PXD057759-1

PXD057759 is an original dataset announced via ProteomeXchange.

Title	Proteomics and peptidomics of breast cancer subtypes
Description	In our study, we applied high-throughput mass spectrometry, bioinformatic, and machine learning approaches to investigate the proteome, including noncoding RNA (ncRNA)–derived micropeptides, of different breast cancer subtypes. In total, 19 tumor and 18 paired nontumor samples were used to obtain the proteome and peptidome. Among these, 5 samples were classified as LABC (plus 5 paired nontumor samples), 4 as LBBC (HER2−) (plus 4 paired nontumor samples), 4 as HER2+ breast cancer (plus 3 paired nontumor samples), and 6 as TNBC (plus 6 paired nontumor samples). We identified that each subtype depends on different protein expression patterns to sustain its malignancy,and also alterations in pathways and processes that can be associated with each subtype and its biological and clinical behaviors. Regarding subtype biomarkers, our panels achieved performances with at least 75% of sensibility and 92% of specificity. In the validation cohort, the panels obtained acceptable to outstanding performances (AUC = 0.740 to 1.00). We identified 58 peptides expressed on breast tissue, including 27 differentially expressed MPs in tumor compared with nontumor samples and MPs exhibiting tumor or subtype specificity. These peptides presented physicochemical features compatible with the canonical proteome and were predicted to influence the tumor immune environment and participate in cell communication, metabolism, and signaling processes. In addition, some MPs presented potential as anticancer, antiinflammatory, and antiangiogenic molecules.
HostingRepository	PRIDE
AnnounceDate	2024-11-12
AnnouncementXML	Submission_2024-11-12_04:33:26.881.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD057759
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Michel Batista
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-11 13:13:50	ID requested
⏵ 1	2024-11-12 04:33:28	announced

Azevedo ALK, Gomig THB, Batista M, Marchini FK, Spautz CC, Rabinovich I, Sebasti, ã, o APM, Oliveira JC, Gradia DF, Cavalli IJ, Ribeiro EMSF, High-throughput proteomics of breast cancer subtypes: Biological characterization and multiple candidate biomarker panels to patients' stratification. J Proteomics, 285():104955(2023) [pubmed]

10.1016/J.LABINV.2024.102150;

10.1016/j.jprot.2023.104955;

10.1016/j.labinv.2024.102150;

10.6019/PXD057759;

de Azevedo ALK, Gomig THB, Batista M, de Oliveira JC, Cavalli IJ, Gradia DF, Ribeiro EMSF, Peptidomics and Machine Learning-based Evaluation of Noncoding RNA-Derived Micropeptides in Breast Cancer: Expression Patterns and Functional/Therapeutic Insights. Lab Invest, 104(12):102150(2024) [pubmed]

submitter keyword: Human, breast cancer, peptidomics, proteomics, LC-MS/MS

Enilze Maria de Souza Fonseca Ribeiro
contact affiliation	Genetics Post-Graduation Program, Genetics Department, Federal University of Paraná, Curitiba, Brazil
contact email	eribeiro@ufpr.br
lab head
Michel Batista
contact affiliation	Fiocruz
contact email	batista.mic@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/2024/11/PXD057759

PRIDE project URI

• PRIDE
  1. PXD057759
     1. Label: PRIDE project
     2. Name: Proteomics and peptidomics of breast cancer subtypes