PXD077038-1

PXD077038 is an original dataset announced via ProteomeXchange.

Title	Proteomic description of CT26 and KPC after FUS treatment and reproducibility
Description	growing colorectal cancer model [1, 2], whereas KPC tumors arise from genetically engineered mutations in Kras and Trp53, resulting in a dense, desmoplastic stroma which is characteristic of the human pancreatic cancer [3, 4]. A prerequisite for successful cancer treatment is effective delivery of therapeutic agents to tumor cells. However, a major limitation of chemotherapy is the low accumulation of injected drug [5]. To address this, multiple strategies have been proposed to enhance drug delivery. Among these, focused ultrasound combined with intravenously administered microbubbles has demonstrated improved delivery and effect of both small molecular drugs and nanoparticles in clinical [6-8] and preclinical [9-12] trials. In studies of CT26 and KPC tumors, ultrasound and microbubbles enhanced the delivery of polymeric nanoparticles in the soft and well-vascularized CT26 tumors, but not in the stiff, poorly vascularized KPC tumors [13]. Development of novel treatment strategies relies on the understanding of the tumor model at multiple scales, including macroscopic features such as extracellular matrix (ECM) composition, tumor stiffness, and perfusion, as well as molecular and protein-level characteristics. Proteomic profiling provides a powerful approach for characterizing such differences at the molecular level. In particular, liquid chromatography-mass spectrometry (LC-MS)-based label-free quantification (LFQ) proteomics enables high-throughput, unbiased measurement of thousands of proteins within complex biological samples [14, 15]. Through gene ontology (GO) enrichment analysis, this comprehensive measurement of proteins can offer valuable insight into biological processes, molecular functions and cellular components [16, 17]. Despite the widespread use of CT26 and KPC models, the characterization of their proteomic landscapes remains insufficient. In this study, we applied LC-MS-based LFQ proteomics to identify molecular, cellular, and biological features that distinguish CT26 and KPC tumors. In addition, we used the reference database SpLICe [18] and CIBERSORTx [19, 20] to create a signature matrix for murine immune cells, and immune cell deconvolution identified important immune cell populations. Reproducibility is critical in preclinical cancer research. It is known that several environmental factors, such as temperature, housing conditions, and handling influence the outcomes of animal experiments by affecting phenotypes, behavior and physiology [21-23]. In addition, measurement techniques such as mass spectrometry–based proteomics introduce further variability [24]. To our knowledge, variation in the proteomic landscape of tumors across independent experimental replicates has not been systematically reported. Therefore, we employed MS-based LFQ proteomics to characterize proteomic profiles across three independent experimental replicates using KPC and CT26 tumor models. This approach enabled us to assess differences in biological, molecular, and cellular features between tumors across independent experiments.
HostingRepository	PRIDE
AnnounceDate	2026-08-25
AnnouncementXML	Submission_2026-08-25_01:59:53.740.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Animesh Sharma
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	deamidated residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-11 09:33:10	ID requested
⏵ 1	2026-08-25 01:59:54	announced

10.1038/S41598-026-68589-1;

submitter keyword: r FUS, pdac, KPC, pancreatic, CT26 ,cancer, colorectal

Lars Hagen
contact affiliation	Daglig leder, PROMEC Institutt for klinisk og molekylær medisin lars.hagen@ntnu.no 73598508 72573342 Laboratoriesenteret, 231.04.008, Øya, Erling Skjalgssons gate 1 PROMEC, Norway
contact email	lars.hagen@ntnu.no
lab head
Animesh Sharma
contact affiliation	Engineer at NTNU, Norway
contact email	sharma.animesh@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/2026/08/PXD077038

PRIDE project URI

• PRIDE
  1. PXD077038
     1. Label: PRIDE project
     2. Name: Proteomic description of CT26 and KPC after FUS treatment and reproducibility