PXD069647-1

PXD069647 is an original dataset announced via ProteomeXchange.

Title	Identification of Neoadjuvant Chemoradiotherapy Resistance-Related Proteins in Locally Advanced Rectal Cancer
Description	Locally advanced rectal cancer (LARC) exhibits heterogeneous responses to neoadjuvant chemoradiotherapy (nCRT), patients resistant to nCRT failing to benefit from to nCRT. The aim of this pilot study is to identify proteins associated with LARC nCRT-resistance. This pilot study retrospectively enrolled 4 representative nCRT-resistant (stable disease/progressive disease) and 4 nCRT-sensitive (complete response/partial response) patients, of which a total of 15 formalin-fixed paraffin-embedded tumor tissues (before and after nCRT) were subjected to data-independent acquisition mass spectrometry for proteomic analysis. Spectronaut software was employed for protein identification and quantification. Principal component analysis (PCA) was used to visualize intergroup differences in detected proteins. Differently abundant proteins in resistant patients (fold change ≥ 1.2 or ≤ 0.83 compare to sensitive patients) were selected for analysis using hierarchical clustering, cluster of orthologous groups, subcellular location, gene ontology, and pathway enrichment assay. A total of 39052 peptides and 6006 proteins were identified. PCA showed PCA clear separation among four groups: pre-treatment sensitive (B_S), pre-treatment resistant (B_R), post-treatment sensitive (P_S), and post-treatment resistant (P_R). Intergroup comparisons revealed before nCRT, 133 proteins were upregulated in the resistant group compared to the sensitive group, mainly localized in cytoplasm (33.08%), secreted (24.81%), and nucleus (24.06%), with functions enriched in cell junctions and metabolic related pathways. Post nCRT, 290 proteins were upregulated in the resistant group compared to the sensitive group, mainly localized in the nucleus (36.55%) and cytoplasm (23.10%), with functions enriched in replication, transcription, translation, and metabolic pathways. This study characterized DAP signatures of LARC with nCRT resistance, specific DAPs in resistant tumor provide references for mechanistic studies on treatment resistance, could be potential biomarker for response and therapeutic targets after further validation in larger cohorts.
HostingRepository	iProX
AnnounceDate	2025-10-17
AnnouncementXML	Submission_2025-10-20_02:04:09.270.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiangyi He
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-20 02:03:44	ID requested
⏵ 1	2025-10-20 02:04:09	announced

Dataset with its publication pending

submitter keyword: Locally advanced rectal cancer, neoadjuvant chemoradiotherapy, therapy resistant, data-independent acquisition mass spectrometry

Jianjun Li
contact affiliation	Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University)
contact email	jianjunli@tmmu.edu.cn
lab head
Jiangyi He
contact affiliation	Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University)
contact email	hejiangyi@tmmu.edu.cn
dataset submitter

iProX dataset URI