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Ena-DATASET-BIOPIC-12-02-2020-09:47:27:678-255 - samples

ABSTRACT: The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This is the droplet data of this study

PROVIDER: EGAD00001005961 | EGA |

REPOSITORIES: EGA

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ena-DATASET-BIOPIC-12-02-2020-09:38:58:819-253 - samples

| EGAD00001005960 | EGA

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

Project description:The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites.A cluster of LAMP3+ dendritic cells (DCs) appeared to be the mature form of conventional DCs and possessed the potential to migrate from tumors to LNs. LAMP3+ DCs also expressed diverse immune-relevant ligands and exhibited potential to regulate multiple subtypes of lymphocytes. Of the macrophages in tumors that exhibited distinct transcriptional states, tumor-associated macrophages (TAMs) were associated with poor prognosis, and we established the inflammatory role of SLC40A1 and GPNMB in these cells. Further, myeloid and lymphoid cells in ascites were predominantly linked to tumor and blood origins, respectively. The dynamic properties of diverse CD45+ cell types revealed by this study add new dimensions to the immune landscape of HCC.

2019-11-13 | GSE140228 | GEO

Differential expression signature of EpiCAM/CD45 positive cells in ascitic fluid from serous ovarian cancer patients

Project description:Differential transcriptome signature of FACS purified cell population (EpiCAM/CD45 dual positive cells vs EpiCAM only) from the ascites of human serous ovarian cancer. Primary objective: To characterize the phenotypic expression of stem cells markers, elucidation of differential gene expression and oncogenic functions in EpiCAM/CD45 dual positive vs EpiCAM cells. Methods: Cell Sorting (FACS) from ascites of human serous ovarian cancer patients, apoptotic assay, Drug sensitivity assay, tumor spheroid assay, Cell invasion and cell migration assay.

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Expression data from the spleen of tumor bearing mice

Project description:We identify a new cell subset Ter119+CD45- small cells that promotes tumor metastasis in hepatocellular carcinoma (HCC)-bearing mice. We used microarrays to detail the gene expression of Ter119+CD45- cells comparing with CD45- cells in the spleen of hepatocellular carcinoma (HCC)-bearing mice. Ter119+CD45- cells in the spleen of hepatocellular carcinoma (HCC)-bearing mice, being sorted by a MoFlo high-speed cell sorter, were prepared for RNA extraction and hybridization on Affymetrix microarrays. The CD45+ cells from the same tumor bearing mice were prepared as control.

2014-12-19 | E-GEOD-58468 | biostudies-arrayexpress

Identification of recurrence related microRNAs from bone marrow in hepatocellular carcinoma (HCC) patients

Project description:To identify the role of miRNAs in patient bone marrow (BM) and explore the function of these molecules during HCC progression, we employed microarray-based profiling to analyze miRNA expression in the BM of patients with HCC. MicroRNA expression in the BW of HCC patients was measured by using microarray-based profiling. BM cells were separated into 3fraction by cell surface markers as follows: CD45+(macrophage), CD14-/CD45+(lymphocyte) and CD14-/CD45-/EpCAM+(epithelial cell).

2015-08-06 | E-GEOD-71762 | biostudies-arrayexpress

Expression data from the spleen of tumor bearing mice

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Extracellular vesicle-mediated communication between hepatocytes and natural killer cells promotes hepatocellular tumorigenesis

Project description:Hepatocellular carcinoma (HCC) is frequently characterized by metabolic and immune remodeling in the tumor microenvironment. We previously discovered that liver-specific deletion of fructose-1, 6-bisphphotase 1 (FBP1), a gluconeogenic enzyme ubiquitously suppressed in HCC tissues, promotes liver tumorigenesis, and induces metabolic and immune perturbations closely resembling human HCC. However, the underlying mechanisms remain incompletely understood. Here we reported that FBP1-deficient livers exhibit diminished amounts of natural killer (NK) cells and accelerated tumorigenesis. Using the diethylnitrosamine-induced HCC mouse model, we analyzed potential changes in the immune cell populations purified from control and FBP1-depleted livers and found that NK cells were strongly suppressed. Mechanistically, FBP1 attenuation in hepatocytes derepresses an EZH2-dependent transcriptional program to inhibit PKLR expression. This leads to reduced levels of PKLR cargo proteins sorted into hepatocyte-derived EVs, dampened activity of EV-targeted NK cells, and accelerated liver tumorigenesis. Our study demonstrated that hepatic FBP1 depletion promotes HCC-associated immune remodeling, partly through the transfer of hepatocyte-secreted, PKLR-attenuated EVs to NK cells.

2023-03-11 | PXD026822 | Pride

The hepatic immunological pattern shaped by dominant-subdominant cellular relationship creates a collective function beyond the function of each cellular constituent to orchestrate the progression of hepatocellular carcinoma

Project description:Abundance of data on the role of inflammatory immune responses in the progression or inhibition of hepatocellular carcinoma (HCC) has failed to offer a curative immunotherapy for HCC. This is largely because of taking reductionist approaches and missing the collective function of the hepatic immune system by focusing on specific immune cell type. To discover the collective immune function, we take systems immunology approach by performing high-throughput analysis of snRNAseq data collected from the liver of DIAMOND mice during the progression of nonalcoholic fatty liver disease (NAFLD) to HCC. We report that mutual signaling interactions of the hepatic immune cells in a dominant-subdominant manner, as well as their interaction with structural cells shape the immunological pattern manifesting a collective function beyond the function of the cellular constituents. Within different immune pattern, the same cytokines manifest different functional signaling pathways. These data suggest that discovery of the immune pattern not only explains dynamic changes in immune cells during the course of diseases but also offers immune modulatory approaches for the treatment of NAFLD and HCC.

2023-04-04 | GSE225381 | GEO

Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity

Project description:Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing we identified 9 peripheral LNs non-endothelial SC subsets. Included are the established subsets Ccl19hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs) and perivascular cells. We also identified Ccl19lo TRCs, likely including cholesterol-25-hydroxylase+ cells located at the T-zone perimeter, Cxcl9+ TRCs in the T-zone and interfollicular region, CD34+ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase+ SCs in the medullary cords and Nr4a1+ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and they provide evidence that many SCs are in an activated state.

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Monocyte-derived IL-1 and IL-6 are differentially required for cytokine release syndrome and neurotoxicity by CAR-T cells.

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