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Quantitative Label Free Ultra Definition Mass-Spectrometry Provides Novel Data on the Proteomic Signature of Oral Squamous Cell Carcinoma

ABSTRACT: There are no early detection biomarkers or prognostic markers for oral squamous cell carcinoma (OSCC) thus many are detected late, with unpredictable disease course. Using systems level analysis on shotgun proteomics with quantitative label-free ultra-definition mass spectrometry, our study aims to find novel proteins involved in both low and high grade OSCC tissue, and to further understand pathways involved in cancer development and progression, using proteomic analysis.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Tongue Epithelium

DISEASE(S): Head And Neck Squamous Cell Carcinoma

SUBMITTER: Sakari Joenväärä

LAB HEAD: Suvi Renkonen

PROVIDER: PXD009244 | Pride | 2022-03-02

REPOSITORIES: Pride

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			Action	DRS
	20161010_SUVI_OSCC_01.raw.zip	Raw
	20161010_SUVI_OSCC_02.raw.zip	Raw
	20161010_SUVI_OSCC_03.raw.zip	Raw
	20161010_SUVI_OSCC_04.raw.zip	Raw
	20161010_SUVI_OSCC_05.raw.zip	Raw

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Publications

Label-free tissue proteomics can classify oral squamous cell carcinoma from healthy tissue in a stage-specific manner.

Dickinson Amy A Saraswat Mayank M Mäkitie Antti A Silén Robert R Hagström Jaana J Haglund Caj C Joenväärä Sakari S Silén Suvi S

Oral oncology 20181003

<h4>Objectives</h4>No prognostic or predictive biomarkers for oral squamous cell carcinoma (OSCC) exist. We aimed to discover novel proteins, altered in OSCC, to be further investigated as potential biomarkers, and to improve understanding about pathways involved in OSCC.<h4>Materials and methods</h4>Proteomic signatures of seven paired healthy and OSCC tissue samples were identified using ultra-definition quantitative mass spectrometry, then analysed and compared using Anova, principal componen ...[more]

PMID: 30409303

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Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Squamous Cell Carcinoma

Project description:Cancer cells often rely on aerobic glycolysis for metabolism, and lactylation, a newly discovered post-translational modification, significantly impacts molecular processes. This study comprehensively analyzes lactylation's role in oral squamous cell carcinoma (OSCC), providing initial insights into its impact on progression. Six pairs of OSCC tissues underwent lactylation modification sequencing. 2,765 lactylation modification sites on 1,033 proteins were identified in OSCC, indicating its widespread presence. These modifications influenced metabolic activities, molecular synthesis, and transport.

2024-08-23 | PXD047535 | Pride

Expression data from oral squamous cell carcinoma (OSCC)-derived cell lines and normal oral keratinocytes

Project description:Oral squamous cell carcinoma (OSCC) is a lethal disease and early death usually occurs as a result of local invasion and regional lymph node metastases. We used microarrays to identify down or upregulated genes in OSCCs compared with non-malignant controls. To identify genes whose transcription is deregulated in OSCC, the gene expression profiles of eight OSCC cell lines (H-series and M9) and three primary cultures of normal oral keratinocytes (NKs) were examined using Affymetrix HG-U133A and HG-U133 Plus 2.0 arrays.

2011-09-01 | E-GEOD-31853 | biostudies-arrayexpress

Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Carcinoma

2024-08-23 | PXD047673 | Pride

NORMALvs late stage OSCC

Project description:In order to identify genes with differential gene expression or alternative splicing between the groups Normal and late stage OSCC (Stage III and IV), we study 16 hybridizations (6 normal; 10 late stage OSCC) on the HumanGene10ST array using mixed model analysis of variance. 1323 genes with significant gene expression differences between the groups and 357 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 129 genes with both gene and possible splicing differences (p<0.01). Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes (p<0.01). Algorithm ANOVA study of 16 HumanGene10ST files. Factorial arrangment NORMALvs late stage OSCC samples

2014-09-30 | E-GEOD-56532 | biostudies-arrayexpress

Whole saliva baseline proteome profile - head and neck cancer

Project description:Oral mucositis (OM) is a common, painful and often treatment-limiting side effect of radiotherapy (RT) for head and neck cancer (HNC) patients. Unstimulated saliva was collected before the first radiotherapy application in 50 HNC patients. 41 out of 50 patients developed OM (grade III) during radiotherapy, of which 14 patients even displayed an early OM (grade III) at low radiation dose of 30 Gy. Nine patients did not develop OM (grade III). Using an LC-MS/MS approach 5,323 tryptic peptides were assigned to 487 distinct proteins (≥2 peptides) in the data set. The levels of 48 proteins differed significantly (p<0.05) between patients developing OM or not. 17 proteins displayed increased levels (≥1.3-fold) and 31 proteins decreased in level in OM, respectively. Furthermore, using partial least square analysis proteins patterns could be used to distinguish subjects which did not develop grade III OM even after 70 Gy total dose (n=9) and those displaying early OM (grade III at <30 Gy total dose, n=14). Using leave one out cross validation 37 of 41 patients (90%) developing OM could be correctly assigned indicating that prognostic proteome signatures may help to identify patients that should be specifically monitored to increase overall effectiveness of RT treatment.

2016-07-04 | PXD003230 | Pride

Array CGH analysis of Oral Squamous Cell Carcinoma

Project description:Array Comparative Genomic Hybridization (CGH) profiling of Oral Sqaumaous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with clinico-pathological parameters. The array CGH hybridizations were performed for 60 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent. Agilent two-color CGH experiment,Organism: Human ,Agilent-014698 Agilent-21764 Human Genome CGH Microarray 105A (G4412A) , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453): 60 OCC patients/samples

2011-03-11 | E-GEOD-23831 | biostudies-arrayexpress

Gene Expression Profiling of Oral Squamous Cell Carcinoma

Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent. The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

2011-10-29 | E-GEOD-23558 | biostudies-arrayexpress

Quantitative proteomic analysis of head and neck squamous cell carcinoma (HNSCC) based on pathological grading using FFPE blocks using high-resolution mass spectrometry

Project description:Oral squamous cell carcinoma is one of the most common cancers occurring worldwide associated with significant mortality and morbidity. Despite the early prognostic factors which such as histological tumor grading, staging, the extent of the tumor invasion, and involvement of regional lymph nodes, there is a demand for development of molecular markers which will help in unraveling molecular carcinogenesis associated with OSCC. In the current study, we carried out an in-depth proteomic analysis using high-resolution mass spectrometry to identify the differentially expressed proteins among the types of OSCC FFPE tissues. This resulted in the identification of 2,399 non-redundant proteins expressed differentially across histologically-classified well, moderate and poorly differentiated OSCC specimens.

2021-09-09 | PXD019456 | Pride

PARVB overexpression increases migration capability and defines high risks for endophytic growth and metastasis in tongue squamous cell carcinoma.

Project description:Tongue squamous cell carcinoma (TSCC) varies in characteristics even in early stages and is mainly classified into three subtypes, which are superficial, exophytic and endophytic types, based on a macroscopic appearance of tumor growth.Of these subtypes, endophytic tumor has a poorer prognosis because of its invasive feature and higher frequency to have metastasis. To understand a molecular mechanism of endophytic subtype and identify biomarkers, we performed comprehensive microarray analysis for mRNAs from clinical biopsy sampleswhich were classified into subtypes and found overexpression of parvin-beta (PARVB) gene significantly related to endophytic type. PARVB is known to play a critical role in actin reorganization and focal adhesions. Knocking down PARVB expression in vitrocaused apparent decreases in cell migration and wound healing, implying that PARVB has a crucial role in cellular motility. Moreover, metastasis-free survival was significantly lowered in patients with higher PARVB expression. Therefore overexpression of PARVB is a candidate biomarker for endophytic tumor and metastasis and may be clinically applicable for decision making of an adjuvant therapy in TSCC. Twenty seven OCT embedded tissues were used to extract total RNA. Then RNAs were amplified, biotinylated, fragmented and hybridized on GeneChip Human Genome U133 plus 2.0 arrays.

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Head and neck squamous cell carcinoma

Project description:Quantitative (iTRAQ 4-plex) proteomic analysis of progressive head and neck cancers

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