Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets

ABSTRACT: Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets

PROVIDER: PRJNA729972 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14536336.fastq.gz	Fastqsanger.gz
	SRR14536337.fastq.gz	Fastqsanger.gz
	SRR14536338.fastq.gz	Fastqsanger.gz
	SRR14536339.fastq.gz	Fastqsanger.gz
	SRR14536340.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets II

Project description:Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets II

| PRJNA730552 | ENA

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets

Project description:We hypothesised that whole transcriptome analysis of human TB granulomas isolated by laser capture microdissection could identify therapeutic targets, and that comparison with a non-infectious granulomatous disease, sarcoidosis, would identify disease-specific pathological mechanisms. Bioinformatic analysis of RNAseq data identified numerous shared pathways between TB and sarcoidosis lymph nodes, and also specific clusters demonstrating TB results from a dysregulated inflammatory immune response. To translate these insights, we compared three primary human cell culture models at the whole transcriptome level, and demonstrated that the 3D collagen granuloma model most closely reflected human TB disease. We investigated shared signaling pathways with human disease and identified twelve intracellular enzymes as potential therapeutic targets. Sphingosine kinase 1 inhibition controlled Mtb growth, concurrently reducing intracellular pH in infected monocytes and suppressing inflammatory mediator secretion. Immunohistochemical staining confirmed that sphingosine kinase 1 is expressed in human lung TB granulomas, and therefore represents a host therapeutic target to improve TB outcomes.

2021-05-15 | GSE174443 | GEO

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets II

2021-05-18 | GSE174566 | GEO

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets.

Project description:Tuberculosis (TB) is a persistent global pandemic, and standard treatment for it has not changed for 30 years. Mycobacterium tuberculosis (Mtb) has undergone prolonged coevolution with humans, and patients can control Mtb even after extensive infection, demonstrating the fine balance between protective and pathological host responses within infected granulomas. We hypothesized that whole transcriptome analysis of human TB granulomas isolated by laser capture microdissection could identify therapeutic targets, and that comparison with a noninfectious granulomatous disease, sarcoidosis, would identify disease-specific pathological mechanisms. Bioinformatic analysis of RNAseq data identified numerous shared pathways between TB and sarcoidosis lymph nodes, and also specific clusters demonstrating TB results from a dysregulated inflammatory immune response. To translate these insights, we compared 3 primary human cell culture models at the whole transcriptome level and demonstrated that the 3D collagen granuloma model most closely reflected human TB disease. We investigated shared signaling pathways with human disease and identified 12 intracellular enzymes as potential therapeutic targets. Sphingosine kinase 1 inhibition controlled Mtb growth, concurrently reducing intracellular pH in infected monocytes and suppressing inflammatory mediator secretion. Immunohistochemical staining confirmed that sphingosine kinase 1 is expressed in human lung TB granulomas, and therefore represents a host therapeutic target to improve TB outcomes.

| S-EPMC8321576 | biostudies-literature

Application of the ISM bioinformatics platform in detection of new therapeutic targets and potential therapeutic molecules

Project description:Application of EIIP / ISM bioinformatics platform in detection of new therapeutic targets and potential therapeutic molecules. Study of the molecular basis of rare human diseases

2020-12-16 | PRJEB42044 | EVA

Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer (RNA-seq)

Project description:To identify novel regulators and therapeutic targets of β-catenin-driven colorectal cancer development, genome-scale CRISPR-cas9 screens of Wnt/β-catenin were conducted and identified KMT2A as a key player of β-catenin-driven CRC progression. RNA-seq data was integrated with CHIP-seq and other experiments to assess the effect of KMT2A knockout on the transcriptomic profiling of CRC cells.

2021-05-26 | GSE156082 | GEO

Biomimetic Virulomics

Project description:An affinity guided approach coupled with multiplexed quantitative proteomics, namely Biomimetic Virulomics, for successful identification of cell-type specific effector proteins of both prokaryotic and eukaryotic pathogens.

2017-02-15 | MSV000080551 | MassIVE

Molecular classification and therapeutic targets in extrahepatic cholangiocarcinoma

Project description:Molecular classification and therapeutic targets in extrahepatic cholangiocarcinoma

| PRJNA547577 | ENA

Functionally-defined Therapeutic Targets in DIPG

Project description:<p>Diffuse Intrinsic Pontine Glioma (DIPG) is a universally fatal childhood cancer. Here, we performed a chemical screen in patient-derived DIPG cell cultures along with RNAseq expression analysis and integrated computational modeling to identify potentially effective therapeutic strategies. Panobinostat, among the more promising agents identified, demonstrated efficacy in pontine orthotopic xenograft models of both H3K27M and histone WT DIPG. These data suggest the potential utility of specific drug combinations and provides evidence of in vivo treatment efficacy of the multi-histone deacetylase inhibitor panobinostat. We are depositing to dbGaP deep sequencing whole exome data for 22 patient tumor samples and 13 matched normals, along with RNAseq data for 12 patient tumor samples and 6 normal pediatric brain tissue samples. In addition, we are depositing 22 RNAseq samples from DIPG cell lines before and after panobinostat treatment.</p>

| phs000900 | dbGaP

Induced pluripotent stem cell modeling of bone marrow failure and MDS identifies therapeutic targets

Project description:Induced pluripotent stem cell modeling of bone marrow failure and MDS identifies therapeutic targets

| PRJNA485356 | ENA