Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1011833 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25868015_1.fastq.gz | Fastqsanger.gz | |||
| SRR25868015_2.fastq.gz | Fastqsanger.gz | |||
| SRR25868016_1.fastq.gz | Fastqsanger.gz | |||
| SRR25868016_2.fastq.gz | Fastqsanger.gz | |||
| SRR25868017_1.fastq.gz | Fastqsanger.gz |
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Project description:The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of kidney in fish immune systems remain to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cell types from zebrafish kidney via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in kidney, suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system, and highlighted the multifaced biology of kidney in ancient vertebrates.
2024-03-15 | GSE242133 | GEO
Project description:The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of the kidney in fish immune systems remains to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cells types from zebrafish kidneys via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in the kidney, suggesting the kidney acts as a secondary lymphoid organ. These results indicated that the fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune systems, and highlighted the multifaced biology of kidneys in ancient vertebrates.
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Project description:Motivation: Identification of eQTL, the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis. Methods: We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual and pleiotropic effects of eQTL in the presence of hidden factors. The HEFT model simultaneously accounts for the effects of genotypes while learning hidden factors, where we make use of the complete likelihood of a unified multivariate regression and factor analysis model to derive a ridge estimator for combined factor learning and detection of eQTL. HEFT requires no pre-estimation of hidden factor effects, no iterative model selection, it provides p-values, and is extremely fast, requiring just a few hours to complete an eQTL analysis of thousands of expression variables when analyzing hundreds of thousands of SNPs on a standard 8 core 2.6G desktop. Results: By analyzing simulated data, we demonstrate that HEFT can correct for an unknown number of hidden factors and outperforms related hidden factor methods for eQTL analysis, where the improved performance is particularly evident in the detection of eQTL with multivariate effects. To demonstrate a real-world application, we applied HEFT to identify eQTL affecting gene expression in human lung tissue for a study that included presumptive hidden factors. The analysis identified a number of eQTL with direct relevance to lung disease that could not be found without a hidden factor analysis, including cis-eQTL for GTF2H1 and MTRR, genes that have been independently associated with lung cancer. We have developed HEFT, a fast multivariate method that detect eQTLs by analyzing thousands of traits simultaneously in the presence of hidden factors. HEFT employs a combined regression factor analysis approach to analyze the gene expression and genotype data sets, looking for univariate or multivariate eQTLs that regulate gene expression, while simultaneously controlling for both orthogonal or non-orthogonal hidden factors. We show by extensive simulation that HEFT outperforms competing methods, and by applying HEFT to a study that included presumptive hidden factors, we identified a number of eQTL with direct relevance to lung disease that could not be found without a hidden factor analysis. HEFT analysis results file (includes all results, not just top hits) linked below as supplementary file.
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