PXD063002-1

PXD063002 is an original dataset announced via ProteomeXchange.

Title	Longitudinal Proteomic Changes in HCT 116 Colon Cancer Spheroids During Growth
Description	The FDA Modernization Act 2.0 permits data from advanced microphysiological systems, such as spheroids, to be used as a testbed for drug candidates entering phase 1 clinical trials. Despite their increasing adoption, spheroids of varying growth durations are often used interchangeably as disease models. While transcriptomic studies have been employed to monitor spheroids over time, proteomics has primarily been used to validate their utility as model systems and assess drug responses, rather than for longitudinal studies. Here, we apply data independent acquisition with gas phase fractionation (DIA-GPF) proteomics to investigate temporal changes in HCT 116 spheroids every two days throughout 18 days of growth, identifying 6,835 proteins across all samples. Differential expression analysis reveals that day 2 spheroids more closely resemble monolayer cells than spheroids cultured for extended periods. Gene ontology (GO) term analysis of differentially expressed proteins indicates that, relative to monolayer cells, DNA replication is downregulated, while glycolysis is upregulated during spheroid maturation. Parallel reaction monitoring (PRM) experiments targeting thymidylate synthase and fructose-bisphosphate aldolase C validate the initial proteomic findings and corroborate the trends observed in GO term analysis. These results highlight the importance of growth duration when utilizing spheroids as a model for avascular tumors.
HostingRepository	PRIDE
AnnounceDate	2025-05-22
AnnouncementXML	Submission_2025-05-22_13:07:51.319.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Catherine Whitney
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	2025-04-15 17:32:01	ID requested
⏵ 1	2025-05-22 13:07:51	announced

Dataset with its publication pending

submitter keyword: HCT 116, colon cancer,3D cell culture, spheroids, longitudinal proteomics

Amanda B. Hummon
contact affiliation	Department of Chemistry and Biocheimstry at The Ohio State University; Comprehensive Cancer Center, The Ohio State University
contact email	hummon.1@osu.edu
lab head
Catherine Whitney
contact affiliation	The Ohio State University
contact email	edgington.66@buckeyemail.osu.edu
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/PXD063002

PRIDE project URI

• PRIDE
  1. PXD063002
     1. Label: PRIDE project
     2. Name: Longitudinal Proteomic Changes in HCT 116 Colon Cancer Spheroids During Growth