Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE211155 | GEO | 2022/08/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [scATAC-seq]

Project description:Regulatory T (Treg) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Here, we show that Treg cells in the tumor microenvironment (TME) of human lung cancers harbor a completely different open chromatin profile compared to effector T cells and peripheral Treg cells. The integrative sequencing analyses revealed that BATF, IRF4, NF-κb, and NR4A were important transcription factors for Treg cell differentiation in the TME. Particularly, BATF was identified as a key regulator, which leveraged Treg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of Treg cells in the TME. BATF deficiency in Treg cells remarkably inhibited tumor growth and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. Our results propose the specific chromatin remodeling and differentiation program of Treg cells in the TME, which can be applied in the development of Treg cell-targeted therapies.

2022-08-22 | GSE211087 | GEO

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [scRNA-seq]

2022-08-22 | GSE211068 | GEO

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [bulk ATAC-seq]

2022-08-22 | GSE211153 | GEO

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [bulk RNA-seq]

2022-08-22 | GSE211044 | GEO

Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [mouse bulk ATAC-seq]

2022-08-22 | GSE211062 | GEO

Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes.

Project description:High throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome, phosphoproteome and transcriptome in two high-grade glioma (HGG) mouse models driven by mutated RTK oncogenes, PDGFRA and NTRK1, analyzing 13,860 proteins and 30,431 phosphosites by mass spectrometry. Systems biology approaches identify numerous master regulators, including 41 kinases and 23 transcription factors. Pathway activity computation and mouse survival indicate the NTRK1 mutation induces a higher activation of AKT downstream targets including MYC and JUN, drives a positive feedback loop to up-regulate multiple other RTKs, and confers higher oncogenic potency than the PDGFRA mutation. A mini-gRNA library CRISPR-Cas9 validation screening shows 56% of tested master regulators are important for the viability of NTRK-driven HGG cells, including TFs (Myc and Jun) and metabolic kinases (AMPKa1 and AMPKa2), confirming the validity of the multiomics integrative approaches, and providing novel tumor vulnerabilities.

| S-EPMC6697699 | biostudies-literature

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-27 | GSE236905 | GEO

Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation

Project description:Midbrain dopaminergic neurons (mDANs) control voluntary movement, cognition, and reward behavior under physiological conditions and are implicated in human diseases such as Parkinson's disease (PD). Many transcription factors (TFs) controlling human mDAN differentiation during development have been described, but much of the regulatory landscape remains undefined. Using a tyrosine hydroxylase (TH) human iPSC reporter line, we here generate time series transcriptomic and epigenomic profiles of purified mDANs during differentiation. Integrative analysis predicts novel regulators of mDAN differentiation and super-enhancers are used to identify key TFs. We find LBX1, NHLH1 and NR2F1/2 to promote mDAN differentiation and show that overexpression of either LBX1 or NHLH1 can also improve mDAN specification. A more detailed investigation of TF targets reveals that NHLH1 promotes the induction of neuronal miR-124, LBX1 regulates cholesterol biosynthesis, and NR2F1/2 controls neuronal activity.

| S-SCDT-10_1038-S44319-023-00024-2 | biostudies-other

An integrated systems biology approach identifies positive cofactor 4 as a pluripotency regulatory factor

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-10-30 | E-GEOD-74156 | biostudies-arrayexpress

An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-13 | GSE233476 | GEO