PXD037548

PXD037548 is an original dataset announced via ProteomeXchange.

Title	HAVOC: Small-scale histomic mapping of biodiversity across entire tumor specimens using deep neural networks
Description	Intra-tumoral heterogeneity can wreak havoc on current precision medicine strategies due to challenges in sufficient sampling of geographically separated areas of biodiversity distributed across centimeter-scale tumor distances. In particular, modern tissue profiling approaches are still largely designed to only interrogate small tumor fragments; which may constitute a minute and non-representative fraction of the overall neoplasm. To address this gap, we developed a pipeline that leverages deep learning to define topographic histomorphologic fingerprints of tissue and create Histomic Atlases of Variation Of Cancers (HAVOC). Importantly, using a number of spatially-resolved readouts, including mass-spectrometry-based proteomics and immunohistochemisy, we demonstrate that these personalized atlases of histomic variation can define regional cancer boundaries with distinct biological programs. Using larger tumor specimens, we show that HAVOC can map spatial organization of cancer biodiversity spanning tissue coordinates separated by multiple centimeters. By applying this tool to guide profiling of 19 distinct geographic partitions from 6 high-grade gliomas, HAVOC revealed that distinct states of differentiation can often co-exist and be regionally distributed across individual tumors. Finally,to highlight generalizability, we further benchmark HAVOC on additional tumor types and experimental models of heterogeneity. Together, we establish HAVOC as a versatile and accessible tool to generate small-scale maps of tissue heterogeneity and guide regional deployment of molecular resources to relevant and biodiverse tumor niches.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:01:34.558.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sofia Melliou
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-19 02:39:27	ID requested
1	2023-08-23 12:55:52	announced
⏵ 2	2024-10-22 06:01:34	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: molecular profiling,Tumor heterogeneity, computer vision, artificial intelligence, deep learning

Phedias Diamandis
contact affiliation	Laboratory Medicine & Pathobiology University of Toronto
contact email	p.diamandis@mail.utoronto.ca
lab head
Sofia Melliou
contact affiliation	University of Toronto
contact email	sophia.melliou@mail.utoronto.ca
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/2023/08/PXD037548

PRIDE project URI

• PRIDE
  1. PXD037548
     1. Label: PRIDE project
     2. Name: HAVOC: Small-scale histomic mapping of biodiversity across entire tumor specimens using deep neural networks