PXD036238 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Molecular characterization of esophageal squamous cell carcinoma using quantitative proteomics |
Description | Esophageal squamous cell carcinoma (ESCC) is a heterogeneous cancer associated with high mortality rate. In India, it is the 6th most common cause of cancer-related mortality. In this study, we employed high-resolution mass spectrometry-based quantitative proteomics to characterize differential protein expression pattern associated with ESCC. We identified several differentially expressed proteins including PDPN, TOP2A, POSTN and MMP2 that were overexpressed in ESCC. In addition, we identified downregulation of esophagus tissue-enriched proteins such as SLURP1, PADI1, CSTA and small proline-rich proteins like SPRR3, SPRR2A, SPRR1A and CSTA, KRT4, KRT13 involved in squamous cell differentiation. We identified several overexpressed proteins belonging to 3q24-29 chromosomal region, corroborating CNV alterations in this region reported by several published studies. For example, we identified overexpression of SOX2, TP63, IGF2BP2 and RNF13 that are encoded by 3q26 region. Functional enrichment analysis revealed proteins involved in cell cycle pathways, DNA replication, spliceosome, and DNA repair pathways. We identified overexpression of multiple proteins that play a major role in alleviating ER stress. SYVN1/SEL1L complex forms the ER quality control machinery clearing misfolded proteins from ER. SYVN1 is an E3 ubiquitin ligase that ubiquitinates ER-resident proteins. There are also other non-canonical substrates of SYVN1 which are known to play a crucial role in tumor progression. Therefore, SYVN1 is a potential therapeutic target in ESCC. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_09:12:31.942.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Harsha Gowda |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF-X |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-08-23 05:16:54 | ID requested | |
1 | 2023-10-24 15:01:20 | announced | |
⏵ 2 | 2023-11-14 09:12:32 | announced | 2023-11-14: Updated project metadata. |
Publication List
Mangalaparthi KK, Patel K, Khan AA, Nair B, Kumar RV, Prasad TSK, Sidransky D, Chatterjee A, Pandey A, Gowda H, Molecular Characterization of Esophageal Squamous Cell Carcinoma Using Quantitative Proteomics. Cancers (Basel), 15(13):(2023) [pubmed] |
Keyword List
submitter keyword: Quantitative proteomics, Cell cycle regulation, SYVN1,Esophageal squamous cell carcinoma, ER stress |
Contact List
Harsha Gowda |
contact affiliation | Institute of Bioinformatics, 7th floor, Discoverer Building, International Tech Park, Bangalore, 560 066, India |
contact email | harsha@ibioinformatics.org |
lab head | |
Harsha Gowda |
contact affiliation | QIMR Berghofer Medical Research Institute |
contact email | harsha@ibioinformatics.org |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD036238
- Label: PRIDE project
- Name: Molecular characterization of esophageal squamous cell carcinoma using quantitative proteomics