PXD038149

PXD038149 is an original dataset announced via ProteomeXchange.

Title	Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction
Description	Understanding the phenotypic alterations that play a role in differential response to drugs will be pivotal in identifying predictive biomarkers and developing efficacious therapies for advanced CRC. The bulk of research to date has focused on the value of organoids as a predictive tool; some have characterized the transcriptomic profile in relation to drug sensitivity in an effort to identify predictive biomarkers, but only a limited number of studies have used quantitative proteomic analysis to characterize PDOs. Extensive literature indicates that transcriptomic and proteomic expression profiles lack correlation due to significant post-transcriptional regulation, which could explain why RNA signatures are rarely useful as drug response predictors in the clinic. In this study we generated PDO models from advanced CRC patients including heavily pre-treated patients and a model of microsatellite instable- (MSI) high CRC, for which pre- and post chemotherapy liver disease PDOs were established and characterized to ensure biological fidelity with the original tumors. Our main objective was to integrate functional drug assays on PDOs with proteotranscriptomic study to explore the mechanisms underlying drug response. To this end, we used SWATH-MS (sequential window acquisition of all theoretical mass spectrometry), a highly accurate proteomic quantification technique and a bulk RNA-seq analysis. This strategy could represent a useful tool to discover new therapeutic targets in advanced CRC and to guide personalized therapies.
HostingRepository	PRIDE
AnnounceDate	2025-02-03
AnnouncementXML	Submission_2025-02-03_04:13:28.193.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luz Valero
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-15 07:17:19	ID requested
⏵ 1	2025-02-03 04:13:28	announced

Dataset with its publication pending

submitter keyword: Colorectal cancer

organoids

quantitative proteomics

precision medicine

drug resistance

transcriptomics

Josefa Castillo
contact affiliation	Department of Biochemistry and Molecular Biology, Universitat de València, 46100 Burjassot, Spain
contact email	Pepa.Castillo@uv.es
lab head
Luz Valero
contact affiliation	Universitat de Valencia
contact email	mluz.valero@uv.es
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/2025/02/PXD038149

PRIDE project URI

• PRIDE
  1. PXD038149
     1. Label: PRIDE project
     2. Name: Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction