Dataset Information

Quantitative Proteomic Atlas of Ubiquitination in Hepatocellular Carcinoma

ABSTRACT: Ubiquitination plays a critical role in human hepatocellular carcinoma (HCC) genesis and metastasis, but how these processes affect systemic ubiquitinome still remains unclear. In this study, our dataset of around 12,000 diGly modified sites was identified providing a valuable insight into HCC. We find both the diGly sites and ubiquitin chains undergo bulk increase in HCC, suggesting the boost of diGly modification activities in tumor genesis. Two of the most significant alterations of ubiquitination modification in HCC concern components of proteasome and antigen presentation activity. Moreover, during the progression of HCC metastasis, we discover a more extensive diGly modified sites with shorter ubiquitin chains and reveal the key role of ubiquitination modification on proteins involving cell-cell adhesion.

ORGANISM(S): Homo Sapiens

SUBMITTER: Lanjuan Li

PROVIDER: PXD011895 | iProX | Tue Apr 14 00:00:00 BST 2020

REPOSITORIES: iProX

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Publications

Integrative proteomics reveals the role of E3 ubiquitin ligase SYVN1 in hepatocellular carcinoma metastasis.

Ji Feiyang F Zhou Menghao M Sun Zeyu Z Jiang Zhengyi Z Zhu Huihui H Xie Zhongyang Z Ouyang Xiaoxi X Zhang Lingjian L Li Lanjuan L

Cancer communications (London, England) 20210701 10

<h4>Background</h4>Tumor metastasis is a major factor for poor prognosis of hepatocellular carcinoma (HCC), but the relationship between ubiquitination and metastasis need to be studied more systematically. We analyzed the ubiquitinome of HCC in this study to have a more comprehensive insight into human HCC metastasis.<h4>Methods</h4>The protein ubiquitination levels in 15 HCC specimens with vascular invasion and 15 without vascular invasion were detected by ubiquitinome. Proteins with significa ...[more]

PMID: 34196494

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Project description:Post-translational control by ubiquitin regulates various aspects of cellular biology. This chemical modification on proteins presents itself in numerous iterations, from a single mono-ubiquitination event to chains of poly-ubiquitin. Among the various types of poly-ubiquitin constructed are untethered species that comprise a series of ubiquitin moieties linked to one another, but free from another protein. The current notion is that these unanchored poly-ubiquitin species are deleterious to the cell and are rapidly deconstructed. We recently examined the toxicity and utilization of untethered poly-ubiquitin in an intact organism by using the fruit fly, Drosophila melanogaster. We found that these ubiquitin species are largely innocuous to flies and that free poly-Ub can be controlled by being degraded by the proteasome or being conjugated onto another protein as a single unit. However, whether the fly is mounting an organismal defense against untethered chains was not explored in detail. Here, we conducted RNA-seq analyses to examine at the transcriptome level the impact of unanchored poly-Ub in the fly. We found ~90 transcripts whose expression is altered in the presence of different types of unanchored poly-ubiquitin. The set of genes identified was mostly devoid of ubiquitin-, proteasome- or autophagy-related components. The largest gene ontology category identified, housing ~15 of the altered genes, was proteolysis. The seeming absence of a large and multipronged response to unanchored ubiquitin chains in the fly supports the conclusion that these species need not be toxic in vivo and underscores the need to reexamine the role of free ubiquitin chains in the cell. We designed two types of poly-Ub chains with six Ub molecules in tandem. They cannot be cleaved by DUBs (there are no "GG" motifs linking the Ub molecules). Ub6-GG can be conjugated in toto onto other proteins; Ub6-Stop cannot. We drove ubiquitous expression using sqh-Gal4, and then performed RNA-Seq on adult flies to determine any cellular response to the presence of our unanchored Ub chains.

Dataset Information

Quantitative Proteomic Atlas of Ubiquitination in Hepatocellular Carcinoma

Publications

Integrative proteomics reveals the role of E3 ubiquitin ligase SYVN1 in hepatocellular carcinoma metastasis.

Similar Datasets

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