent studies on single-cell transcriptomes of fish have already identified previously unnoticed expression signatures and provided astonishing insights into the diversity of teleost leukocytes and the evolution of vertebrate immunity. Without a doubt, scRNA-seq in tandem with bioinformatics tools and state-of-the-art methods, will facilitate studying the teleost immune system by not only defining key markers, but also teaching us about lymphoid tissue organization, development/differentiation, cell-cell interactions, antigen receptor repertoires, states of health and disease, all across time and space in fishes. These advances will invite more researchers to develop the tools necessary to explore the immunology of fishes, which remain non-conventional animal models from which we have much to learn.

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“…Numerous studies involving single-cell studies in health and disease have identified new endothelial cell subtypes and functions 5 – 10 . Several scRNA-Seq studies using zebrafish embryos have revealed cellular heterogeneity and developmental trajectory during tissue and organ development in zebrafish 11 . In addition, a single cell transcriptomic atlas of day one to five zebrafish embryos has been generated recently 12 .…”

Section: Introductionmentioning

confidence: 99%

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Gurung

Restrepo

Chestnut

et al. 2022

Sci Rep

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Vascular endothelial cells exhibit substantial phenotypic and transcriptional heterogeneity which is established during early embryogenesis. However, the molecular mechanisms involved in establishing endothelial cell diversity are still not well understood. Zebrafish has emerged as an advantageous model to study vascular development. Despite its importance, the single-cell transcriptomic profile of vascular endothelial cells during zebrafish development is still missing. To address this, we applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hpf stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes. Furthermore, we validated our findings by characterizing novel markers for arterial, venous, and endocardial cells. We experimentally confirmed the presence of two transcriptionally different venous cell subtypes, demonstrating heterogeneity among venous endothelial cells at this early developmental stage. This dataset will be a valuable resource for future functional characterization of vascular endothelial cells and interrogation of molecular mechanisms involved in the establishment of their heterogeneity and cell-fate decisions.

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Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Cited by 60 publications

References 63 publications

Insight into 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced disruption of zebrafish spermatogenesis via single cell RNA-seq

Insight into 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced disruption of zebrafish spermatogenesis via single cell RNA-seq

RNA-Seq of Single Fish Cells – Seeking Out the Leukocytes Mediating Immunity in Teleost Fishes

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

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