PXD060201-1

PXD060201 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer
Description	Chemoradiation prior to surgery in locally advanced rectal cancer is the current standard therapy. Unfortunately, this is not effective in all rectal cancer patients and associated with severe side effects, thus, prognostic marker molecules predicting the effectiveness of radiation would be of great interest. Aim of this study was to investigate pathophysiological mechanisms underlying radioresistance. Therefore, FFPE rectal tumor (n=50) and control tissue (n=39) of non-responders and responders to chemoradiation were analyzed using LC-MS-based proteomics. As a result, 1683 proteins were robustly identified. Comparing tumor with corresponding control samples revealed 199 significantly regulated proteins with FTL, PCOLCE and RCN3 being most striking in tumor tissue. While CAECAM 1, 5 and 6 as well as MCM protein complex components were significantly up-regulated in tumor tissue of non-responders compared to all types of responders, ER-stress and autophagic activity-related proteins, namely HYOU1, PDIA4 and RAB1B were only found significantly regulated when compared to complete responders, suggesting their importance in radioresistance mechanisms. Analyzing not only tumor but also surrounding control tissue allowed us to highlight the contribution of stroma to radioresistance. This study demonstrates the suitability of FFPE samples for proteomic analysis and presents potential molecular mechanisms mediating resistance to chemoradiation in rectal cancer.
HostingRepository	PRIDE
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-24_21:57:36.782.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Gerner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-25 01:21:48	ID requested
⏵ 1	2025-08-24 21:57:37	announced

Zott T, Wolf M, Plessl-Walder G, Regele H, Bergmann M, Meier-Menches SM, Gerner C, Silberhumer GR, Bileck A, Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer. J Proteome Res, 24(8):3990-4001(2025) [pubmed]

10.1021/acs.jproteome.5c00114;

submitter keyword: proteome profiling, radioresistance, LC-MS, resistance mechanisms,Colorectal cancer, radiotherapy, ER stress, tumor-associated stroma, FFPE tissue

Christopher Gerner
contact affiliation	University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry
contact email	christopher.gerner@univie.ac.at
lab head
Christopher Gerner
contact affiliation	University of Vienna
contact email	christopher.gerner@univie.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060201
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer