PXD005157-2

PXD005157 is an original dataset announced via ProteomeXchange.

Title	Differential proteomic comparison of the breast cancer secretome using a quantitative paired analysis workflow
Description	Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that secrete the nipple aspirate fluid (NAF). In cancer patients, this breast secretome contains proteins associated with the tumor microenvironment. NAF studies are challenging because inter-individual variability is substantial. To better address this limitation, we introduced a paired-proteomic strategy that relies on NAF sample analysis from both breasts of patients with unilateral breast cancer. We developed a software extension to the PatternLab for Proteomics software to take advantage of this setup. Briefly, the software relies on a peptide-centric approach and uses the binomial distribution to attribute a probability for each peptide as being linked to the disease or not; these probabilities are then propagated to a final protein p-value according to the Stouffer’s Z-score method. Our approach was applied to both a discovery-driven (shotgun) analysis of NAF samples and a hypothesis-driven (targeted) assessment of 19 cancer-related proteins described in the literature. Shotgun results culminated in the reliable quantitative proteomic profiling of NAF samples from healthy and cancer cohorts. A total of 1,083 proteins were identified, of which 77 were differentially abundant, being mainly involved in glycolysis (Warburg effect) and immune system activation (activated stroma). Additionally, in the estrogen receptor-positive subgroup, proteins related to the lipid metabolism and the complement cascade displayed higher abundance, as expected for this well-differentiated subtype of cancer. The targeted analysis of NAF samples from triple negative patients revealed three differentially abundant proteins related to cell migration/attraction and tumor cell differentiation. In summary, we debuted a paired differential bioinformatics workflow, performing a proof-of-principal differential proteomic analysis of NAF samples in unilateral breast cancers patients. The results revealed a promising statistical paired analysis workflow, thus validating NAF as a treasure-trove for studying this paired-organ cancer type.
HostingRepository	PRIDE
AnnounceDate	2019-04-23
AnnouncementXML	Submission_2019-04-23_02:27:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Giselle Brunoro
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-14 07:31:02	ID requested
1	2019-04-23 02:11:37	announced
⏵ 2	2019-04-23 02:27:35	announced	Updated publication reference for PubMed record(s): 30999875.

Brunoro GVF, Carvalho PC, Barbosa VC, Pagnoncelli D, De Moura Gallo CV, Perales J, Zahedi RP, Valente RH, Neves-Ferreira AGDC, Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow. BMC Cancer, 19(1):365(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: breast cancer, paired analysis, tumor microenvironment

Jonas Perales
contact affiliation	Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Av. Brasil 4365, Manguinhos 21040-360, Rio de Janeiro, Brazil
contact email	jonasperales@gmail.com
lab head
Giselle Brunoro
contact affiliation	Fundação Oswaldo Cruz
contact email	gisellebrunoro@gmail.com
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/2019/04/PXD005157

PRIDE project URI

• PRIDE
  1. PXD005157
     1. Label: PRIDE project
     2. Name: Differential proteomic comparison of the breast cancer secretome using a quantitative paired analysis workflow