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Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]

ABSTRACT: Recent advances in single-cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here, we utilized massively parallel single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally-distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs, il2rgaY91fs and double homozygous mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells, classically-defined and erythroid-primed hematopoietic stem and progenitor cells, mucin secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish.

ORGANISM(S): Danio rerio

PROVIDER: GSE100910 | GEO | 2017/08/04

SECONDARY ACCESSION(S): PRJNA393429

REPOSITORIES: GEO

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Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA-seq]

Project description:Recent advances in single-cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here, we utilized massively parallel single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally-distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs, il2rgaY91fs and double homozygous mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells, classically-defined and erythroid-primed hematopoietic stem and progenitor cells, mucin secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish.

2017-08-04 | GSE100912 | GEO

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart-seq]

2017-08-04 | GSE100911 | GEO

tp53 deficiency causes a wide tumor spectrum and elevates embryonal rhabdomyosarcoma metastasis in zebrafish

Project description:We generated tp53 deletion mutant zebrafish that spontaneously develop malignant peripheral nerve-sheath tumors, angiosarcomas, germ cell tumors, and an aggressive Natural Killer cell leukemia not previously reported in zebrafish. Each tumor type efficiently engrafted into syngeneic recipient zebrafish and shared gene expression signatures with predicted cells of origin.

2018-09-05 | GSE109581 | GEO

Methylation and Hydroxymethylation profile of zebrafish tet2 mutant

Project description:Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type

2020-09-01 | GSE136761 | GEO

Gene expression profile of zebrafish tet2 mutant

Project description:Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type

2020-09-01 | GSE136349 | GEO

Single nucleus inDrops to profile adult human kidney

Project description:Single nucleus inDrops to profile adult human kidney

2018-06-19 | GSE114156 | GEO

scRNA-seq of kidney marrow cells from Gata2b deficient and wild type zebrafish

Project description:GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells (HSCs). Due to early embryonic lethality of Gata2 deficiency in mice, its role during adult hematopoiesis is incompletely understood. In zebrafish, mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells (HSPCs), whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation, but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells, we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow (KM) of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single-cell RNA sequencing. To enrich the scarce HSC population, we used pooled KM from two WT and Gata2b deficient Tg(CD41:GFP) zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.

2022-04-09 | E-MTAB-10370 | biostudies-arrayexpress

Differential requirement for Nfil3 during NK cell development

Project description:Natural killer (NK) cells can be grouped into distinct subsets that are localized to different organs and exhibit different capacity to secrete cytokines and mediate cytotoxicity. Despite these hallmarks that reflect tissue-specific specialization in NK cells, little is known about the factors that control the development of these distinct subsets. The basic leucine zipper transcription factor nuclear factor interleukin 3 (Nfil3; E4bp4) is essential for bone marrow-derived NK cell development but it is not clear whether Nfil3 is equally important for all NK cell subsets nor how it induces NK lineage commitment. Here we show that Nfil3 is required for the formation of Eomesodermin (Eomes)-expressing NK cells, including conventional medullary and thymic NK cells, whereas TRAIL+ Eomes- NK cells develop independent of Nfil3. Loss of Nfil3 during the development of bone marrow-derived NK cells resulted in reduced expression of Eomes and, conversely, restoration of Eomes expression in Nfil3-/- progenitors rescued NK cell development and maturation. Collectively, these findings demonstrate that Nfil3 drives the formation of mature NK cell by inducing Eomes expression and reveal the differential requirements of NK cell subsets for Nfil3. RNA-sequencing of natural killer (NK) cell subsets

2014-05-07 | E-GEOD-54291 | biostudies-arrayexpress

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Project description:Single-cell measurements of osteolineage cells within the bone marrow cell niche

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Clinical Efficacy and Safety of NKT Cell Infusion in Patients With Advanced Solid Tumor

Project description:Natural killer T (NKT) cells are a unique subset of lymphocytes that present a mixed T-NK phenotype. Our hypothesis is that Natural killer T cells may decrease the tumor burden and improve overall survival. The purpose of this study is to determine whether Natural killer T (NKT) cells are effective and safe in the treatment of patients with unresectable advanced solid tumor.

| 2199117 | ecrin-mdr-crc

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