Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Serum N-glycopeptidomics of oral squamous cell carcinoma patients and healthy controls: N-glycopeptidomics

ABSTRACT: The serum N-glycopeptidomics of 41 oral squamous cell carcinoma patients and 44 healthy controls were compared in this project. This project is the second part of a two-part project, where proteomics and N-glycopeptidomics were analyzed in-parallel. The quantitation of N-glycopeptides was performed with MSE in sensitivity mode and the identification with MS2 Fast DDA.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Oral Squamous Cell Carcinoma

SUBMITTER: Sakari Joenväärä

LAB HEAD: Prof. Risto Renkonen

PROVIDER: PXD055600 | Pride | 2026-02-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20200922_OSCC_SEC_GP_04.raw.zip	Raw
	20200922_OSCC_SEC_GP_05.raw.zip	Raw
	20200922_OSCC_SEC_GP_06.raw.zip	Raw
	20200922_OSCC_SEC_GP_07.raw.zip	Raw
	20200922_OSCC_SEC_GP_08.raw.zip	Raw

Items per page:

1 - 5 of 304

Publications

Disease-specific N-glycopeptides in serum of patients with oral squamous cell carcinoma.

Tohmola Tiialotta T Joenväärä Sakari S Dickinson Amy A Mäkitie Antti A Silén Suvi S

Scientific reports 20250902 1

The incidence of oropharyngeal cancers is increasing due to human papilloma virus (HPV); however, this phenomenon does not explain the rising incidence of oral cancers, for which the reason remains unknown. These cancers are typically diagnosed at an advanced stage, which adversely affects the prognosis. Improved methods for early detection, such as blood-based biomarkers, could significantly improve patient outcomes. We investigated quantitative and qualitative differences in serum protein N-gl ...[more]

PMID: 40890283

Similar Datasets

Label-free LC-MS proteomics of oral squamous cell carcinoma patients and healthy controls: proteomics

Project description:This study compared serum proteomic expressions of 41 oral squamous cell carcinoma patients and 44 healthy controls. The data was acquired with UDMSE in resolution mode and targeted fragmentation with DIA. This project consist of two parallel projects: proteomic and N-glycopeptidomic projects. This is the proteomic project. Due to in-parallel N-glycoproteomic analysis the abundant serum proteins were included in the proteomics.

2026-02-09 | PXD055139 | Pride

Gene profiling of the cell death induced by heat stress in HSC-3 human oral squamous carcinoma cells

Project description:Hyperthermia is widely used to treat patients with various cancers. The 42.5˚C is well known as inflection point of hyperthermia and generally up to 42˚C of hyperthermia is used in clinical case to combine with other therapy. Here, the effects of heat stress at 42 or 44˚C for 90 min on the gene expression in HSC-3 human oral squamous carcinoma cells were investigated using an Affymetrix GeneChip system. The cells were treated with heat stress (42 or 44°C for 90 min) and followed by incubation for 0, 6, or 12 h at 37°C. The percentage of cell death was 5.0 ± 1.5 (mean ± SD) at 42°C for 12 h and 17.4 ± 0.6 at 44°C for 12 h. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with heat stress at 42 and 44°C.

2010-10-20 | GSE24783 | GEO

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_baseline]

Project description:Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells. These patients frequently develop malignant serous effusions (MSE). The value of MSE-based tumor cell characterization for guiding precision oncology is, however, currently unclear. Here, we present a comprehensive characterization of a pan-cancer cohort of 150 MSE samples at the cellular, molecular, and functional level. Our integrative analysis reveals dynamic cellular heterogeneity in MSE, and uncovers links between tumor driver mutations and ex vivo growth patterns. Strong concordance between genomic and transcriptional profiles of MSE and their corresponding solid tumors validates their use as a model system for solid tumor biology. We link baseline gene expression patterns to global ex vivo drug sensitivity, and demonstrate that drug-induced transcriptional changes in MSE are highly indicative of compound mode of action. Two case studies exemplify the utility of our approach in investigating acquired resistance to targeted therapy and identifying treatment options for relapsed solid tumors. In summary, our study provides a functional multi-omics view on a pan-cancer MSE cohort and underlines the utility of MSE-based precision oncology.

2024-08-26 | GSE240952 | GEO

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_drug_treated]

2024-08-26 | GSE240951 | GEO

Transcriptomic analysis of immortalized oral keratinocytes (n=2) and oral squamous cell carcinoma cells (n=5)

Project description:Due to betel nut chewing habit, oral cancer is the fourth leading cause of cancer death among Taiwanese men. In addition, oral cancer is the most common malignancy observed in men with 25-44 years old, alerting an urgent need to curb this disease. It is hypothesized that betel nut ingredients exhibit carcinogenic effects on the oral epithelium and alter local immune system. As a step to identify potential oncogenic gene fusions in Taiwanese oral cancer cells, total RNAs of two immortalized oral keratinocytes (CGHNK2, -K6) and five oral squamous cell carcinoma cell lines (C9, OC3, OEC-M1, TW2.6) were subjected to RNA-sequencing analysis, followed by an in-house bioinformatic pipeline for fusion gene detection.

2020-07-07 | GSE150469 | GEO

Differential expression of microRNAs between oral squamous cell carcinoma and healthy control tongues

Project description:In order to identify aberrantly expressed microRNAs in oral squamous cell carcinomas (OSCCs), we have employed microRNA microarray profile using healthy tongue samples as control. All seventeen human OSCCs and three normal tongue tissues were collected from the Tissue Bank at the Moffitt Cancer Center and approved by the University of Florida institutional review board. Majority (15 out of 17) of the OSCCs were derived from tongue cancers. The tumor samples contained greater than 80% of cancerous cells, confirmed by microscopic examination by a head and neck pathologist. The normal tongues were taken from a non-cancerous region. Tissues were snap-frozen and stored at -80°C until further use. Total RNAs were isolated from human tissues using mirVana miRNA Isolation kit (Ambion/Applied Biosystems, Austin, TX) according to the manufacturer’s instruction. NanoDrop® ND-100 spectrophotometer (Thermo Scientific, Wilmington, DE) was used to quantify the isolated RNA. The Agilent 2100 Bioanalyzer from the Interdisciplinary Center for Biotechnology Research at the University of Florida was used to detect the size distribution of total RNA and to determine the quality as well. Expression of microRNAs from this signature was quantified in the same RNA samples by real-time PCR, confirming the expression pattern. Human tissues of oral squamous cell carcinoma and healthy normal tongues were used for microRNA microarray profile to identify aberrantly expressed microRNAs in oral squamous cell carcinomas.

| S-ECPF-GEOD-28100 | biostudies-other

Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa.

Project description:Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.

| S-EPMC5458226 | biostudies-literature

AML patients samples compared to Healthy Human CD34+ cells (LFQ LC-MSMS)

Project description:Cryopreserved normal CD34 + bone marrow cells were derived from eight healthy Caucasians (four men and four women; PromoCell GMBH; Heidelberg, Germany), and their age did not differ significantly from the AML patients analysed in the study. The submitted samples have been analyzed together with raw files derived from 50 different AML patient samples (9 patients samples in this project and 41 patient samples in project PXD014997).

2025-05-07 | PXD058846 | Pride

A maple syrup extract alleviates liver injury in type 2 diabetic model mice

Project description:A recent study showed that 54% of type 2 diabetes (T2D) patients have nonalcoholic fatty liver disease, which is a risk factor for aggravation diabetic symptoms. Previous studies suggested components in maple syrup alleviated liver injury and found polyphenols as food components to improve the symptoms and complications of diabetes. Therefore, we hypothesized that a polyphenol fraction in maple syrup improves the symptoms and complications of diabetes. To address the hypothesis, we investigated the effects of a polyphenol-rich maple syrup extract (MSE) on a T2D model mice. KK-Ay mice were fed a normal or 0.1% MSE-supplemented diet for 43 days. The results showed that the levels of serum alanine aminotransferase and aspartate aminotransferase were significantly reduced in mice that ingested MSE. Hepatic genes related to lipogenesis and lipolysis were down- and upregulated, respectively, in mice that ingested MSE. These results suggest that MSE intake alleviates liver injury and suppresses lipid accumulation in the livers of T2D mice.

2020-01-13 | GSE134185 | GEO

Laser Capture Microdissection of Normal Kidney Biopsy Glomeruli and Tubulointerstitium Characterized by LC-MS/MS

Project description:The Kidney Precision Medicine Project (KPMP) is funded by the NIDDK for "the purpose of understanding and finding new ways to treat chronic kidney disease and acute kidney injury. " To accomplish this goal, the KPMP chose several technologies to successfully deliver their goals. One of the technologies chosen was using a combination of laser capture microdissection (LCM) in combination with LC -MS /MS to characterize quantitative protein changes in the diseased kidney. The data presented here is from the initial pilot study using normal kidney biopsies for proof of principal. Samples analyzed were either LCM collected glomeruli or tubulointerstitium. Protein was retrieved from the LCM collected tissue, proteins were trypsinized and samples run on the fusion orbitrap.

2022-04-13 | MSV000089251 | MassIVE