Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synergistic immunochemotherapy exerts efficiently anti-hepatocellular carcinoma effect to induce SAMD4B-APOA2 axis for inhibition of tumor immune evasion [NM-seq]

ABSTRACT: RNA modifications are a type of post-transcriptional modification and involved in many biological processes of immune cells, thus regulating immune response and participating in immune related diseases. 2'-O-methylation is one of the most common modifications. However, whether 2’-O-methylation is involved in immune evasion via regulating programmed death ligand 1 (PD-L1) is unclear. Here, we were the first to propose a new treatment strategy for patients with advanced hepatocellular carcinoma (HCC), provided evidence that synergistic immunochemotherapy had a better prognosis, and revealing the mechanism of immune regulation through 2'-O-methylation modification mediated by SAMD4B, as a tumor suppressor gene.

ORGANISM(S): Homo sapiens

PROVIDER: GSE223622 | GEO | 2024/01/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Synergistic immunochemotherapy exerts efficiently anti-hepatocellular carcinoma effect to induce SAMD4B-APOA2 axis for inhibition of tumor immune evasion

Project description:The purpose of this study is to speculate TCC (Thalidomide+carmofur+ Cantharidin), may be a promising treatment strategy for patients with advanced HCC.However, there is few research on this novel clinical combination therapy, especially the mechanism of its anti-hepatocellular effect. Therefore, it is necessary to further explore the specific mechanism of triple drug combination in HCC treatment.Here, we prospectively collected the clinical data of 92 patients with unresectable HCC, observed the effective efficacy of TCC in clinical practice, and confirmed in 6 PDX models in mice.Later on, we collected the resected tumors conducted single cell sequencing (scRNA-seq). We found that SAMD4B, especially its expression level, could affect the immune microenvironment. In order to understand the details of its immune regulation mechanism, such as which immune cells PD1 (i.e. PD-L1 receptor regulated by SAMD4B) comes from, we selected 4 patients from low- and high-SAMD4B groups for scRNA-seq.

2024-01-08 | GSE222791 | GEO

Nm-Mut-seq: The base-resolution quantitative method for mapping transcriptome-wide 2’-O-methylations

Project description:2’-O-methylation (Nm) is a prevalent post-transcriptional RNA modification present in many cellular RNAs and plays a critical role in modulating both the physical properties and regulation of eukaryotic RNAs. Studies of Nm modifications in RNA have long been hampered by a lack of effective mapping methods. Previously reported approaches can work well for detecting Nm modifications on abundant RNAs, but face challenges when applied to low-abundant RNAs, such as mRNA, lack stoichiometric information, and are challenged by issues of RNA sample degradation due to chemical treatment. Here, we present Nm-Mut-seq, a mutation signature-based Nm mapping method, which uses a custom reverse transcriptase (RT) that installs mutations at Am, Cm, and Gm-modified sites (Um is undetectable by this method). Our work provides a much-needed approach to detect Nm at base resolution in low abundant RNAs and to estimate the stoichiometry of each modified site transcriptome-wide.

2023-06-01 | GSE174518 | GEO

TIGIT Blockade Exerts Synergistic Effects on Microwave Ablation against Cancer

Project description:Combination immunotherapy based on immune checkpoint inhibitors (ICIs) has shown great success in the treatment of many types of cancers and has become the mainstream in the comprehensive treatment of cancers. Ablation in combination with immunotherapy has achieved tremendous efficacy in some preclinical and clinical studies. To date, our team proved that ablation in combination with ICIs was a promising antitumor therapeutic strategy for the liver metastasis of colorectal cancer (CRC). Moreover, we found that the expression of T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) expression was up-regulated after microwave ablation (MWA), indicating that TIGIT was involved in immunosuppression, and the combination of MWA and TIGIT blockade represented a potential clinical treatment strategy. In this study, we analyzed the single-cell RNA sequencing (scRNA-seq) data from the MWA and MWA plus anti-TIGIT groups. We found that TIGIT blockade in combination with MWA significantly promoted the expansion and functions of CD8+ TILs and reshaped myeloid cells in the tumor microenvironment (TME). In conclusion, TIGIT blockade in combination with MWA was a novel treatment strategy for the liver metastasis of CRC, and this combination therapy could reprogram the TME toward an antitumor environment.

2022-03-30 | GSE194209 | GEO

m6A IP sequencing analysis of m6A mRNA methylation regulation by arsenic in keratinocytes

Project description:N6-methyladenosine (m6A) RNA methylation is the most abundant internal chemical modifications in eukaryotic messenger RNA (mRNA) as well as long non-coding RNA (lncRNA). Recently, m6A RNA methylation research was revived by the discovery of the fat mass- and obesity-associated protein (FTO) as the first RNA demethylase, implicating that m6A RNA methylation is a reversible and dynamic modification and may have critical biological functions. Emerging evidence has shown that m6A modifications in mRNAs and lncRNAs play crucial roles in regulating RNA fate and function in biological processes in the past several years. The goal is to determine the targets of arsenic damage including m6A RNA methylation in keratinocytes.

2021-03-01 | GSE145923 | GEO

Asparagine hydroxylation is likely to be a reversible post-translational modification

Project description:Amino acid hydroxylation is a common post-translational modification, which generally regulates protein interactions or adds a functional group that can be further modified. Such hydroxylation is currently considered irreversible, necessitating the degradation and re-synthesis of the entire protein to reset the modification. Here we present evidence that the cellular machinery can reverse FIH-mediated asparagine hydroxylation on intact proteins. These data suggest that asparagine hydroxylation is a flexible and dynamic post-translational modification akin to modifications involved in regulating signalling networks, such as phosphorylation, methylation and ubiquitylation.

2020-03-23 | PXD013116 | Pride

Systemically administered HMGN1 immunostimulatory peptide with anti-PD-L1 antibody exerts synergistic antitumor effects

Project description:In this study, we explore a new combination therapy of anti-PD-L1 antibody with an immunostimulatory peptide derived from an alarmin high mobility group nucleosome binding protein 1 (HMGN1). Combination treatement of HMGN1 immunostimulatory peptide with anti-PD-L1 antibody exerted robust anti-tumor effects in Colon26 subtaneous murine model. To understand transcriptomic differences of immune cell population in the tumor-bearing mice after treated with single-agent or combination therapy of HMGN1 with anti-PD-L1 antibody, we performed transcriptome analysis on tumor tissue using 5’end Serial Analysis of Gene Expression (SAGE)-sequencing with an Ion 540 Chef kit, an Ion 540 Chip kit, and an Ion S5 Sequencer (Thermo Fisher Scientific).

2021-11-02 | GSE139291 | GEO

Targeted DNA demethylation using TALE-TET1 fusion proteins

Project description:Recent large-scale studies have defined genomewide, cell type-specific patterns of DNA methylation, a modification known to be important for regulating gene expression in both normal development and disease states. However, determining the functional significance of specific methylation events remains a challenging problem due to the current lack of targeted methodologies for removing these modifications. Here we describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator-like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, we demonstrate that modification of certain critical methylated promoter CpG positions can be associated with substantial increases in endogenous human gene expression. Our results delineate a general strategy for defining the functional significance of specific CpG methylation marks in the context of endogenous gene loci and validate new programmable DNA demethylation reagents with broad utility for research and potential therapeutic applications. Bisulfite sequencing of three different loci in three different cell lines (Klf4 in K562s, HBB in K562s and RHOXF2 in 293s and HeLas. Biological triplicates of all samples and controls (off-target and GFP controls).

2013-09-23 | E-GEOD-50761 | biostudies-arrayexpress

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [WGBS]

Project description:DNA methylation and histone modifications cooperate to shape the epigenetic landscape for transcription regulation, but their orchestration is not fully understood due to the lack of met1 drm1 drm2 cmt2 cmt3 mutants (mddcc), in which total DNA methylation were eliminated. This is the first time to generate mddcc that allow us to elucidate the roles of DNA methylation in the upheaval of histone modification landscape, transposon activity and gene expression. We found that DNA methylation elimination-triggered genome-wide transcriptional reprogramming is largely orchestrated by the redistribution and conversion of histone modifications. We also distinguished the contribution of CG and non-CG methylation to the histone modification landscape. Furthermore, we reveal histone modifications can serve as an independent regulatory system despite the influence of DNA methylation. Taken together, we provide comprehensive insights into the roles of DNA methylation in shaping epigenomic landscape for genome transcription, which deep understanding of epigenomic regulation.

2022-08-19 | GSE183986 | GEO

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [RNA-Seq]

2022-08-19 | GSE183985 | GEO

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [ChIP-Seq]

2022-08-19 | GSE183957 | GEO