Browse
Submit Data
Databases
API
Help

Dataset Information

169 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human breast cancer cell line and tissue, ISE-affinity proteogenomics

ABSTRACT: Introducing a clinical-practical, alternative splicing activity-based proteogenomic method that identifies, in their oncogenically active states, biomarker genes bearing patient-specific GE or copy-number alterations of prognostic significance. This integrated multi-omics method uses intronic splicing enhancers (ISEs) probes to sort in situ ISE-interacting trans-acting protein factors (trans-interactome) directly from a heterogeneous tumor for subsequent mass spectrometry (MS) characterization.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast, Cell Culture, Breast Cancer Cell Line

DISEASE(S): Breast Cancer

SUBMITTER: Li Wang

LAB HEAD: Xian Chen

PROVIDER: PXD008642 | Pride | 2018-03-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AS_RNA10.raw	Raw
	AS_RNA11.raw	Raw
	AS_RNA12.raw	Raw
	AS_RNA13.raw	Raw
	AS_RNA14.raw	Raw

Items per page:

1 - 5 of 118

Publications

Novel RNA-Affinity Proteogenomics Dissects Tumor Heterogeneity for Revealing Personalized Markers in Precision Prognosis of Cancer.

Wang Li L Wrobel John A JA Xie Ling L Li DongXu D Zurlo Giada G Shen Huali H Yang Pengyuan P Wang Zefeng Z Peng Yibing Y Gunawardena Harsha P HP Zhang Qing Q Chen Xian X

Cell chemical biology 20180301 5

To discriminate the patient subpopulations with different clinical outcomes within each breast cancer (BC) subtype, we introduce a robust, clinical-practical, activity-based proteogenomic method that identifies, in their oncogenically active states, candidate biomarker genes bearing patient-specific transcriptomic/genomic alterations of prognostic value. First, we used the intronic splicing enhancer (ISE) probes to sort ISE-interacting trans-acting protein factors (trans-interactome) directly fr ...[more]

PMID: 29503206

Similar Datasets

A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression.

Project description:Structural Maintenance of Chromosomes Hinge Domain Containing 1 (SMCHD1) is a chromatin repressor, which is mutated in >95% of Facioscapulohumeral dystrophy (FSHD) type 2 cases. In FSHD2, SMCHD1 mutations ultimately result in the presence of the cleavage stage transcription factor DUX4 in muscle cells due to a failure in epigenetic repression of the D4Z4 macrosatellite repeat on chromosome 4q, which contains the DUX4 locus. While binding of SMCHD1 to D4Z4 and its necessity to maintain a repressive D4Z4 chromatin structure are well documented, it is unclear how SMCHD1 is recruited to D4Z4, and how it exerts its repressive properties on the chromatin. Here, we employ a quantitative proteomics approach to identify and characterize novel SMCHD1 interacting proteins, and assess their functionality in D4Z4 repression. We identify 47 robust SMCHD1 interactors, of which 19 are present in D4Z4 chromatin. We demonstrate that one of these SMCHD1 interacting proteins in D4Z4, RuvB-like 1 (RUVBL1) is indeed required for maintaining DUX4 silencing in FSHD myocytes. We also confirm the interaction of SMCHD1 with EZH inhibitory protein (EZHIP), which prevents global H3K27me3 deposition by the Polycomb repressive complex PRC2, providing novel insights into the potential function of SMCHD1 in the repression of DUX4 in the early stages of embryogenesis. The SMCHD1 interactome outlined herein can thus provide further direction into research on the potential function of SMCHD1 at genomic loci where SMCHD1 is known to act, such as D4Z4 repeats, the inactive X chromosome, autosomal gene clusters, imprinted loci and telomeres.

2021-12-15 | PXD023993 | Pride

Single-cell RNA-sequencing of spinal cord ependymal cells from FOXJ1-EGFP mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. Ependymal cells are, however, heterogeneous and we know little about what this reflects. To gain new insights into ependymal cell heterogeneity, we microdissected the ependymal cell layer from the thoracic spinal cord of 4 FOXJ1-EGFP transgenic mice (2.5-to-3-month old). After after dissociating the tissue into a cell suspension, we sorted single GFP-positive ependymal cells into lysis plates. cDNA synthesis was performed using Smart-seq2 technology.

2022-12-13 | E-MTAB-11563 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in high glucose condition

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in a high glucose concentration media

2024-08-31 | E-MTAB-14308 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in low glucose condition at 6 hours, 8 hours, and 1 week

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in low glucose condition at 6 hours, 8 hours, and 1 week

2024-08-31 | E-MTAB-14309 | biostudies-arrayexpress

Altered microbiota-host mutualism and bloom of Atopobium define severe pediatric Crohn's disease

Project description:Microbial dysbiosis has been identified in adult inflammatory bowel disease (IBD) patients. However, microbial composition and functional interplay between host genetics and microorganisms in early IBD onset remain poorly defined. Here, we identified and demonstrated the causal effect of Atopobium parvulum and the gut microbiota in pediatric IBD. Microbiota and proteomic profiling revealed that the abundance of A. parvulum, a potent H2S producer, was associated with increased disease severity and a concurrent reduction in the expression of the host H2S detoxification pathway. In the Il10-/- mouse model of inflammation, A. parvulum induced severe pancolitis that was dependent on the presence of the gut microbiota. In addition, we demonstrated that administration of bismuth, an H2S scavenger, prevented A. parvulum-induced colitis. Our findings identified Atopobium parvulum as a major mediator of inflammation severity, and revealed an alteration of the balance between the production and detoxification of H2S in the gastrointestinal tract.

2022-02-22 | PXD000690 | Pride

Single-cell RNA-sequencing of mouse thymic epithelial cells across the first year of life

Project description:The thymus shapes the T cell receptor repertoire, and is one of the first organs to rapidly age, with gross changes in cellularity and architecture. To resolve the nature of these changes we used SMART-Seq2 on FACS purified thymic epithelial cells (TEC) across the first year of mouse life. We sorted 4 TEC populations in each of 5 mice at each age (1 week, 4 weeks, 16 weeks, 32 weeks and 52 weeks old).

2020-09-14 | E-MTAB-8560 | biostudies-arrayexpress

Multi-omic dissection of oncogenically active epiproteomes identifies drivers of proliferative or invasive breast tumors

Project description:Here we present a functional multi-omics method, interaction-Correlated Multi-omic Aberration Patterning or iC-MAP, which dissects intra-tumor heterogeneity and identifies in situ in real time the oncogenic consequences of multi-omics aberrations that drive proliferative/invasive tumor in individuals with poor prognosis. First, given epigenetic aberrations resulting from complex interactions between genetic susceptibility and environmental influences are the primary driving force of tumorigenesis, we applied our chromatin activity-based chemoproteomics (ChaC) method to characterize the tumor-phenotypic epiproteomes (epigenetic regulatory proteomes) in breast cancer (BC) patient tissues. A biotinylated ChaC probe UNC0965 that specifically binds to the oncogenically active histone methyltransferase G9a enabled the sorting/enrichment of a G9a-interacting epiproteome representing the predominant BC subtype in a tissue, which is separated from other cell types, especially non-malignant cells where G9a is less enzymatically active. ChaC then identified UNC0965-captured G9a interactors that are mostly involved in the oncogenic pathways associated with tumor cell viability and invasion. Using BC patient transcriptomic/genomic data we retrospectively identified the G9a interactor-encoding genes that show individualized iC-MAP in BC-subtypic patients with incurable metastatic disease, revealing essential drivers of proliferative or invasive BC phenotypes. Our iC-MAP findings can not only act as new diagnostic/prognostic markers to identify patient subsets with metastatic disease but also create precision therapeutic strategies that can match proliferative or invasive potential of individual patients.

2019-07-26 | PXD013795 | Pride

Functional enhancers at the gene-poor 8q24 cancer-linked locus

Project description:Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate, breast, and colon. These regions are far from any annotated gene and their biological activities have been unknown. Here we profiled a 5-megabase chromatin segment encompassing all the risk regions for RNA expression, histone modifications, and locations occupied by RNA polymerase II and androgen receptor (AR). This led to the identification of several transcriptional enhancers, which were verified using reporter assays. Two enhancers in one risk region were occupied by AR and responded to androgen treatment; one contained a single nucleotide polymorphism (rs11986220) that resides within a FoxA1 binding site, with the prostate cancer risk allele facilitating both stronger FoxA1 binding and stronger androgen responsiveness. The study reported here exemplifies an approach that may be applied to any risk-associated allele in non-protein coding regions as it emerges from genome-wide association studies to better understand the genetic predisposition of complex diseases. 20 Normal Prostate cDNA samples (no replicates), 4 cell line cDNA samples (each cell line in duplicate), 4 cell line Acetylated H3 ChIP (each line in duplicate), 2 cell line various histone modification and protein ChIPs (6 Abs LNCaP, 5 Abs PC3, each in duplicate). All samples were hybridized with matching genomic DNA as reference.

2009-12-18 | E-GEOD-19561 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

Single-nucleus RNA-seq of adult female and male mouse livers for sex-biased gene expression analyses

Project description:To obtain new insight into the sexual dimorphism of mammalian livers, single-nucleus RNA-seq was performed on the liver samples from two female and two male adult mice. The single-nucleus libraries were generated on the 10X Chromium Next GEM Single Cell 3ʹ platform and sequenced on Illumina NextSeq 550. We used the data to understand the heterogeneity and sex-biased gene expression of liver cell types. The data revealed significant sex differences primarily focused on hepatocytes. Specifically, from the sex-biased genes detected at the bulk tissue level, we observed that male-biased genes are more highly expressed in male hepatocytes, and female-biased genes are more highly expressed in female hepatocytes.

2023-08-03 | E-MTAB-12180 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data