PXD055170

PXD055170 is an original dataset announced via ProteomeXchange.

Title	High resolution proteome profiling of multiple neighboring regions with each tumor tissue of patients with melanoma brain metastasis using bulk tumor sequencing.
Description	Our study provides a comprehensive multiomics overview of each patient’s tumor, revealing tumor cell types, proteomics, and transcriptomic changes related to melanoma brain metastasis (MBM). Here, we have applied the HiRIEF pre-fractionation and tandem mass tags (TMT)-16plex based peptide quantification to generate proteomes of multiple neighboring regions within each MBM tumor tissue. PCA and Hierarchical clustering analysis illustrated higher inter-tumoral heterogeneity than intra-tumoral heterogeneity of MBM at the protein levels, as lesions from the same patients are grouped into a single cluster. The treatment-naive patient (P3) exhibited high intra-tumoral heterogeneity (ITH) compared to treated ones, with ITH levels varying across neighboring regions in patient tumors. Differential expression analysis highlighted enriched protein and gene clusters for all patient comparisons, including innate immune proteins, macrophage activation, T- and B-cell signaling, and key cancer pathways (e.g., epithelial-mesenchymal transition, cell adhesion, notch signaling, oxidative phosphorylation and cell cycle checkpoints). Genes involved in functional processes characteristic of MBM cell types, tumor-immune interactions, and signaling mechanisms were more highly correlated with their protein levels. Overall, our results provide a comprehensive spatial and molecular view of intra-tumoral and inter-tumoral heterogeneity in MBM.
HostingRepository	PRIDE
AnnounceDate	2025-07-21
AnnouncementXML	Submission_2025-07-20_23:48:42.645.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nidhi Sharma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-24 08:49:04	ID requested
⏵ 1	2025-07-20 23:48:44	announced

10.1016/j.tranon.2025.102468;

Sharma N, R, á, jov, á J, Mermelekas G, Thrane K, Lundeberg J, Shamikh A, Vikstr, ö, m S, Baba, č, i, ć H, Jensdottir M, Lehti, ö J, Pernemalm M, Eriksson H, In-depth patient-specific analysis of tumor heterogeneity in melanoma brain metastasis: Insights from spatial transcriptomics and multi-region bulk sequencing. Transl Oncol, 59():102468(2025) [pubmed]

submitter keyword: PD-1, proteomics, multi-omics, immunotherapy, immune signaling, transcriptomics, targeted therapy,melanoma brain metastases

Janne Lehtiö
contact affiliation	Department of Oncology-Pathology, Karolinska Institute and Scilifelab, Solna, Sweden
contact email	janne.lehtio@gmail.com
lab head
Nidhi Sharma
contact affiliation	Karolinska Institute
contact email	nidhi.cct@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/2025/07/PXD055170

PRIDE project URI

• PRIDE
  1. PXD055170
     1. Label: PRIDE project
     2. Name: High resolution proteome profiling of multiple neighboring regions with each tumor tissue of patients with melanoma brain metastasis using bulk tumor sequencing.