PXD054500

PXD054500 is an original dataset announced via ProteomeXchange.

Title	Comprehensive proteomic profiling of the differences between Cancer Associated Fibroblasts and KRAS mutated cancer cell lines
Description	Cancer associated fibroblasts (CAFs) are a key component of tumors. We aimed to profile the proteome of cancer cell lines representing three common cancer types (lung, colorectal and pancreatic) and a representative CAF cell line from each tumor type to gain insight into CAF function and identify new CAF biomarkers. We used liquid chromatography and tandem mass spectrometry to evaluate the proteome of 9 cancer and 3 CAF cell lines. Functions of selected differentially expressed proteins in CAF cell lines were studied using siRNA and expression of new CAF biomarkers identified in cell lines were studied by immunohistochemistry in 30 human tumor specimens. Of the 9460 proteins evaluated, functional enrichment analysis revealed N-glycan biosynthesis and extracellular membrane proteins to be upregulated in CAFs and not in cancer cells. 85 proteins had 16-fold higher expression in CAFs compared to cancer cells. These included previously known CAF markers like ACTA2, FAP and SDC2. Novel biomarkers overexpressed in CAFs were noted, including HSPB6 and PTGS1. SiRNA knockdown of these genes encoding these proteins did not reduce contractility in lung CAFs, suggesting they were not crucial to this function despite high expression. Immunohistochemical analysis of 30 tumor samples (10 lung, 10 colorectal and 10 pancreatic) showed HSPB6 and PTGS1 expression were restricted to the stroma. An unbiased analysis of the differences in the proteome of cancer cells compared to CAFs revealed increased expression of HSPB6 and PTGS1 in CAFs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:57:50.769.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Graeme Benstead-Hume
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-01 07:56:29	ID requested
1	2024-09-09 09:56:49	announced
⏵ 2	2024-10-22 06:57:51	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2023.104973;

Lau R, Yu L, Roumeliotis TI, Stewart A, Pickard L, Riisanes R, Gurel B, de Bono JS, Choudhary JS, Banerji U, Unbiased differential proteomic profiling between cancer-associated fibroblasts and cancer cell lines. J Proteomics, 288():104973(2023) [pubmed]

submitter keyword: Cancer Associated Fibroblasts, KRAS, CAFs

Jyoti Choudhary
contact affiliation	Functional Proteomics, ICR
contact email	jyoti.choudhary@icr.ac.uk
lab head
Graeme Benstead-Hume
contact affiliation	ICR
contact email	ghume@icr.ac.uk
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/2024/08/PXD054500

PRIDE project URI

• PRIDE
  1. PXD054500
     1. Label: PRIDE project
     2. Name: Comprehensive proteomic profiling of the differences between Cancer Associated Fibroblasts and KRAS mutated cancer cell lines