Gene Expression
Nebulas
Gene Expression NebulasSummary: The liver plays a critical role in both immune defense and tolerance in the body. The liver-resident immune cells (LrICs) determine the immune properties, but the unique composition and heterogeneity of these cells are incompletely understood. Here, we dissect the diversity of LrICs by a comprehensive transcriptomic profiling using the unbiased single-cell RNA-sequencing (scRNA-seq). A total of 70, 706 of CD45+ immune cells from the paired liver perfusion, spleen and peripheral blood as references were profiled. We identified 33 discrete cell populations comprising 14 of T and NK cell, 7 of B cell, 4 of antibody-secreting cell (ASC) and 8 of myeloid cell subsets in human liver and donor-paired spleen and blood, and characterized their tissue distribution, gene expression and functional modules. Especially, four of CXCR6+ T and NK cell subsets were found to be present preferentially in the liver, where they manifested heterogeneity, distinct function and prominent homeostatic proliferation. We propose a universal category system of T and NK cells based on distinct chemokine receptors, confirmed subsequently by phenotype, transcriptional factors and functionality. We also identified adaptive changes by the spleen and liver-resident monocyte and macrophage populations. Finally, we give a global glimpse on B cell and ASC subsets in human spleen and liver. We, therefore, reveal the heterogeneity and functional diversity of LrICs in human. This study presents comprehensively the landscape of LrICs and will enable further study on their roles in various human diseases.
Overall Design: Using 10x genomics to measure CD45+ immune cells in healthy human liver and paired spleen and PBMCs from the same donors access to liver transplantation.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Immune cells from human samples were isolated according to the previous protocols. In brief, peripheral blood mononuclear cells (PBMCs) and bone marrow cells were isolated by ficoll-hypaque density gradient centrifugation from heparinized blood of enrolled subjects. Spleen was first grinded on ice and the cells were then collected and filtered. Liver perfusion was directly filtered and concentrated by centrifugation (750 g, 15 min, 20℃), and were layered onto Ficoll. Upon isolation, human CD45+ cells were isolated with the anti-CD45 magnetic-activated cell sorting (MACS) kit. Then the cells were counted three times by three individuals independently and the mean 22, 000-24, 000 live cells were used for 10x genomics. The left cells were cryopreserved in 90% fetal calf serum plus 10% of DMSO for subsequent assay. Single cells were lysed in droplets using the 10X Chromium instrument Reverse transcription was performed in droplet |
| Library Construction Protocol: | library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq X Ten |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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