PXD062678

PXD062678 is an original dataset announced via ProteomeXchange.

Title	Identification of potential salivary biomarkers and enriched protein domain/motif families for early detection and lymph node invasion in OSCC patients of the Indian population
Description	Oral squamous cell carcinoma (OSCC) is a major public health concern, particularly in India, where it is the leading cause of cancer-related mortality among men and the fourth among women, resulting in approximately nine deaths per hour. Despite advancements in clinical management, the prognosis for OSCC remains poor due to late-stage detection and the absence of specific, reliable biomarkers for early diagnosis and disease monitoring. This study aims to identify potential salivary biomarkers and enriched protein domain/motif families for the early detection of OSCC and its progression, including lymph node invasion. A comparative salivary proteomics approach was employed using diaPASEF mode on 45 saliva samples from healthy individuals, pre-malignant (PM) lesions, and OSCC patients (with and without lymph node invasion), followed by targeted proteomics validation in 40 additional saliva samples. Data analysis was performed using FragPipe, Perseus, and InterPro/SMART for domain and motif enrichment. Signal peptides were predicted using SignalP, while pathway and protein interaction analyses were conducted via STRING. Multi-classifier biomarkers were identified using LASSO and logistic regression, with validation through targeted proteomics and TCGA datasets. A total of 1,068 proteins were identified, with differential expression patterns observed across disease stages (PM vs. Healthy, OSCC vs. PM). Several protein domain/motif families were significantly enriched, including SERPINS, ITI family, Lipocalins, Calcium-binding EF-hand motifs, Trypsin-like serine proteases, and Annexin repeats. Functional analysis highlighted pathways related to negative regulation of wound healing and calcium ion binding. Key potential biomarkers, such as ITIH4, RBP4, NUCB2, TXN, and ELANE, exhibited an AUC > 0.7 in classification models. These findings provide novel insights into salivary biomarkers and enriched protein domain families that may aid in the early detection of OSCC and prediction of lymph node invasion, offering a promising non-invasive diagnostic tool for the Indian population.
HostingRepository	PRIDE
AnnounceDate	2025-08-08
AnnouncementXML	Submission_2025-08-08_07:35:07.583.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Avinash singh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-07 04:00:54	ID requested
⏵ 1	2025-08-08 07:35:07	announced

Dataset with its publication pending

submitter keyword: Oral cancer, DIA-pasef, OSCC,Salivary Proteomics, LC-MS/MS

Sanjeeva Srivastava
contact affiliation	Proteomics Lab, Dept. of Biosciences and Bioengineering, IIT Bombay, INDIA, 400076
contact email	sanjeeva@iitb.ac.in
lab head
Avinash singh
contact affiliation	PhD student
contact email	singhavi739@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062678
     1. Label: PRIDE project
     2. Name: Identification of potential salivary biomarkers and enriched protein domain/motif families for early detection and lymph node invasion in OSCC patients of the Indian population