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USP13 dictates RAN turnover and vulnerability to ferroptosis in diffused large B cell lymphoma (DLBCL)

ABSTRACT: To identify the substrates of deubiquitinase USP13, we used a protein label-free quantitation technique, which involves mass spectrometry analysis of peptides from protein digests using liquid chromatography, to identify candidate substrates of USP13 that interact with it from co-immunoprecipitation (Co-IP) of HEK293T cells and candidate substrates of USP13 that are upregulated by its overexpression in HEK293T cells, from the data sets of the full protein profile and protein-protein interactions.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Large B-cell Lymphoma

SUBMITTER: Xuan Qiao

LAB HEAD: Boheng Li

PROVIDER: PXD056804 | Pride | 2025-12-08

REPOSITORIES: Pride

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Publications

USP13 dictates Ran turnover and vulnerability to ferroptosis in diffuse large B cell lymphoma (DLBCL).

Qiao Xuan X Yang Xingmeng X Diao Yuanhao Y Li Qiuxiang Q Wang Xianhuo X Li Chong C Yang Zailin Z Chng Wee Joo WJ Li Boheng B

Cell death & disease 20251128 1

Diffuse large B-cell lymphoma (DLBCL) is one of the most common and lethal B-cell malignancies worldwide, with high relapse rate after standard treatment, and the relapsed cases are often difficult to treat. Ubiquitination has a pivotal role in cellular protein homeostasis and tumorigenic deubiquitinases (DUBs) stabilize oncoproteins during carcinogenesis. In this study, we have identified USP13 as one of the abnormally-overexpressed and stage-related DUBs in DLBCL critical to disease pathogenes ...[more]

PMID: 41315297

Similar Datasets

USP13 dictates RAN turnover and vulnerability to ferroptosis in diffused large B cell lymphoma (DLBCL)

Project description:To identify the substrates of deubiquitinase USP13, we used a protein label-free quantitation technique, which involves mass spectrometry analysis of peptides from protein digests using liquid chromatography, to identify candidate substrates of USP13 that interact with it from co-immunoprecipitation of HEK293T cells and candidate substrates of USP13 that are upregulated by its overexpression in HEK293T cells, from the data sets of the full protein profile and protein-protein interactions.

2025-12-08 | PXD056840 | Pride

Interrogating kinase-substrate relationships with proximity labeling and phosphorylation enrichment

Project description:Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase “ON” and kinase “OFF” conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification. TMT1: pAPEX-MAPK1 experiment in HEK293T cells TMT2: pAPEX-MAPK1 experiment in HCT116 cells TMT3: pAPEX-PKA experiment in HEK293T cells

2022-03-11 | PXD028150 | Pride

Internally Tagged Ubiquitin: a Tool to Identify Linear Polyubiquitin-modified Proteins by Mass Spectrometry

Project description:Even though ubiquitination controls a plethora of cellular processes, modifications by linear polyubiquitin have so far only been linked with acquired and innate immunity, lymphocyte development and genotoxic stress response. Until now, a single E3 ligase complex (LUBAC), one specific deubiquitinase (Otulin) and a very few substrates have been identified. The existing methods for the study of lysine-based polyubiquitination are not suitable for the detection of linear polyubiquitin-modified proteins. Here, we present a novel approach to discovering linear polyubiquitin-modified substrates by combining lysine-less internally tagged ubiquitin (INT-Ub.7KR) with SILAC-based mass spectrometry. We applied our approach in TNFα-stimulated T-Rex HEK293T cells and afterwards validated newly identified linear polyubiquitin targets. Moreover, we demonstrated that linear polyubiquitination of the novel LUBAC substrate TRAF6 is essential for the NFkappaB signalling. Overall, we have established a powerful method for the detection of linear polyubiquitin substrates.

2017-03-21 | PXD005878 | Pride

Differential expression of genes after over expression of miR-23a~27a~24-2 cluster in human embryonic kidney cells

Project description:The experiment was deigned to identify the genes which get altered after the over expression of miR-23a~27a~24-2 cluster in HEK293T cells. The HEK293T cells plated in 6-well plate were transfected with two different concentrations of cloned miRNA cluster i.e 2micrograms and 4micrograms per well. Biological duplicates of 3 samples were used viz. control HEK293T cells, HEK293T cells transfected with 2micrograms of the cloned cluster and HEK293T cells transfected with 4micrograms of the cloned cluster.

2010-07-30 | E-GEOD-20158 | biostudies-arrayexpress

USP13 dictates RAN turnover and vulnerability to ferroptosis in diffused large B cell lymphoma (DLBCL)

Project description:USP13 dictates RAN turnover and vulnerability to ferroptosis in diffused large B cell lymphoma (DLBCL)

| PRJNA1177845 | ENA

Genetic analysis reveals a longevity associated protein modulating endothelial function and angiogenesis

Project description:Transcriptome analysis in HEK293T transfected with plasmid carrying different isoforms of BPIFB4 gene. This gene was previously associated with exceptional longevity in a GWAS study performed on three different populations. Results indicate an up-regulation of stress response genes and proteostasis genes in HEK293T transfected with plasmid carrying the longevity-associated variant (LAV) of BPIFB4. Total RNA obtained from HEK293T over-expressing wild-type or mutated form of BPIFB4.

2015-06-12 | E-GEOD-63912 | biostudies-arrayexpress

Gene expression analysis of HEK293T cells after CHMP5 gene modulation

Project description:Microarray-based gene expression analysis identified genes differentially expressed in HEK293T cells after CHMP5 gene modulation. In this study, HEK293T cells, silenced for CHMP5 using sh-CHMP5 was compared to genome wide expression changes when compared to cellular transfections with a sh-luciferase control by Significance Analysis of Microarray data. Further, overexpression of CHMP5 using the vector pCMV_CHMP5 was compared to cellular transfections with an empty vector pCMV in the cell line HEK293T

2010-07-08 | E-GEOD-17003 | biostudies-arrayexpress

The deafness gene DFNA5 induces programmed cell death through mitochondria and MAPK-related pathways [HEK293T]

Project description:The function of DFNA5 remained unknown for a long time, but previous functional studies by Op de Beeck et al. (2011) revealed that DFNA5 induces a growth defect in mutDFNA5- transfected HEK293T cells, as well as other cells, leading to PCD (Op de Beeck et al., 2011). The cell death-inducing capacity of DFNA5 was not only restricted to human cell lines, but was also observed in the yeast model Saccharomyces cerevisiae (Van Rossom et al., 2012). This inspired us to perform a transcriptomic analysis using two different model organisms (mammalian, HEK293T, and yeast, S.cerevisiae) to further elucidate the mechanisms related to DFNA5. Comparison of two HEK293T transfected cell populations, either with a WT or mutated DFNA5 gene. There are 5 biol reps for the WT transfected cells and 6 biol reps for the mut DFNA5 transfected cells.

2015-06-24 | E-GEOD-70167 | biostudies-arrayexpress

CUT&RUN Negative Controls in Human and Mouse

Project description:We performed 8 C&R tests in HEK293T human cells and 8 in mouse embryonic tissues from JAX Swiss mice by using either IgG or anti-HA antibodies. To increase diversity in this test, we used both the original C&R protocol and our recently developed C&R-LoV-U version for non-DNA-binding transcriptional co-factors. The aim was to experimentally validate our generated CUT&RUN blacklists containing problematic high signal regions.

2022-12-11 | E-MTAB-12411 | biostudies-arrayexpress

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

Project description:Idax/Cxxc4 is the CXXC domain protein that preferentially binds unmethylated CpG sites in vitro. By performing genome-wide mapping of Idax/Cxxc4, we report here that Idax is preferentially enriched in CpG-rich regions in genome including the promoters containing CpG islands. ChIP-seq binding site detection of Myc-Idax and Myc-IdaxDBM over cells expressing an empty vector in stable HEK293T cell lines; two replicates per condition (2x ChIP Myc-Idax, 2x ChIP Myc-IdaxDBM, 2xChIP empty vector)

2013-04-03 | E-GEOD-42958 | biostudies-arrayexpress

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