PXD029186

PXD029186 is an original dataset announced via ProteomeXchange.

Title	Spatial immunophenotypes orchestrate prognosis in triple negative breast cancer with Miller Payne grade 4
Description	Some triple-negative breast cancer (TNBC) patients evaluated as Miller-Payne 4 with ypN0 after neoadjuvant chemotherapy (NACT) who have better prognosis should avoid escalation of therapy. We aim to identify these patients through evaluating pretherapeutic spatial distributions of immunophenotypes. Our retrospective study in patients with TNBC assessed as Miller-Payne grade 4/5 with ypN0 showed that Miller-Payne 4 with ypN0 group had poorer 5-year disease-free survival (DFS, 63.8% vs 83.0%, p=0.003) and the 5-year overall survival (OS, 71.0% vs 85.5%, p=0.007) than Miller-Payne 5 with ypN0 group. High TILs were significantly associated with better DFS and OS in patients with Miller-Payne 4 and ypN0 (both p=0.016). Spatially, detected by multiplexed ion beam imaging by time of flight combined with proteomics, tumors assessed as Miller-Payne 4 and ypN0 with good prognosis exhibited an inflamed phenotype, with dominant CD8+ T cells on tumor center, few scattered CD68+ myeloid-derived cells far away from T cells, and deposit of increased activated molecules of lymphocyte. While those with poor prognosis presented excluded phenotype, with few CD8+ T cells restricted to invasive margin and a high density of CD14+CD68+CD11c+ myeloid cells. A good classifier model based on 29 spatial immunophenotypes was established by the random forest algorithm (AUC=0.975), for identifying patients with Miller-Payne 4 and ypN0 who had favorable prognosis. We also observed similar signatures in patients with Miller-Payne 5 and ypN0. Taken together, spatial immunophenotypes may assess the prognosis in TNBC patients with Miller-Payne 4 and ypN0 after NACT.
HostingRepository	PRIDE
AnnounceDate	2024-02-12
AnnouncementXML	Submission_2024-02-12_09:03:43.853.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	qingyuan zhang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Thermo Fisher Scientific instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-18 01:53:24	ID requested
⏵ 1	2024-02-12 09:03:44	announced

10.1038/S41523-023-00565-8;

submitter keyword: IMC,GLUT1, early-relapsed follicular lymphoma, PI3K/Akt /mTOR signaling, tumor immunomicroenvironment, proteomic

qingyuan zhang
contact affiliation	Department of Medical Oncology, Harbin Medical University Cancer Hospital, Heilongjiang Cancer Institute, Harbin 150081, Heilongjiang Province, People闁炽儲鐛� Republic of China.
contact email	0566@hrbmu.edu.cn
lab head
qingyuan zhang
contact affiliation	Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, People’s Republic of China.
contact email	0566@hrbmu.edu.cn
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/2023/07/PXD029186

PRIDE project URI

• PRIDE
  1. PXD029186
     1. Label: PRIDE project
     2. Name: Spatial immunophenotypes orchestrate prognosis in triple negative breast cancer with Miller Payne grade 4