PXD019549

PXD019549 is an original dataset announced via ProteomeXchange.

Title	SWATH-MS based proteomic profiling of Pancreatic Ductal Adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways
Description	Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become by 2030 the second leading cause of cancer-related deaths. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with worse severity and outcomes. The purpose of this study was to map the proteomic and genomic landscape of a cohort of PDAC patients of African ancestry. Thirty tissues (15 tumours and 15 normal adjacent tissues) were obtained from consenting South African PDAC patients. Optimisation of the sample preparation method allowed for the simultaneous extraction of high-purity protein and DNA for SWATH-MS and OncoArray SNV analyses. We quantified 3402 proteins with 49 upregulated and 35 downregulated proteins at a minimum 2.1 fold change and FDR adjusted p-value (q-value) ≤ 0.01 when comparing tumour to normal adjacent tissue. Many of the upregulated proteins in the tumour samples are involved in extracellular matrix formation (ECM) and related intracellular pathways. Proteins such as EMIL1, ZCCHV and KBTB2 involved in the regulation of ECM proteins were observed to be dysregulated in pancreatic tumours. Approximately 11% of the dysregulated proteins, including ISLR, BP1, PTK7 and OLFL3, were predicted to be secretory proteins. Additionally, we identified missense mutations in some upregulated proteins, such as MYPN, ESTY2 and SERPINB8. These findings help in further elucidating the biology of PDAC and may aid in identifying future plausible markers for the disease.
HostingRepository	PRIDE
AnnounceDate	2020-09-30
AnnouncementXML	Submission_2020-09-29_23:42:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Previn Naicker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-03 15:00:45	ID requested
⏵ 1	2020-09-29 23:42:47	announced

Dataset with its publication pending

submitter keyword: Pancreatic cancer, SWATH-MS, Extracellular matrix

Stoyan Stoychev
contact affiliation	NextGen Health, Council for Scientific and Industrial Research, South Africa
contact email	sstoychev@csir.co.za
lab head
Previn Naicker
contact affiliation	Council for Scientific and Industrial Research
contact email	pnaicker1@csir.co.za
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/2020/09/PXD019549

PRIDE project URI

• PRIDE
  1. PXD019549
     1. Label: PRIDE project
     2. Name: SWATH-MS based proteomic profiling of Pancreatic Ductal Adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways