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Gene expression analysis of hPSC derived macrophages (iMacs) co-cultured with hepatic cells

ABSTRACT: Purpose: to analyze change in gene expression of hPSC derived macrophages upon co-culture with hepatic cells including Huh7 and primary human hepatocytes Methods: SMART-seq2 amplified polyA RNA from sorted iMacs in the co-cultures. Results: the transcriptome of iMacs changed after co-culture with Huh7 cells or pHHs, and changed after the HCV infection of the co-cultured Huh7 cells. Conclusions: the gene expression profiles of co-cultured iMacs indicated that the culture conditions and the microenvironments could reprogrammed iMacs to adopt tissue-specific features and perform specifc functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE234572 | GEO | 2024/05/23

REPOSITORIES: GEO

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Gene expression analysis of hPSC-derived macrophages (iMACs) encountering Streptococcus pneumoniae.

Project description:Purpose: to analyze gene expression changes of iMACs encountering S. pneumoniae. Methods: SMART-seq2 amplified polyA RNA from sorted iMACs in the co-cultures. Results: the transcriptome of iMACs changed after encountering S. pneumoniae. Conclusions: the gene expression profiles of S. pneumoniae stimulated iMACs indicated iMACs undergoing inflammatory response and the immune response was distinct with iMACs encountering other pathogens such as HCV or SARS-CoV-2.

2024-05-23 | GSE253876 | GEO

ScRNA-seq and scATAC-seq analysis of human pluripotent stem cell (hPSC) derived macrophages iMacs

Project description:Purpose: to depict the single-cell map and reveal the heterogeneity of hPSC derived macrophages Methods: Differentiation day 14 iMacs were dissociated to obtain a single-cell suspension. scRNA-seq and scATAC-seq library preparation and sequencing were done by CapitalBio Technology (https://www.capitalbiotech.com/). scRNA-seq, the cell suspension was immediately loaded onto the Chromium Single Cell Controller (10× Genomics) for droplet formation. cDNA and subsequent sequencing library were generated using Chromiun Single Cell 3’ Reagent Kit (v3 Chemistry) (10× Genomics) according to the instruction manual. For sc-ATAC-seq, cell nuclei were extracted with Chromiun Nuclei Isolation Kit (v2 Chemistry) (10x Genomics) and then loaded onto the Chromium Single Cell Controller for droplet formation. Results: ScRNA-seq and scATAC-seq data of differentiation day 14 iMacs from hPSCs Conclusions: day 14 differentiation culture, which consisted primarily of monocytes and macrophages.

2024-05-23 | GSE234577 | GEO

Comparison between infant and adult primary human hepatocytes (PHHs) in terms of their responsiveness to FAC (FBS + A83-01 + CHIR99021)

Project description:Infant PHHs (IPHHs) and adult PHHs (APHHs) were cultured in the presence of FBS only or FAC, and their transcriptomic changes throughout the 2-week culture were assessed by mRNA microarray.

2019-08-01 | GSE134672 | GEO

The Second Generation of CAR-iMACs with Enhanced Polarization, CAR-mediated Efferocytosis and Superior Potency against Solid Tumors

Project description:Chimeric antigen receptor (CAR)-T cell therapies have shown great success in treating hematologic malignancies. Nonetheless, their therapeutic effect on solid tumors remains to be improved. Recently, macrophages have attracted great attention, given their ability to infiltrate solid tumors, phagocytize tumor cells as well as their immunomodulatory capacities. The first generation of CD3ζ-based CAR-macrophages demonstrated that the CAR could stimulate macrophage phagocytosis in a tumor antigen-dependent way. Here, we genetically engineered induced pluripotent stem cell (iPSC)-derived macrophages (iMACs) with TLR4 intracellular TIR domain-containing CARs against EGFRvIII and GPC3, which yielded markedly enhanced antitumor effect in two different solid tumor models including glioblastoma, and hepatocellular carcinoma in which complete remission was achieved with CAR-iMACs alone or in combination with CD47 antibody. Moreover, the tandem CD3ζ-TIR-CAR, or the “second-generation” design of TIR-based dual signaling CAR, endowed iMACs with both target engulfment/efferocytosis capacity against antigen-expressing solid tumor cells, and potency of antigen-dependent M1 state polarization and M2 state resistance in an NF-κB dependent manner. We also illustrated a surprising mechanism of tumor cell elimination by CAR-induced efferocytosis against tumor cell apoptotic bodies. Taken together, we established the next generation CAR-iMACs equipped with orthogonal phagocytosis and polarization capacity for better antitumor functions in treating solid tumors.

2023-09-29 | GSE214140 | GEO

Long-term maintenance of functional primary human hepatocytes using small molecules

Project description:Primary human hepatocytes (PHHs) were cultured with or without a cocktail of four small molecules, Y-27632, PD0325901, A83-01 and CHIR99021 (termed YPAC), and their transcriptomes after a long-trm culture were compared.

2019-09-01 | GSE135011 | GEO

RNA-seq data for Huh7 cells in spheroid culture and adherent culture

Project description:Anchorage-independent spheroid cells of HCC possess stemness properties. Huh7 cells are cultured in ultra-low attachment surface plates with serum-free medium. RNA-sequencing (RNA-seq) was applied in spheroid culture cells and adherent culture cells.

2022-06-01 | GSE199940 | GEO

Gene expression profiles in human liver organoid-derived hepatocytes

Project description:Human liver organoids are expected to be a hepatocyte source for preclinical in vitro studies. Although these organoids show long-term proliferation, their hepatic functions remain low. Here, we propose a novel method for two dimensional (2D)-cultured hepatic differentiation from human liver organoids. When cultured under a 2D condition, the single cells from human liver organoids were seeded on collagen type I-coated plates. Then, optimal conditions for hepatic differentiation were screened using several reagents. We determined the 2D-cultured hepatocyte differentiation method from human liver organoids. Hepatic gene expressions in human liver organoids-derived hepatocytes (Org-HEPs) were greatly increased, compared to those in human liver organoids. The metabolic activities of cytochrome P450 (CYP) 1A2, CYP2C8, CYP2E1 and CYP3A4 were at levels comparable to those in primary human hepatocytes (PHHs). These results suggested that human liver organoids could be differentiated into highly functional hepatocytes in 2D culture. We also treated Org-HEPs and PHHs with hepatotoxic drugs. The cell viability of Org-HEPs was almost the same as that of PHHs, suggesting that Org-HEPs could be used for hepatotoxicity tests. Thus, Org-HEPs will be useful for pharmaceutical research.

2024-08-29 | GSE234459 | GEO

Global transcriptomic analysis of hepatocyte cells infected with Ebola virus (EBOV)

Project description:We performed transcriptomic analysis of a Ebola virus (EBOV) infected hepatocyte cells. We utilized primary human hepatocytes (PHHs), iPSC-derived hepatocytes (iHeps), and immortalized hepatocarcinoma cell line Huh7 cells. Cells were infected with a multiplicity of infection of 10 and harvested after 1 day. Corresponding Mock infected samples were also included in this study.

2022-09-01 | GSE184638 | GEO

hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts

Project description:We systematically compared autopsy samples from non-COVID-19 donors and COVID-19 patients using RNA-seq and immunohistochemistry. We observed strikingly increased expression levels of CCL2 as well as macrophage infiltration in heart tissues of COVID-19 patients. We generated an immuno-cardiac co-culture platform containing human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) and macrophages. We found that macrophages induce increased reactive oxygen species (ROS) and apoptosis in CMs by secreting IL-6 and TNF-α after SARS-CoV-2 exposure. Using this immuno-cardiac co-culture platform, we performed a high content screen and identified ranolazine and tofacitinib as compounds that protect CMs from macrophage-induced cardiotoxicity. We established an immuno-host co-culture system to study macrophage-induced host cell damage following SARS-CoV-2 infection, and identified FDA-approved drug candidates that alleviate the macrophage-mediated hyper-inflammation and cellular injury.

2021-04-16 | GSE169241 | GEO

Expression levels of mature miRNAs from Huh7 cell treated with ROCK inhibitor

Project description:We used microarray to determine the miRNA whose expression was changed at 12 hours after Y27632 treatment Two-condition experiment; Huh7 control vs Huh7 treated with Y27632 for 12 hours

2014-04-21 | E-GEOD-33876 | biostudies-arrayexpress

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