PXD059079

PXD059079 is an original dataset announced via ProteomeXchange.

Title	Single-Cell Proteomic and Transcriptomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes
Description	This study delves into the proteomic intricacies of drug-resistant cells (DRCs) within prostate cancer, which are known for their pivotal roles in therapeutic resistance, relapse, and metastasis. Utilizing single-cell proteomics (SCP) with an optimized high-throughput Data Independent Acquisition (DIA) approach with the throughput of 60 sample per day, we characterized the proteomic landscape of DRCs in comparison to parental PC3 cells. This optimized DIA method allowed for robust and reproducible protein quantification at the single-cell level, enabling the identification and quantification of over 1,300 proteins per cell on average. Distinct proteomic sub-clusters within the DRC population were identified, closely linked to variations in cell size. The study uncovered novel protein signatures, including the regulation of proteins critical for cell adhesion and metabolic processes, as well as the upregulation of surface proteins and transcription factors pivotal for cancer progression. Furthermore, by integrating SCP and single-cell RNA-seq (scRNA-seq) data, we identified six upregulated and ten downregulated genes consistently altered in drug-treated cells across both SCP and scRNA-seq platforms. These findings underscore the heterogeneity of DRCs and their unique molecular signatures, providing valuable insights into their biological behavior and potential therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2025-03-20
AnnouncementXML	Submission_2025-03-20_08:30:22.830.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jongmin Woo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF HT; Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-20 00:25:52	ID requested
⏵ 1	2025-03-20 08:30:23	announced

10.1016/J.MCPRO.2025.100949;

submitter keyword: single-cell proteomics

drug resistant prostate cancer cells

scRNA-seq

Hui Zhang
contact affiliation	Department of Pathology, Department of Urology, Department of Oncology, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231
contact email	huizhang@jhu.edu
lab head
Jongmin Woo
contact affiliation	Johns Hopkins University
contact email	jongminw@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/2025/03/PXD059079

PRIDE project URI

• PRIDE
  1. PXD059079
     1. Label: PRIDE project
     2. Name: Single-Cell Proteomic and Transcriptomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes