Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of proteasome inhibition on total and poly-ubiquitylated proteomes of human A549 lung adenocarcinoma cells in different proliferation states

ABSTRACT: Cellular stress responses are crucial for survival in sub-optimal conditions, and almost invar-iably involve proteome-wide alterations at the levels of protein abundance and post-translational modification with poly-ubiquitin chains (poly-ubiquitylation). However, most of our understanding of human cell stress responses at the protein level stems from experiments in rapidly-dividing cell culture models. Here, we used the A549 human diploid lung adenocarci-noma cell line (alveolar, type-2) in proliferating or bleomycin-induced senescent states, to ex-plore their responses to a severe proteotoxic stress with the proteasome inhibitor bortezomib (100 nM for 24 hours) at the total and poly-ubiquitylated proteome levels.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Harvey Johnston

LAB HEAD: Rahul Samant

PROVIDER: PXD067220 | Pride | 2025-10-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	File_description_summary.xlsx	Xlsx
	Ref1023_TMT18_A549_BTZ.msf	Msf
	Ref_1024-10_FAIMS_RTS_MS3.raw	Raw
	Ref_1024-11_FAIMS_RTS_MS3.raw	Raw
	Ref_1024-12_FAIMS_RTS_MS3.raw	Raw

Items per page:

1 - 5 of 21

Similar Datasets

Effect of heat-shock on total and poly-ubiquitylated proteomes of human A549 lung adeno-carcinoma cells in different proliferation states

Project description:Cellular stress responses are crucial for survival in sub-optimal conditions, and almost invar-iably involve proteome-wide alterations at the levels of protein abundance and post-translational modification with poly-ubiquitin chains (poly-ubiquitylation). However, most of our understanding of human cell stress responses at the protein level stems from experiments in rapidly-dividing cell culture models. Here, we used the A549 human diploid lung adenocarci-noma cell line (epithelial, alveolar type-2) in proliferating or bleomycin-induced senescent states, to explore their responses to a severe heat-shock (44 degrees Celsius for 2 hours) at the total and poly-ubiquitylated proteome levels

2025-10-08 | PXD067153 | Pride

Effect of heat-shock on total, poly-ubiquitylated, and insoluble proteomes of human IMR-90 fibroblasts in different proliferation states

Project description:Cellular stress responses are crucial for survival in sub-optimal conditions, and almost invar-iably involve proteome-wide alterations at the levels of protein abundance, post-translational modification with poly-ubiquitin chains (poly-ubiquitylation), and solubility. However, most of our understanding of human cell stress responses at the protein level stems from experi-ments in rapidly-dividing cell culture models. Here, we used primary human diploid lung fibro-blasts (IMR-90) in proliferating, contact-inhibited quiescent, or doxorubicin-induced senes-cent states, to explore their responses to a severe heat-shock (44 degrees Celsius for 2 hours) at the total, poly-ubiquitylated, and insoluble proteome levels.

2025-10-08 | PXD067225 | Pride

Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers

Project description:The mammalian SWI/SNF helicase SMARCA4 is frequently mutated in cancer and inactivation results in a cellular dependence on its paralog, SMARCA2, thus making SMARCA2 an attractive synthetic lethal target. However, published data indicates that achieving a high degree of SMARCA2 selectivity is likely essential to afford an acceptable therapeutic index and this has been a considerable challenge due to the homology between paralogs. Herein we report the discovery of the first potent and selective SMARCA2 proteolysis-targeting chimera (PROTAC) molecule. Selective degradation was achieved in the absence of selective PROTAC binding and translated to potent in vitro growth inhibition and in vivo efficacy in SMARCA4 mutant models, compared to wild type models. Global ubiquitin mapping and proteome profiling revealed no unexpected off-target degradation. Our study thus highlights the ability to transform a non-selective SMARCA2-binding ligand into a selective and efficacious in vivo SMARCA2 PROTAC, providing a potential therapeutic opportunity for SMARCA4 mutant patients.

2022-09-22 | PXD036865 | Pride

Modeling CRL4A ligase complex to predict target protein ubiquitination induced by CRBN-recruiting PROTACs

Project description:PROteolysis TArgeting Chimeras (PROTACs) are bifunctional small molecules that can simultaneously recruit target protein and E3 ligase to form a ternary complex (target protein / PROTAC / E3 ligase), leading to target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities enabling targeting of previously "undruggable" proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by CRBN-based PROTACs,

2022-05-19 | PXD030213 | Pride

Ubiquitin remenants identification following in vitro assay of 20S and 26S proteasome using naked and ubiquitined cyclin

Project description:A systematic and comparative study of the proteolysis products generated by purified human 26S and 20S proteasome following the in vitro cleavage of non-modified (naked), mono-ubiquitinated and poly-ubiquitinated cyclin B.

2021-11-02 | PXD028912 | Pride

Multiplexed phosphoproteomics of low cell numbers using SPARCE

Project description:Understanding cellular diversity and disease mechanisms requires global analysis of proteins and their modifications. Ultrasensitive mass spectrometry-based proteomics enables unbiased protein-level analysis of low cell numbers, down to single cells. However, phosphoproteomics remains limited to high-input samples due to sample losses and poor reaction efficiencies associated with processing low cell numbers. In this study, we have used isobaric stable isotope labelling as a promising approach for reproducible and accurate quantification of low abundant phosphopeptides. Here, we introduce SPARCE (Streamlined Phosphoproteomic Analysis of Rare CElls) for multiplexed phosphoproteomic analysis of low cell numbers. SPARCE outperforms traditional methods by enhancing labelling efficiency and phosphoproteome coverage. To demonstrate the utility of SPARCE, we analysed four patient-derived glioblastoma stem cell lines, reliably quantifying phosphosite changes from 1,000 FACS-sorted cells. This workflow expands the possibilities for signalling analysis of rare cell populations.

2025-04-01 | PXD056902 | Pride

Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B Cell Lymphoma

Project description:Polatuzumab Vedotin (Pola-V) is an antibody-drug conjugate directed to the CD79B subunit of the B cell receptor (BCR). When combined with conventional immunochemotherapy, Pola-V improves outcomes in DLBCL. To identify molecular determinants of sensitivity to Pola-V, we used CRISPR-Cas9 screening for genes that modulated the toxicity of Pola-V for lymphomas or the surface expression of its target, CD79B. Our results reveal a striking impact of CD79B glycosylation on Pola-V epitope availability on the lymphoma cell surface and on Pola-V toxicity. Genetic, pharmacological, and enzymatic approaches that remove terminal sialic acid residues from N-linked glycans enhanced lymphoma killing by Pola-V. Pola-V toxicity was also modulated by KLHL6, a ubiquitin ligase that targets CD79B for degradation in normal and malignant germinal center B cells, explaining its recurrent inactivation in germinal center-derived lymphomas. Our findings suggest precision medicine strategies to optimize Pola-V as a lymphoma therapeutic.

2024-07-12 | PXD043670 | Pride

Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

Project description:Turnover of nucleoplasmic transcripts by the multi-subunit RNA exosome is mediated by two adaptors; the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely been based on long-term factor depletion strategies. Here, we rapidly deplete a NEXT, a PAXT and a core-exosome component, uncovering direct consequences of their losses. Global proteome analyses displayed only minor changes, yet exposed the immediate co-depletion of exosome and adaptor subunits, reflecting possible sub-complex compositions. Parallel high-resolution 3’end sequencing of newly synthesized RNA confirmed earlier established long-term depletion phenotypes. Still, rapid NEXT depletion displayed a narrower phenotype, illustrated by its restricted effect on snoRNA-hosting introns, whereas long-term NEXT depletion data had suggested a more general role of the complex in mediating intron turnover. While this validates snoRNA-hosting introns as primary NEXT targets, our data suggest that nuclear 5’-3’ RNA decay is altered after prolonged NEXT depletion, obscuring interpretation. Further analysis of snoRNA-hosting introns also uncovered an unusual mode of core exosome-independent RNA decay. Due to its non-processive nature, we speculate that this reflects a hitherto undisclosed exosome-independent activity of the EXOSC10 ribonuclease.

2021-12-23 | PXD026774 | Pride

Signature cleavage in vitro assay of 20S and 26S proteasome using naked and ubiquitined cyclin

2021-11-02 | PXD018711 | Pride

TAG-TMTpro, a hyperplexing quantitative approach for high-throughput proteomic studies

Project description:Isobaric labeling is the most widely used multiplexing quantitative approach in proteomic studies, enabling the comparison of up to 18 samples in a single MS analysis. Expanding the multiplexing capacity is of great necessity for high-throughput proteomic studies. Herein, we establish a novel TAG-TMTpro approach by introducing Ala or Gly residues to peptides prior to TMTpro labeling, which is able to triple the quantitative capacity of TMTpro. We systematically evaluated the Boc-Ala-OSu and Boc-Gly-OSu reaction and optimized the conditions for labeling, side-product elimination and Boc deprotection. We validated the identification and quantification performance using E. coli and HeLa cell lysates. We demonstrated that the TAG-TMTpro approach resulted in good identification reproducibility and reliable quantitative accuracy. The TAG-TMTpro is able to triple the multiplexing capacity of TMTpro reagents, and is a versatile quantitative approach for high-throughput proteomic studies.

2022-10-14 | PXD033711 | Pride