Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

ABSTRACT: A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

PROVIDER: PRJNA798367 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17653700_1.fastq.gz	Fastqsanger.gz
	SRR17653700_2.fastq.gz	Fastqsanger.gz
	SRR17653701_1.fastq.gz	Fastqsanger.gz
	SRR17653701_2.fastq.gz	Fastqsanger.gz
	SRR17653702_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 52

Similar Datasets

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

Project description:A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

| PRJNA747256 | ENA

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

Project description:We first treated liver cancer cells with vehicle or HHT for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated liver cancer cells. HHT-induced expression changes were obtained based on the resultant data.

2022-01-21 | GSE193897 | GEO

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

Project description:We first treated LX-2 cells with vehicle or HHT (1μM and 5μM) for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated LX-2 cells. HHT-induced expression changes were obtained based on the resultant data.

2021-07-18 | GSE180243 | GEO

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer.

Project description:Pharmacologic perturbation projects, such as Connectivity Map (CMap) and Library of Integrated Network-based Cellular Signatures (LINCS), have produced many perturbed expression data, providing enormous opportunities for computational therapeutic discovery. However, there is no consensus on which methodologies and parameters are the most optimal to conduct such analysis. Aiming to fill this gap, new benchmarking standards were developed to quantitatively evaluate drug retrieval performance. Investigations of potential factors influencing drug retrieval were conducted based on these standards. As a result, we determined an optimal approach for LINCS data-based therapeutic discovery. With this approach, homoharringtonine (HHT) was identified to be a candidate agent with potential therapeutic and preventive effects on liver cancer. The antitumor and antifibrotic activity of HHT was validated experimentally using subcutaneous xenograft tumor model and carbon tetrachloride (CCL4)-induced liver fibrosis model, demonstrating the reliability of the prediction results. In summary, our findings will not only impact the future applications of LINCS data but also offer new opportunities for therapeutic intervention of liver cancer.

| S-EPMC8893721 | biostudies-literature

Establishment of Primary Liver Cancer Organoids and Application on Sorafenib Resistance

Project description:Current in vitro models of primary liver cancer fail to recapitulate the key characteristics of original cancer. We construct the long-term organoids culture from tumor tissue of primary liver cancer (PLC) patients with varieties of subtypes. PLC organoids retain the histopathological features of originating tumor. Organoids transplantation proved that the tumorogenic potential and histological characteristics of PLC organoids are well preserved in vivo. PLC organoids are amenable for preclinical drug screening test and identification of mammalian target of rapamycin (mTOR) inhibitor compound as a potential therapeutic treatment for PLC. Besides, we also establish sorafenib-resistant hepatocellular carcinoma (HCC) organoids to clarify the mechanisms that drive resistance. In conclusion, PLC organoids models provide a platform for drug development for PLC and theoretical basis for HCC resistance.

2023-02-22 | GSE182593 | GEO

Centromere repositioning in Schizosaccharomyces pombe

Project description:Centromere repositioning in Schizosaccharomyces pombe

| PRJNA484011 | ENA

Nucleosome Repositioning: Nicotine- and Cocaine-induced Changes

Project description:SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug-naive positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse. SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Two independently grown biological replicates for each time point and condition, and two controls were processed.

2015-08-07 | E-GEOD-71795 | biostudies-arrayexpress

A technique to identify context-based protein biomarkers: Application to a mouse liver cancer model

Project description:To date, most proteomic analyses towards cancer biomarker discovery have been based on protein quantification. However, proteins function in association with other proteins to form modules that are localized in specific subcellular compartments. Cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells1,2. Here, we describe a strategy for biomarker detection based on a mitochrondrial enrichment score (mtES), which is sensitive to protein abundance as well as protein translocation between mitochondria and cytosol. The mtES score integrates protein expression data from total cellular lysates and enriched mitochondrial fractions and provides important information for the classification of cancer samples, which is not apparent from conventional quantitative protein measurements. We apply the new strategy to a panel of wild-type and mutant mice that are either healthy or present liver cancer. We show that proteome changes based on mtES scores outperform protein abundance measurements in discriminating liver cancer from healthy liver tissue and that they are uniquely robust against strong genetic perturbation. Overall, our method provides a more sensitive approach to cancer biomarker discovery that takes into account contextual information of tested proteins.

2019-05-09 | PXD008758 | Pride

Alterations in soybean gene expression profile after foliar application of lipo-chitooligosaccharide (LCO) from Bradyrhizobium japonicum under sub-optimal temperature

Project description:Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChipÂ® Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data. Soybean seedlings grown at optimal temperature (25 Â°C) were exposed to sub-optimal temperature (15 Â°C). After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Total RNA was extracted and microarray analysis was performed using Affymetrix GeneChipÂ® Soybean Genome Arrays.

2010-03-20 | E-GEOD-20972 | biostudies-arrayexpress

Establishment of Primary Liver Cancer Organoids and Application on Sorafenib Resistance

Project description:Establishment of Primary Liver Cancer Organoids and Application on Sorafenib Resistance

| PRJNA756985 | ENA