Ontology highlight
ABSTRACT:
PROVIDER: PRJNA722859 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14270600_1.fastq.gz | Fastqsanger.gz | |||
| SRR14270600_2.fastq.gz | Fastqsanger.gz | |||
| SRR14270601_1.fastq.gz | Fastqsanger.gz | |||
| SRR14270601_2.fastq.gz | Fastqsanger.gz | |||
| SRR14270602_1.fastq.gz | Fastqsanger.gz |
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Project description:Globally, oral cavity squamous cell carcinoma (OSCC) is one of the most common fatal illnesses. Its high mortality is ascribed to the fact that the disease is often diagnosed at a late stage, which indicates an urgent need for approaches for the early detection of OSCC. The use of salivary autoantibodies (autoAbs) as OSCC biomarkers has numerous advantages such as easy access to saliva samples and efficient detection of autoAbs using well-established secondary reagents. To improve OSCC screening, we identified OSCC-associated autoAbs with the enrichment of salivary autoAbs combined with affinity mass spectrometry (MS). The salivary IgA of healthy individuals and OSCC patients was purified with peptide M-conjugated beads and then applied to immunoprecipitated antigens (Ags) in OSCC cells. Using tandem MS analysis and spectral counting-based quantitation, the level of 10 Ags increased in the OSCC group compared with the control group. Moreover, salivary levels of autoAbs to the 10 Ags were determined by a multiplexed bead-based immunoassay. Among them, 7 were significantly higher in early-stage OSCC patients than in healthy individuals. A marker panel consisting of autoAbs to LMAN2, PTGR1, RAB13, and UQCRC2 was further developed to improve the early diagnosis of OSCC.
2025-06-04 | PXD036897 | Pride
Project description:Oral cavity cancer is one of the most common cancer worldwide and oral cavity squamous cell carcinoma (OSCC) accounts for up to 90 percent of oral cancers. In Taiwan, OSCC is the fifth most common malignancy of male and causes more than 250 deaths per year. The poor outcome of OSCC patients is principally ascribed to the fact that this disease is often advanced at the time of diagnosis, suggesting that early detection and prevention of OSCC are urgently needed to reduce the cancer burden. Analysis of cancer-related body fluids is one of promising approaches to identify cancer-related molecules and biomarker candidates. To identify salivary biomarkers of OSCC, salivary samples of OSCC patients, individuals with oral potentially malignant disorders (OPMD), and healthy volunteers were collected. With isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry (MS) analysis, 1838 proteins were identified. The levels of 102 proteins are found to be elevated in the saliva samples of OSCC patients compared to that of OPMD and healthy groups. To improve the feasibility of biomarkers, we used a two-phase verification to measure these candidates. Among them, salivary levels of AHSG, CFH, FGA, and SERPINA1 were determined to be significantly higher in the OSCC patients than in the healthy or in the OPMD group with both of MRM-MS and ELISA. Furthermore, the levels of these proteins were highly related to tumor size, lymph-node metastasis, and cancer stages. The results of this study not only provides a powerful strategy for verification of biomarker candidates, but also suggested that AHSG, CFH, FGA, and SERPINA1 could act as salivary biomarkers for OSCC detection.
2019-08-15 | PXD008655 | Pride
Project description:Patients with oral cavity squamous cell carcinoma (OSCC) are frequently first diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. Early detection of OSCC using body fluid-accessible biomarkers may help improve the prognosis and survival rate of OSCC patients. As tumor interstitial fluid (TIF) is a proximal fluid enriched with cancer-related proteins, it is therefore a valuable reservoir suitable for the discovery of cancer biomarkers as well as dysregulated biological pathways in tumor microenvironment. Thus, we harvested and analyzed the paired tumor (TIF) and adjacent noncancerous (NIF) interstitial fluids from ten OSCC patients using one-dimensional gel electrophoresis coupled with the nano-liquid chromatography-tandem mass spectrometry (GeLC-MS/MS) approach and label-free spectral counting method. The results showed that 113 proteins were up-regulated in at least six OSCC TIFs compared to their respective NIFs, and that the aminoacyl tRNA biosynthesis was statistically enriched in TIFs by Gene Set Enrichment Analysis (GSEA). The enrichment of aminoacyl tRNA biosynthesis in OSCC was verified that four members (IARS, KARS, WARS, and YARS) were revealed to be elevated in OSCC by IHC (n = 12). Among the 113 up-regulated proteins, two candidates (NID1 and SERPINH1) were selected based on an integrated bioinformatics analysis and verified that the salivary NID1 levels were significantly higher in OSCC patients (n = 48) compared to health (n = 51) and OPMD individuals (n = 53). Moreover, the IHC results (n = 222) showed that the expression of NID1 was higher in OSCC compared to adjacent noncancerous epithelium and correlated with pathological T, N, and overall stage as well as survivals of OSCC patients. These results collectively indicate that the analysis of TIF is help to understand the tumor microenvironment, and that salivary NID1 is a potentially useful biomarker for the OSCC.
2019-08-15 | PXD008654 | Pride
Project description:Background: The differential abundance of cell-free RNAs in bodily fluids is emerging as a promising tool for the non-invasive molecular diagnosis of cancer. Human saliva is considered a promising source of non-invasive biomarkers of diagnostic value for oral cancer detection. This study aims to identify diagnostic potent salivary RNAs in oral squamous cell carcinoma (OSCC)-patients by RNA-Sequencing. Method: Unstimulated saliva was collected from 5 normal control (NC) individuals and 9 OSCC patients (PS) with prior consent and ethical committee approvals. Total RNA isolated from cell-free saliva (CFS) supernatant was used to prepare small RNA libraries and sequenced on the Ion Torrent S5 platform. The sequencing reads were aligned to the human genome (hg19) using Bowtie 2, and the differential expression analysis was performed using RUVSeq and DESeq2. Mapped reads were screened across miRBase (v22) annotations for miRNAs and Gencode (v19) annotation for other RNAs. Reads were quantified by the Featurecount (v1.4.6) module of the R-package. The microbial-RNA enrichment analysis was determined using the One Codex platform. Result: RNA-sequencing detected protein-coding transcripts (PCTs), long-intergenic RNAs (lincRNAs), microRNAs (miRNAs), small nuclear RNAs (snRNAs), transfer RNAs (tRNAs) and pseudogenes from the saliva of PS and HC samples. Transcriptome analyses revealed 89 PCTs, 18 lincRNAs and 6 miRNAs differentially expressed between PS and HC with a log2fold change ≥ 1 or ≤ -1 and p-value < 0.05. Gene ontology and pathway enrichment analyses indicated a significant correlation of the identified PCTs and miRNAs to various cancer-related pathways that may have implications in the pathogenesis of OSCC. Interestingly, unmapped non-human reads aligned to the microbial reference genomes. Further analyses of these microbial sequence reads revealed a significant microbial dysbiosis differentiating PS from HC. Metabolic pathways and functional analysis of the identified microbial phylotypes showed gene ontologies associated with inflammation, cell proliferation, ROS generation, and a range of metabolic processes. Conclusion: We report novel panels of differentially expressed PCTs, miRNAs and lincRNAs distinguishing PS from HC. Importantly, our results also provide evidence for oral microbial dysbiosis that appears to have pathological implications in OSCC. Summarily, this study provides a comprehensive landscape of salivary RNAs that can be exploited as non-invasive biomarkers for OSCC detection.
2023-01-30 | GSE176077 | GEO
Project 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.
2025-08-08 | PXD062678 | Pride
Project description:Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide including the Asian subcontinent. Oral carcinoma exhibits inherent heterogeneity in terms of the sites involved, etiology and pathology. They occur at multiple sites such as tongue, buccal mucosa, maxilla. Effective approaches towards improving survival rates in OSCC patients are primarily focused on early detection of the disease. The early clinical indication of the disease follows the development of potentially malignant lesions (leukoplakia/erythro-leukoplakia) with varied rates of transformation. Currently histopathological evaluation of oral biopsy is generally practiced to evaluate potential malignancy. However, human saliva has been considered to be a valuable medium for discovering biomarker molecules for malignancy. Exfoliated cancer cells may release protein or RNA molecules into the saliva or free molecules may be secreted or leaked from cancer cells representing gene expression changes associated with tumor development. Salivary proteins thus provide a strong option for development of non-invasive, point-of-care assays for screening/early detection of oral cancers. Dysplastic leukoplakia (LP) of the oral cavity is a potentially malignant condition for oral squamous cell carcinoma (OSCC), early detection of which is an unmet clinical need. In an effort to develop non-invasive biomarker based method for early detection of the disease, we have used quantitative mass spectrometry to identify differently abundant salivary proteins in OSCC (buccal mucosa) patients and individuals with potential to develop cancer (oral dysplastic leukoplakia) in comparison to healthy controls (with risk habits such as tobacco chewing or smoking).
2019-11-12 | PXD015722 | Pride
Project description:Background: Cervical lymph node metastasis is a potent prognostic factor in oral squamous cell carcinoma (OSCC). However, lymph nodes resected by sentinel node biopsy or neck dissection are usually diagnosed by examining only one or two sections of the maximal cut surface. Accurate diagnosis of the metastasis in lymph nodes is important but depends on a heavy workload of the pathologist. In this study, we have attempted to identify novel molecular markers to find the harboring cancer cells in the lymph node and establish rapid detection method. Methods: We determined the gene expression profiles of 7 metastatic lymph nodes from patients with OSCC and 1 normal lymph node and 5 salivary glands from non-cancerous patients by microarray analysis. We found the overexpression genes in all metastatic lymph nodes. Subsequently, we examined the expression of these genes in newly 23 metastatic lymph nodes and 9 normal lymph nodes by real-time quantitative RT-PCR (qRT-PCR) assay. Moreover, the rapid detection of lymph node metastasis by these genes was examined using the reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Result: Among the 4 genes identified by microarray analysis, annexin A8 (ANXA8) and desmoglein 3 (DSG3) were detected in all metastatic lymph nodes at a much higher level but not in normal lymph nodes at all by qRT-PCR. Furthermore, RT-LAMP method targeting ANXA8 rapidly detected almost lymph nodes with metastasis. Conclusions: ANXA8 could be a useful marker for detecting lymph node metastasis in OSCC. Using AB1700 system, we determined the gene expression profiles of lymph nodes with metastasis of OSCC. Normal lymph node and salivary gland tissues were used as control samples.
2015-12-21 | E-GEOD-70604 | biostudies-arrayexpress