PXD004941

PXD004941 is an original dataset announced via ProteomeXchange.

Title	Integrative analysis of proteome and ubiquitylome reveals unique features of protein ubiquitylation and mitochondria in gefitinib resistant non-small cell lung cancer cells
Description	Even though gefitinib, a tyrosine kinase inhibitor, widely used in treating non-small cell lung cancer (NSCLC) patients carrying EGFR activating mutations, most patients will develop gefitinib resistance. Protein ubiquitylation is one of major posttranslational modifications affecting the stability or function of the protein. However, the role of protein ubiquitylation in gefitinib resistance is poorly understood. To systematically identify the global change in protein ubiquitylation during gefitinib resistance, we carried out quantitative global proteome and ubiquitylome study by using cells with stable isotopic labeling with amino acid in cell culture (SILAC) followed by affinity enrichment of ubiquitylated peptides and subsequent liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis. Our study quantified are differentially regulated in ubiquitylation between gefitinib resistant and sensitive cells. Among them, 799 lysine sites were up-regulated in ubiquitylation in resistant cells, which are enriched in pathways, such as SNARE interaction in vesicle transport, endocytosis, phagosome, and lysosome, etc. In addition, we also found cells. The proteins carry these sites are involved in pathways including metabolic pathways, gap junction, and biosynthesis of amino acids, etc, This data indicate that gefitinib resistance dramatically alters the landscape of ubiquitylation in the cells. Furthermore, by integrating the genome-wide transcriptome data, we discovered that complexes I and IV in the electron transport chain of the mitochondria are up-regulated, while complexes II and III are down-regulated in resistant cells. Overall, these results reveal the unique features of ubiquitylation and mitochondria during gefitinib resistance, which will help to a better understanding of the role(s) of ubiquitylation, and to identify new therapeutic targets in overcoming gefitinib resistance.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:32:35.076.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	zhu taotao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-12 03:59:11	ID requested
1	2018-07-05 04:52:46	announced
⏵ 2	2024-10-22 04:32:37	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201700388;

Li W, Wang H, Yang Y, Zhao T, Zhang Z, Tian Y, Shi Z, Peng X, Li F, Feng Y, Zhang L, Jiang G, Zhang F, Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib-Resistant Non-Small Cell Lung Cancer Cells. Proteomics, 18(15):e1700388(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, LC_MSMS, lung, non-small cell lung cancer cells

Zhang Fan
contact affiliation	Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of 6 Medicine, 507 Zhengmin Road, Shanghai 200433, China
contact email	fzhang@tongji.edu.cn
lab head
zhu taotao
contact affiliation	PTM biolab (Hangzhou)
contact email	taotao_zhu@ptm-biolab.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004941
     1. Label: PRIDE project
     2. Name: Integrative analysis of proteome and ubiquitylome reveals unique features of protein ubiquitylation and mitochondria in gefitinib resistant non-small cell lung cancer cells