Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TET1 Functions as a Tumor Suppressor in Lung Adenocarcinoma Through Epigenetic Remodeling and Immune Modulation.

ABSTRACT: TET genes have been characterized as tumor suppressors because their expression levels are reduced in many human cancers including lymphoma, prostate, and pancreas, and TET2 gene mutations are common in hematological cancers. In contrast, TET1 was recently reported to be overexpressed in triple negative breast cancer and to act as a protooncogene in lung cancer. In our study, TET1 knock out and overexpressed H441 cells were isolated for multi-omics analyses.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Epithelial Cell

DISEASE(S): Lung Adenocarcinoma

SUBMITTER: Monica Kruk

LAB HEAD: Natalia Y. Tretyakova

PROVIDER: PXD066092 | Pride | 2026-01-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Global_H441_TET1KO_Fraction_W1.raw	Raw
	Global_H441_TET1KO_Fraction_W10.raw	Raw
	Global_H441_TET1KO_Fraction_W11.raw	Raw
	Global_H441_TET1KO_Fraction_W12.raw	Raw
	Global_H441_TET1KO_Fraction_W13.raw	Raw

Items per page:

1 - 5 of 66

Publications

TET1 functions as a tumor suppressor in lung adenocarcinoma through epigenetic remodeling and immune modulation.

Rahim Abdur A Ruis Brian L BL Rajczewski Andrew T AT Kruk Monica E ME Tretyakova Natalia Y NY

Epigenetics & chromatin 20250811 1

<h4>Background</h4>Ten-Eleven Translocation (TET1-3) dioxygenases oxidize 5-methylcytosine (5mC) in DNA to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), initiating DNA demethylation. Since their discovery in 2009, there have been contradictory reports regarding the roles of TET proteins in cancer. TET genes have been characterized as tumor suppressors because their expression levels are reduced in many human cancers including lymphoma, prostate, ...[more]

PMID: 40790761

Similar Datasets

PRM of Ganoderma lucidum dikaryon and monokaryons

Project description:PRM was performed to validate TMT-based quantification of Ganoderma lucidum dikaryon and monokaryons proteome to probe the profiles of different biological processes and their coordination that contribute to the dikaryon growth advantage.

2025-07-09 | PXD051874 | Pride

An integrated multi-omic workflow reveals markers of host-microbe dynamics in clinical cystic fibrosis samples

Project description:Airway microbiota composition correlates with cystic fibrosis (CF) progression, however, microbial drivers of disease remain unclear. MS-based metaproteomics of bronchoalveolar lavage fluid (BALF) offers insights into both host and microbe dynamics and potential interactions. However, detection of microbial proteins, and analysis of their interaction with host proteins is analytically challenging. As a solution, we have developed a novel, integrated workflow coupling deep MS-based BALF analysis, with customized bioinformatic processing of both host and microbial proteins, generating a panel of verified host and microbe peptide candidates suitable for targeted analysis within individual patient samples. We have utilized this workflow in our ongoing work to identify a promising host and microbe peptide panel for application to CF disease progression studies.

2024-06-25 | PXD041457 | Pride

Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast

Project description:In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-CDK activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in protein production rate, which do not scale with cell size dynamics, but -following the intrinsic metabolic dynamics- peak around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population level, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells, across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.

2019-10-29 | PXD015327 | Pride

Neurodegeneration and humoral response proteins in cerebrospinal fluid associate with pediatric-onset multiple sclerosis -- Validation

Project description:The pathogenesis of multiple sclerosis (MS) remains to be elucidated. Pediatric-onset MS (POMS) represents the earliest stage of the disease. CSF proteins in POMS may therefore provide causal information. Therefore, the aim of the current study was to analyze CSF proteins in children with an initial CNS acquired demyelinating syndrome (ADS) and to make a comparison between POMS and monophasic ADS (mADS). Patients were selected from two prospective pediatric ADS studies. Liquid chromatography-mass spectrometry was performed in a Dutch discovery cohort (POMS n=28; mADS n=39). Parallel reaction monitoring-mass spectrometry was performed on selected proteins more abundant in POMS with ≥ 8 unique peptides in a combined Dutch and Canadian validation cohort (POMS n=48; mADS n=106).

2022-09-30 | PXD031022 | Pride

Data-independent Acquisition - Parallel Reaction Monitoring (DIA-PRM) Acquisition Reveals Alteration of Lysosomal Hydrolases in a Mouse Model of Metachromatic Leukodystrophy

Project description:For the reproducible analysis of peptides by mass spectrometry-based proteomics, data-independent acquisition (DIA) and parallel/multiple reaction monitoring (PRM/MRM) deliver unrivalled performance with respect to sensitivity and reproducibility. Both approaches come, however, with distinct advantages as well as shortcomings. While DIA enables the unbiased analysis of a large fraction of a sample’s proteome, it shows limitations with respect to dynamic range and the reproducible identification/quantification of low-abundant proteins. PRM, on the other hand, is ideally suited to reproducibly and sensitively quantify selected peptides originating from the proteins of interest, even if they are low-abundant, but no knowledge of the remaining sample is obtained. Here, we combine both methods into a mixed DIA-PRM acquisition approach, thereby merging the benefits of each method, while operating at reduced machine run times and sample amount, relative to individual measurements. We demonstrate the feasibility of the approach by merging a scheduled PRM assay for 59 low-abundant lysosomal hydrolases, covered through 103 peptides, with a DIA data acquisition scheme. After benchmarking DIA-PRM against mouse embryonic fibroblast (MEF) whole cell lysates, we use the approach to investigate disease progression in brain tissues of a mouse model of metachromatic leukodystrophy (MLD). In these tissues, we found a progressive increase in lysosomal hydrolases in MLD as compared to healthy control mice .

2025-05-07 | PXD052313 | Pride

Tet1 as a Negative Regulator of Somatic Cell Reprogramming

Project description:Tet1 is a hydroxylase known for its role in the conversion of 5-methylcytosines (5mC) to 5-hydroxymethylcytosines (5hmC) involved in the possible active demethylation process and gene expression regulation1-5.M-BM- As somatic cell reprogramming involves the re-activation of pluripotency genes and the silencing of somatic ones6, it remains unclear whether Tet1 plays a positive or negative role in the reprogramming process. Here we show that Tet1 deficiency enhances reprogramming and its overexpression impairs reprogramming. Mechanistically, we demonstrated that Tet1 represses the early obligatory process of mesenchymal to epithelial transition (MET) during reprogramming7,8. Thus, our findings not only define a negative role for Tet1 in somatic cell reprogramming, but also suggest that the Tet enzymes regulate cell fate through distinctive mechanisms. Examination of genome DNA hmC modifications in 2 conditions: individually overexpressed Tet1CD or Tet2CD during MEF reprogramming; Examination of mRNA levels in five different conditions: individually overexpressed DR or Tet1CD or Tet1CDmut or Tet2CD or Tet2CDmut, during MEF reprogrammig.

2013-03-08 | E-GEOD-44935 | biostudies-arrayexpress

Quantification of calcyclin and heat shock protein 90 in sera from women with and without preeclampsia by mass spectrometry

Project description:Maternal serum levels of calcyclin and heat shock protein 90 were compared throughout pregnancy from the first trimester till term among women with preeclampsia (PE) and age-matched normotensive pregnant controls (C). Serum samples from two different studies, a nested case-control study embedded in the Rotterdam periconception cohort and the Lepra Study both conducted at the Erasmus MC in Rotterdam. They were collected in the first, second and third trimester of pregnancy in 43 patients with preeclampsia, consisting of 20 early-onset and 23 late-onset preeclampsia, and 46 normotensive pregnant controls. A serum based 2D LC-MS assay on Parallel Reaction Monitoring mode using a high resolution tribrid mass spectrometer was used to quantify both calcyclin and heat shock protein 90.

2018-11-21 | PXD009025 | Pride

Phosphoproteins in extracellular vehicles as candidate markers for breast cancer

Project description:The state of protein phosphorylation can be a key determinant of cellular physiology such as early stage cancer, but the development of phosphoproteins from biofluids for disease diagnosis remains elusive. Here we demonstrate, for the first time, a strategy to isolate and identify phosphoproteins in extracellular vehicles from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides, representing 2108 phosphoproteins, in EVs isolated from small volume of plasma samples. Using label-free quantitative proteomics, we quantified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer than in healthy controls. Multiple novel biomarkers were validated in 13 patients using Paralleled Reaction Monitoring and antibody- and non-antibody based assays. The study demonstrated that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.

2017-03-23 | PXD005214 | Pride

Blood Proteome profiling for protein biomarker discovery in Broilers

Project description:Analysis of the blood proteome allows identification of proteins related to changes upon certain physiological conditions. The pathophysiology of necrotic enteritis (NE) has been extensively studied. While intestinal changes have been very well documented, data addressing NE-induced alterations in the blood proteome are scant, although these might have merit in diagnostics. Considering recent technological advancements in proteomics and pressing need for tools to access gut health, the current study employs mass-spectrometry (MS) proteomics to identify biomarkers for gastrointestinal health of broilers chickens. Untargeted proteomics investigation was conducted on chicken blood plasma in animals under NE challenge. Two MS-strategies were used for analysis: DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition). DIA showed superior completeness and quantification of the acquired data, despite high degree of agreement in identification and quantification between both approaches. Identified differentially expressed proteins shared by DDA and DIA represent responses of animals to infection and may serve as potential biomarkers. Experimental validation through ELISA immunoassays for selected regulated proteins confirmed medium-to-high levels of inter-protein correlation, along with positive correlation between the methods. Functional analysis showed enhanced defense, immune, and acute phase responses, alongside reduced signaling, regulatory, and cell adhesion activities in infected animals.

2025-05-07 | PXD061607 | Pride

Targeted quantification of flg22-responsive BSU1 phosphorylation sites

Project description:To confirm the flg22-induced BSU1 phosphorylation site, we performed targeted quantification by PRM analysis with SILIA IP-MS sample. The isotopes switched in replicate experiments.

2023-03-10 | PXD016257 | Pride

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