PXD036238

PXD036238 is an original dataset announced via ProteomeXchange.

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

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.

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]

submitter keyword: Quantitative proteomics, Cell cycle regulation, SYVN1,Esophageal squamous cell carcinoma, ER stress

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD036238

PRIDE project URI

• PRIDE
  1. PXD036238
     1. Label: PRIDE project
     2. Name: Molecular characterization of esophageal squamous cell carcinoma using quantitative proteomics