PXD046857

PXD046857 is an original dataset announced via ProteomeXchange.

Title	Investigative needle core biopsies support multimodal deep-data generation in glioblastoma
Description	Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis with few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both our understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The adaptation of stereotactic biopsy tissue for complex and integrated investigative multi-modal molecular analyses (‘Multi-omics”) in the context of GBM regional heterogeneity is not routinely performed, Most of the tissue is consumed with standard of care clinical testing and the amount and quality of remaining cells, particularly in the context of recurrent GBMs that have failed previous treatments, has not previously been shown to be amenable to complex analyses. Here we performed highly resolved multi-modal analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonal analysis, and immunopeptidomics on needle biopsy cores obtained from a single patient during the same procedure. In a second patient, we analyzed multi-regional core biopsies to decipher spatially associated tissue and genomic variance. Finally in a separate cohort of patients we investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models. Dataset integration across modalities showed good correspondence between spatial modalities and revealed tumor and immune cell associated metabolic profiles and cell signalling pathways. In conclusion, stereotactic needle biopsy cores are of sufficient quality for the purposes of investigative biopsy and can generate multi-omics data, providing data rich insight into a patient’s disease to interrogate the tumor immune microenvironment.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_11:14:01.697.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046857
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ryuhjin Ahn
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-10 17:09:12	ID requested
⏵ 1	2025-05-06 11:14:02	announced

10.6019/PXD046857;

10.1038/s41467-025-58452-8;

Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, Couturier C, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim BYS, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Chiocca EA, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR, Wiley J, Partridge K, Gocheva V, Chukwueke UN, Michor F, Ogilvie S, Mineo M, Hossain MA, Rincon-Torroella J, Vogelzang J, Vasquez KL, Solomon IH, Soni H, Ball A, Piranlioglu R, Triggs D, Ling AL, Masud N, Landivar AM, Polk MJ, Elharouni D, Ayoub G, Hu J, Larsen AG, Sharma P, Douville C, Investigative needle core biopsies support multimodal deep-data generation in glioblastoma. Nat Commun, 16(1):3957(2025) [pubmed]

submitter keyword: stereotactic biopsy, multi-omics, single cell sequencing, metabolomics, sampling variance,Glioblastoma, immunopeptidomics, spatial

Forest White
contact affiliation	Biological Engineering, MIT
contact email	fwhite@mit.edu
lab head
Ryuhjin Ahn
contact affiliation	Massachusetts Institute of Technology
contact email	ryuhjin.ahn@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/2025/05/PXD046857

PRIDE project URI

• PRIDE
  1. PXD046857
     1. Label: PRIDE project
     2. Name: Investigative needle core biopsies support multimodal deep-data generation in glioblastoma