CircZKSCAN1 suppresses stemness in hepatocellular carcinoma (HCC) by competing against RNA-binding protein FMRP
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA432661 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6666070_1.fastq.gz | Fastqsanger.gz | |||
| SRR6666070_2.fastq.gz | Fastqsanger.gz | |||
| SRR6666071_1.fastq.gz | Fastqsanger.gz | |||
| SRR6666071_2.fastq.gz | Fastqsanger.gz | |||
| SRR6666072_1.fastq.gz | Fastqsanger.gz |
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2022-07-23 | GSE208358 | GEO
Project description:Background & Aims: Extracellular vesicles (EVs) play a pivotal role in connecting tumor cells and their local and distant microenvironment. Here, we aimed to understand the role and molecular basis of patient-derived EVs in modulating cancer stemness and tumorigenesis in the context of hepatocellular carcinoma (HCC). Methods: EVs were isolated, quantified and characterized from patients’ sera. EVs were tested vigorously, both in vitro and in vivo, by various functional assays. Proteomic analysis was performed to identify the functional components of EVs. The expression level of polymeric immunoglobulin receptor (pIgR) in circulating EVs, tumor and non-tumorous tissues of HCC patients was determined by ELISA, immunoblotting, immunohistochemistry and quantitative PCR. The functional role and underlying mechanism of EVs with an enhanced pIgR expression was elucidated. Blockage of EV-pIgR with neutralizing antibody was performed in nude mice implanted with patient-derived tumor xenograft (PDTX). Results: Circulating EVs of late-stage HCC (L-HCC) patient had significantly elevated pIgR expression when compared to the EVs released by control individuals. The augmenting effect of L-HCC patient in cancer stemness and tumorigenesis was hindered by anti-pIgR antibody. EVs enriched with pIgR consistently promoted cancer stemness and cancerous phenotypes in the recipient cells. Mechanistically, EV-pIgR-induced cancer aggressiveness was abrogated by Akt and β-catenin inhibitors, ascertaining the role of EV-pIgR through the activation of PDK1/Akt/GSK3β/β-catenin signaling axis. Furthermore, anti-pIgR neutralizing antibody attenuated the tumor growth in mice implanted with PDTX. Conclusion: The study illustrates an unrevealed role of EV-pIgR in regulating cancer stemness and aggressiveness, in which EV-pIgR activates PDK1/Akt/GSK3β/β-catenin signaling cascades. The blockage of intercellular communications mediated by EV-pIgR in the tumor microenvironment may provide a new therapeutic strategy for cancer patients.
2023-10-24 | PXD025522 | Pride
Project description:To investigate the role of RALYL in HCC development and stemness, RALYL was overexpressed in PLC-8024 HCC cell line. Transcriptome sequencing was performed to investigate subsequent target and signaling pathway of RALYL.
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Project description:BACKGROUND & AIMS: Expression of microRNAs (miRNAs) in metastatic foci of hepatocellular carcinoma (HCC) is unknown. We identified metastasis-related miRNAs in recurrent cases after living donor liver transplantation (LDLT). Methods: We performed a comprehensive analysis of primary HCC (T), noncancerous liver (N), and resected recurrent (metastatic) HCC (M) using microarray analyses to identify metastasis-related miRNAs in in three patients with post-transplant recurrence. The RNA samples from three cases that underwent resection of recurrences after LDLT were made available for miRNA microarray analysis. The three cases included a 57-year-old man (case 1) with peritoneal recurrence and infected by hepatitis B virus (HBV), and a 48-year-old woman (case 2) and a 51-year-old man (case 3) with lung recurrences and hepatitis C virus (HCV) infection. Microarray analysis was performed for each RNA sample from the (T), (N) in the explanted liver, and (M). A sample containing equal amounts of RNAs from histologically normal livers of three living donors (NL: normal liver) was analyzed as a control. The RNA samples from three cases that underwent resection of recurrences after living donor liver transplantation were made available for microRNA microarray analysis. Microarray analysis was performed for each RNA sample from the primary HCC (T), noncancerous liver (N) in the explanted liver, and resected recurrent metastatic HCC (M). A sample containing equal amounts of RNAs from histologically normal livers of three living donors (NL: normal liver) was analyzed as a control.
2013-10-25 | E-GEOD-41874 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) RNA modification is the most common and conserved epigenetic modification in mRNA and has been shown to play important roles in cancer biology. As the m6A reader YTHDF1 has been reported to promote progression of hepatocellular carcinoma (HCC), it represents a potential therapeutic target. In this study, we evaluated the clinical significance of YTHDF1 using human HCC samples and found that YTHDF1 was significantly upregulated in HCCs with high stemness scores and was positively associated with recurrence and poor prognosis. Analysis of hepatoma spheroids revealed that YTHDF1 was highly expressed in liver cancer stem cells (CSCs). Stem cell-specific conditional Ythdf1 knock-in (CKI) mice treated with diethylnitrosamine showed elevated tumor burden compared with wild type mice. YTHDF1 promoted CSC renewal and resistance to the multiple tyrosine kinase inhibitors lenvatinib and sorafenib in patient-derived organoids and HCC cell lines, which could be abolished by catalytically inactive mutant YTHDF1. RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing identified NOTCH1 as a direct downstream of YTHDF1. YTHDF1 bound to m6A modified NOTCH1 mRNA to enhance its stability and translation, which led to increased NOTCH1 target genes expression. NOTCH1 overexpression rescued HCC stemness in YTHDF1 deficient cells in vitro and in vivo. Lipid nanoparticles targeting YTHDF1 significantly enhanced the efficacy of lenvatinib and sorafenib in HCC in vivo. Taken together, YTHDF1 drives HCC stemness and drug resistance through a YTHDF1-m6A-NOTCH1 epitranscriptomic axis, and YTHDF1 is a potential therapeutic target for treating HCC.
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Project description:c-Met induces tumor initiation and stemness in HCC cells through the regulation of CD44s via AKT signaling. Over-expression of CD44s in c-Met and CD44s negative cells induce both a stemness and mesenchymal phenotype independent of c-Met. The down regulation of CD44s or c-Met was compared to Scrambled control to investigate the effects of CD44s or c-Met on global changes of mesenchymal or stemness markers.
2012-05-30 | E-GEOD-38343 | biostudies-arrayexpress
Project description:Background:
There are about 100 trillion microbial cells in a person s gut. This is called the human gut microbiota. When this is disrupted, it can lead to many diseases. Studies show that the gut microbiota in people with cancer is different than that found in healthy people. Researchers want to study links between the gut microbiota and the immune system in people with a liver disease called hepatocellular carcinoma (HCC).
Objective:
To study links between gut microbiota and the immune system in people with HCC.
Eligibility:
People at least 18 years old with HCC. They must be scheduled to have tumors removed by surgery.
Design:
* People having surgery for primary liver tumors at the Mount Sinai Medical Center will be screened for this study.
* At the initial visit, blood, rectal swabs, urine, and stool will be collected. Participants will answer questions about their medical condition.
* Before surgery, blood, rectal swabs, urine, and stool will be collected. This will be done at a routine visit.
* When they have surgery, a piece of liver tissue with the tumor will be collected. This will be sent to the National Cancer Institute for tests.
* After surgery, blood, rectal swabs, urine, and stool will be collected 3 times. This will be done at routine visits.
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Project description:DNA copy number profiling for all primary tumor samples and HCC cell lines was performed by ROMA, a form of comparative genomic hybridization. The aim was to identify commonly amplifiied and deleted regions across human HCC. 88 primary HCC samples and 12 human HCC cell lines were analyzed.
2011-01-10 | E-GEOD-22916 | biostudies-arrayexpress
Project description:Fragile X syndrome (FXS) is a rare disease but is the most common form of inherited intellectual disability and a leading cause of autism. FXS is due to the absence of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein mainly involved in translational control. Even if this molecular defect is known, no specific therapy is available for FXS. The first alteration observed in the brain of FXS patients and of Fmr1 KO mice, model for FXS, is represented by an abnormal dendritic morphology that is associated with an altered synaptic plasticity. These findings led to numerous studies focused on mature neurons. However, recently, an increasing body of evidence is pointing out the importance of FMRP in the early steps of brain development. Thus, with the purpose to decipher the earliest molecular events leading to FXS we developed a stem-cell-based disease model by knocking-down the expression of Fmr1 in mouse embryonic stem (ES) cells. To gain insights in the pathways that are affected when FMRP is repressed, we performed a gene expression profile analysis comparing total RNA from shFmr1 and shControl ES cells using whole genome mouse microarrays. Transcripts were clustered according to their Gene Ontology classification using the DAVID software. Surprisingly, the most altered functional category was Nervous system development and function, highlighting the role of FMRP also during the earliest steps of neural development. To study the precise role of FMRP in Embryonic stem (ES) cells, we used an RNAi-based loss-of-function strategy by transducing mouse ES cells with a lentivirus expressing GFP and a shRNA targeting the constitutive exon 1 of Fmr1 (shFmr1). A random shRNA (shCT) was used as a control sequence. Transduced cells were sorted by flow cytometry and established as non-clonal cell populations. RNA samples were harvested and profiling experiments were performed in â??dye-balanceâ?? as indicated for each replicate.
2016-07-04 | E-GEOD-71184 | biostudies-arrayexpress