PXD039704

PXD039704 is an original dataset announced via ProteomeXchange.

Title	UBE2O targets a novel substrate IFIT3 for ubiquitination and degradation, impeding the interferon pathway activation and interferon sensitization in hepatocellular carcinoma
Description	Abstract Rationale: Interferon (IFN) plays a key role in immunotherapy by acting through interferon-stimulated genes. Interferon resistance limits its efficacy. Ubiquitination modification of key proteins is a popular research direction in hepatocellular carcinoma (HCC), and it is also one of the important mechanisms of interferon resistance. This study is dedicated to discovering the link between the pathogenesis of interferon resistance and ubiquitination modifications in HCC. Methods: We first combined the TCGA LIHC dataset and genes from the iUUCD 2.0 database to screen the most promising ubiquitination-related gene, UBE2O, in HCC using a bioinformatics approach. A combination of proteomic analysis, mass spectrometry, and survival analysis was used to screen for pathways and proteins negatively regulated by UBE2O. The effect of silencing UBE2O on interferon sensitivity in HCC cells was assessed using in vitro clone formation, migration, and wound healing assays and in vivo subcutaneous tumor xenograft models. Changes in the half-life of substrates following inhibition of UBE2O were assessed using a cycloheximide method. Two databases were used to predict ubiquitination sites on IFIT3. After rescue experiments to exclude the effect of substrate, proteomic analysis was reperformed to analyze the effect on the interferon pathway and phenotype. The effect on substrate and interferon sensitivity was observed using arsenic trioxide (ATO) to inhibit UBE2O. Results: Initially, UBE2O was deduced from 807 UUCRGs in the TCGA LIHC dataset by six consecutive screening steps. UBE2O was significantly overexpressed in HCC cell lines and tissues compared to the corresponding normal group, and low expression of UBE2O was associated with a better prognosis. UBE2O was knocked down for proteomic analysis, and the results suggested that UBE2O negatively regulates the interferon-alpha/beta signaling (p＜0.01) and the interferon pathway (p＜0.01). IFIT3 in the interferon pathway was identified as a possible ubiquitinated substrate of UBE2O by combining mass spectrometry, the human protein atlas (HPA), and TCGA-based survival analysis. There was a significant negative correlation between UBE2O and IFIT3, including survival analysis showing opposite trends and a negative correlation in protein expression. UBE2O binds to IFIT3, and interferon-α promotes this binding. The stability of IFIT3 protein increased with decreasing UBE2O (p＜0.05), and these effects disappeared with the mutational inactivation of UBE2O. K236 of IFIT3 is the active site of ubiquitination. By increasing IFIT3, the knockdown of UBE2O increases the sensitivity of HCC cells to interferon, leading to reduced proliferation and migration (all p＜0.05). These effects disappeared after the elimination of IFIT3. Additionally, ATO inhibited UBE2O and therefore increased interferon sensitivity in HCC cells. Conclusions: UBE2O exerts a protumor role and targets a new substrate, IFIT3, for ubiquitination and degradation, impeding the interferon pathway activation and interferon sensitization in HCC. The findings will shed light on the interferon-based targeted or combination therapeutic strategies for HCC in the future.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_07:14:49.708.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	li heng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-27 10:49:59	ID requested
⏵ 1	2024-01-26 07:14:50	announced

10.1038/s41419-023-06369-9;

Li H, Liu Y, Cheng C, Wu Y, Liang SH, Wu L, Wang H, Tu CY, Yao HH, Meng FZ, Zhang B, Wang W, Wang JB, Liu LX, via degradation of IFIT3 in hepatocellular carcinoma. Cell Death Dis, 14(12):854(2023) [pubmed]

submitter keyword: UBE2O, interferon pathway,Hepatocellular carcinoma, IFIT3, interferon sensitivity

Wang Jiabei
contact affiliation	Cheeloo College of Medicine, Shandong University, Jinan 250002, PR.China. Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China. Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei 230001, China. Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei 230001, China.
contact email	jbwang16@ustc.edu.cn
lab head
li heng
contact affiliation	Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC) West District/Anhui Provincial Cancer Hospital, Hefei, China.
contact email	drliheng@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD039704
     1. Label: PRIDE project
     2. Name: UBE2O targets a novel substrate IFIT3 for ubiquitination and degradation, impeding the interferon pathway activation and interferon sensitization in hepatocellular carcinoma