Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Saliva

DISEASE(S): Head And Neck Squamous Cell Carcinoma

SUBMITTER: Avinash singh

LAB HEAD: Sanjeeva Srivastava

PROVIDER: PXD062678 | Pride | 2025-08-08

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	C10_AS_30102024_S1-C10_1_221.d.rar	Other
	C11_AS_01112024_S1-C5_1_239.d.rar	Other
	C12_AS_01112024_S1-D4_1_263.d.rar	Other
	C13_AS_30102024_S1-C1_1_229.d.rar	Other
	C3_AS_30102024_S1-C1_1_171.d.rar	Other

Items per page:

1 - 5 of 65

Similar Datasets

Project description:This is a pilot study. We are trying to detect potential salivary biomarkers in mice with a pancreatic tumor. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. Recent studies have demonstrated that discriminatory salivary biomarkers can be readily detected upon the development of systemic diseases such as pancreatic cancer, breast cancer, lung cancer and ovarian cancer. However, the utility of salivary biomarkers for the detection of systemic diseases has been undermined due to the absence of biological and mechanistic rationale why distal diseases from the oral cavity would lead to the development of discriminatory biomarkers in saliva. Here, we examine the hypothesis that pancreatic tumor-derived exosomes are mechanistically involved in the development of pancreatic cancer-discriminatory salivary transcriptomic biomarkers. We first developed a pancreatic cancer mouse model that yielded discriminatory salivary biomarkers by implanting the mouse pancreatic cancer cell line Pan02 into the pancreas of the syngeneic host C57BL/6. The role of pancreatic cancer-derived exosomes in the development of discriminatory salivary biomarkers was then tested by engineered a Pan02 cell line that is suppressed for exosome biogenesis, implanted into the C56BL/6 mouse and examine if the discriminatory salivary biomarker profile was ablated or disrupted. Suppression of exosome biogenesis results in the ablation of discriminatory salivary biomarker development. This study supports that tumor-derived exosomes provide a mechanism in the development of discriminatory biomarkers in saliva and distal systemic diseases. We analyzed saliva from 6 healthy mice and 6 mice with a pancreatic tumor using the Affymetrix Mouse Exon Genome 430 2.0 platform. Array data was processed by dChip. No techinical replicates were performed.

Dataset Information

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

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets