Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human RBM33_HNSC_LC-MS/MS in project "RBM33 Acts as an m6A Reader Required for ALKBH5-mediated m6A Demethylation"

ABSTRACT: To identify the potential RBM33 interaction proteins, we established UM-SCC-1 cells stably expressing pCDH-Strep-Vec, or Strep-RBM33. After strep-tactin beads enrichment of RBM33 and its ascociated proteins, all the pull-downed proteins are subjected to LC-MS/MS analysis.

INSTRUMENT(S): LCQ Classic

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Keratinocyte

SUBMITTER: Fang Yu

LAB HEAD: Zhijian Qian

PROVIDER: PXD033861 | Pride | 2023-05-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Coomassie_staining_gel.tif	Other
	Publication_Report_for_PM-859-search.xls	Xls
	RBM33-UM-SCC-1.sf3	Other
	Strep-RBM33.mgf	Mgf
	Strep-RBM33.raw	Raw

Items per page:

1 - 5 of 8

Similar Datasets

Genetic aberrations in MAP kinase pathway play an important role in erlotinib resistance in head and neck cancer

Project description:Epidermal growth factor receptor (EGFR), a receptor tyrosine kinase is overexpressed in 90% of Head and neck squamous cell carcinoma (HNSCC) patients. Clinical trials with EGFR-targeted tyrosine kinase inhibitors such as erlotinib have shown a modest activity in HNSCC alternate mechanisms of resistance are acquired. To investigate these acquired mechanisms of resistance and identify novel therapeutic targets we employed whole exome sequencing of an isogenic pair of erlotinib sensitive (SCC-S) and resistant (SCC-R) HNSCC cell line. We observed single nucleotide variations and copy number alterations in genes related to RAS-RAF-MEK-ERK pathway. To assess the effects of these variations on cellular kinome and we employed SILAC-based phosphoproteomic analysis of SCC-S and SCC-R cell lines. Quantitative phosphoprotein profiling led to identification of 5558 unique phosphopeptides and 5025 unique phosphosites corresponding to 2344 proteins. We observed, 903 phosphopeptides belonging to 579 proteins and 518 phosphopeptides belonging to 368 proteins to be hyper and hypophosphorylated (≥2 fold) in SCC-R cells, respectively. Bioinformatics analysis of differentially phosphorylated proteins showed enrichment of proteins involved in MAPK pathway downstream of EGFR. We identified and validated activation of proteins related to MAPK pathway and its downstream targets in SCC-R cells. We further demonstrated that MAP2K1 inhibitor can be used as an alternative to erlotinib in HNSCC.

2019-12-18 | PXD007785 | Pride

SILAC-based proteomic approach to delineate molecular alterations associated with erlotinib resistance in head and neck squamous cell carcinoma

Project description:Although Epidermal growth factor receptor (EGFR) is overexpressed in 90% of Head and neck squamous cell carcinoma (HNSCC) patients. Clinical trials with EGFR-targeted small molecule inhibitors such as erlotinib have shown a modest activity in recurrent or advanced HNSCC. To investigate the acquired mechanisms of erlotinib resistance we employed SILAC-based total proteomic analysis of an isogenic pair of erlotinib sensitive (SCC-S) and resistant (SCC-R) HNSCC cell line. This resulted in the identification of 5,427 proteins of which 532 proteins were overexpressed and 527 proteins were downregulated in SCC-R cells as compared to SCC-S cells (≥2 fold). Several proteins known to mediate erlotinib resistance in HNSCC and lung cancer were found to be dysregulated. Bioinformatics analysis of differentially expressed proteins showed enrichment of proteins involved in focal adhesion kinase (FAK) pathway downstream of EGFR. We identified CUB-domain containing protein 1 (CDCP1) and integrin β1 as upstream regulators of FAK signalling pathway to be overexpressed. We further demonstrated that CDCP1 and FAK can be targeted in combination as an alternative to erlotinib in HNSCC.

2019-12-18 | PXD007768 | Pride

miRNA expression profiling in squamous cell carcinoma (SCC)

Project description:Despite its prevalence, the molecular basis of squamous cell carcinoma (SCC) remains poorly understood. We recently identified the developmental transcription factor Grhl3 as a potent tumor suppressor of SCC, and demonstrated that targeting of Grhl3 by a miR-21-dependent proto-oncogenic network underpins SCC in humans. Reduced levels of GRHL3 and its target gene PTEN are evident in human skin, and head and neck SCC, associated with increased expression of miR-21, which targets both tumor suppressors. Our data defines the miR-21-GRHL3-PTEN-axis as a critical tumor suppressor pathway in SCC. Total RNA was isolated from two SCC primary tissue samples and their matched normal skin controls.

2013-01-18 | E-GEOD-32868 | biostudies-arrayexpress

SILAC-based quantitative tyrosine phosphoproteomic profiling identifies alternative therapeutic targets to erlotinib in head and neck squamous cell carcinoma

Project description:Epidermal growth factor receptor (EGFR), a receptor tyrosine kinase is overexpressed in 90% of Head and neck squamous cell carcinoma (HNSCC) patients. Clinical trials with EGFR-targeted tyrosine kinase inhibitors such as erlotinib have shown a modest activity in HNSCC alternate mechanisms of resistance are acquired. To investigate these acquired mechanisms of resistance and identify novel therapeutic targets we employed SILAC-based tyrosine phosphoteomic analysis of an isogenic pair of erlotinib sensitive (SCC-S) and resistant (SCC-R) HNSCC cell line. Quantitative phosphotyrosine profiling revealed 98 phosphopeptides belonging to 64 proteins and 66 phosphopeptides belonging to 52 proteins to be hyper and hypophosphorylated (≥2 fold) in SCC-R cells, respectively. Several proteins such MET proto-oncogene, receptor tyrosine kinase (MET) and CRK like proto-oncogene, adaptor protein (CRKL) known to mediate erlotinib resistance in HNSCC and lung cancer were found to be dysregulated. Bioinformatics analysis of differentially phosphorylated proteins showed enrichment of proteins involved in focal adhesion kinase (FAK) pathway downstream of EGFR. We identified and validated activation of several phosphorylation sites of protein tyrosine kinase 2 (PTK2) in SCC-R cells and its downstream targets. We further demonstrated that CUB-domain containing protein 1 (CDCP1), an upstream regulator of PTK2 activity and PTK2 can be targeted in combination as an alternative to erlotinib in HNSCC.

2022-10-13 | PXD007769 | Pride

FTO: linking m6A demethylation to adipogenesis.

Project description:Polymorphism of the FTO gene encoding an N(6)-methyladenosine (m(6)A) RNA demethylase was robustly associated with human obesity; however, the mechanism by which FTO affects metabolism, considering its emerging role in RNA modification, is still poorly understood. A new study published in Cell Research reports novel functions implicating FTO in the regulation of mRNA alternative splicing in the control of adipogenesis.

| S-EPMC4650590 | biostudies-other

ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas (RNA-Seq I)

Project description:After characterizing super-enhancer-associated chromatin dynamics accompanied by malignant progression of skin stem cells, we show that ETS family members auto-regulate themselves and a cohort of cancer-associated super-enhancer transcription factors which together are essential for tumor maintenance. Mouse skin squamouse cell carcinoma (SCC) tumor-initiating stem cells (SCC-SC), hair follicle stem cells (HF-SC) and epidermal stem cells (Epi-SC) were FACS-prufied for RNA-sequencing.

2015-11-22 | E-GEOD-72146 | biostudies-arrayexpress

Altered DNA Methylation Patterns in Human Oral Squamous Cell Carcinoma Cells

Project description:To gain insight into the DNA methylation changes during OSCC carcinogenesis, we utilized cytosine conversion and next generation sequencing based technique- enhanced reduced representation bisulfite sequencing (ERRBS) - to assess DNA methylation in cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells. OKF6-TERT1R cells and SCC-9 cells were plated in 10 cm2 tissue culture plates at the density of 2 M-CM-^W 106 cells/plate. Total genomic DNA was extracted from OKF6-TERT1R and SCC-9 cells using DNeasy Blood & Tissue Kit (Qiagen, Germantown, MD, USA), including an RNAse treatment step.

2014-10-28 | E-GEOD-51752 | biostudies-arrayexpress

The m6A reader YTHDC1-mediated lncRNA CTBP1-AS2 m6A modification accelerates cholangiocarcinoma progression.

Project description:BackgroundCholangiocarcinoma (CCA) is a serious malignancy originating from the bile ducts and the second most common primary liver cancer. Long non-coding RNA (lncRNA) is a functional lncRNA that plays an important role in human cancers. However, the role and underlying mechanisms of CTBP1-AS2 in CCA remain unknown.PurposeIn this study, we investigated the functional role and mechanism of long-stranded non-coding RNA (lncRNA) C-terminal binding protein 1 antisense RNA 2 (CTBP1-AS2) in CCA progression.ResultIn the present study, the bioinformatics analysis revealed that YTHDC1 and CTBP1-AS2 were significantly upregulated, and it was confirmed in cholangiocarcinoma tissues from CCA patients. Meanwhile, we demonstrated that knockdown of YTHDC1 or lncRNA CTBP1-AS2 inhibited CCA cell proliferation, migration and invasion, blocked the cell cycle in G2/M phase and promoted apoptosis of CCA cells. In addition, lncRNA CTBP1-AS2-mediated N6-methyladenosine (m6A) methylation levels were significantly elevated in cholangiocarcinoma tissues, whereas knockdown of YTHDC1 resulted in a significant down-regulation of m6A methylation levels by lncRNA CTBP1-AS2.ConclusionOur results suggest that YTHDC1 affects cholangiocarcinoma progression by modifying the lncRNA CTBP1-AS2 m6A, and CTBP1-AS2 may be a promising therapeutic target for CCA.

| S-EPMC10559219 | biostudies-literature

Functional and Mechanistic Studies of XPC DNA-Repair Complex as Transcriptional Coactivator in Embryonic Stem Cells

Project description:We recently identified the DNA repair complex XPC-RAD23B-CETN2 as a stem cell coactivator (SCC) required for OCT4 and SOX2 transcriptional activation. Here we investigate genome-wide the role of SCC in murine ESCs by mapping regions bound by its RAD23B subunit in wild type and Xpc-/- ESCs, and analyzing transcriptional profiles of SCC-depleted ESCs. RAD23B ChIP-seq in wild type murine ESCs was performed in two replicates; normal IgG were used as controls. RAD23B ChIP-seq in Xpc-/- mESCs was compared to normal IgG. Antibodies to immunoprecipitate RAD23B were raised in guinea pigs against the 108-177 peptide of murine RAD23B protein (NP_033037). Anti-sera were affinity-purified. For RNA-seq, we compared wild type JM8.N4 cells with either Rad23b-/- cells, Rad23b-/-Xpc KD1 or Rad23b-/-Xpc KD2 cells. Xpc was knocked down with two independent shRNAs (KD1 and KD2).

2015-04-20 | E-GEOD-64040 | biostudies-arrayexpress

Proteins identified by LC-MS/MS analysis to associate with RecJ4-StrepII (vs. empty vector).

Project description:RecJ4 association with RecJ3, RNase J and Cdc48A investigated by pullingown strep tagged-RecJ4 with its partner proteins

2023-06-22 | PXD019933 | Pride