Gene expression signatures in human oral squamous cell carcinoma (OSCC) cell lines
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ABSTRACT:
PROVIDER: PRJNA809590 | ENA |
REPOSITORIES: ENA
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Project description:Oral squamous cell carcinoma (OSCC) is a main reason of oral cancer mortality and morbidity. Cancer of oral cavity in central south Asia, ranks among third most common kinds of cancer. The discovery of candidate markers to differentiate normal from malignant cells in clinical diagnosis of OSCC would be of critical importance because this malignancy has poor prognosis. To improve the clinical outcome in OSCC patients, the present study was aimed at identifying robust candidate biomarkers for early OSCC diagnosis and to enhance understanding of the mechanisms of disease progression and pathogenesis. Of particular interest are proteins that can be found in tissue lysates of OSCC tumor vs normal adjacent mucosa samples and secreted in cell line Secretomes of HNSCC for non-invasive detection. We analysed 17 paired human malignant OSCC tissues and normal adjacent tissue in addition to secretomes of 9 HNSCC cell lines. The proteome dataset of OSCC and normal tissues consisted of 5,123 protein groups, including 299 proteins with strong differential expression (p-value <0.01, fold change barrier to ˃+2 and <-2, 205 upregulated and 94 down regulated) and 134 common proteins were also found out of total dataset of 4473 identified proteins of HNSCC cell line secretomes. Functional data analysis revealed that these differential proteins were significantly associated with multiple biological processes. Myogenesis, Fatty Acid Metabolism and KRAS Signaling DN were associated with the proteins downregulated in cancer tissues, while Protein Secretion, Unfolded Protein Response, Spliceosomal complex assembly, Protein localization to endosome and Interferon Gamma Response were enriched in the set of upregulated proteins and these regulated proteins may be classically or non-classically secreted. Furthermore, we found differential enrichment of Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP transcription factors potentially regulating these major pathways.
2022-04-04 | PXD025701 | Pride
Project description:Epigenome analysis of normal oral keratinocytes cells and oral squamous cell carcinoma (OSCC) cells
2024-05-29 | GSE262310 | GEO
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
Project description:OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls. RNA from 167 OSCC, 17 dysplasia and 45 normal oral tissues were extracted and hybridized to Affymetrix U133 2.0 Plus GeneChip arrays. The differentially expressed genes were identified using GenePlus software and the validation was done using RT-PCR, using independent internal and external datasets.
2011-07-21 | E-GEOD-30784 | biostudies-arrayexpress
Project description:OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls.
2011-07-22 | GSE30784 | GEO
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.
2011-09-02 | GSE31853 | GEO
Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. Oral carcinogenesis is a multifactorial process involving numerous genetic changes that affect the activity of oncogenes, tumor suppressor genes and other classes of disease-related genes.Therefore, to identify the responsive genes for progression of oral dysplasia or OSCC, we here performed CGH analysis to DNA from oral dysplasia and OSCC by microdissection Copy number analysis of Affymetrix 250K SNP arrays was performed for 8 oral dysplasia samples, 8 oral squamous cell carcinoma samples, using microdissection
2013-10-22 | E-GEOD-51265 | biostudies-arrayexpress
Project description:To elucidate the potential role of small ncRNAs, such as piRNAs and miRNAs in oncogenesis of Oral squamous cell carcinoma (OSCC), we performed genome wide profiling in three human OSCC cell lines, H357 (tongue squamous cell carcinoma), KB (mouth cancer), Hep-2 (laryngeal cancer), and HOK (Normal human oral keratinocyte) using high-throughput RNA sequencing (RNA-Seq) of small RNAs. We discovered 4854 piRNAs in H357, 5184 in KB, 8340 in Hep-2, and 4735 in HOK, while miRNAs in H357, KB, Hep-2, and HOK were 1538, 1533, 1257, and 1468, respectively. This is the first study to identify both piRNAs and miRNAs in OSCCs, which will serve as a future resource for understanding the molecular mechanisms underlying the complex neoplastic events mediated by these small RNAs. Furthermore, these piRNAs and miRNAs have the potential to be used as biomarkers for OSCC.
2022-10-01 | GSE196674 | GEO
Project description:Next-generation sequencing (NGS) has transformed systems-based analysis in the molecular landscapes of various cancer types. The goals of this study are to obtain transcriptomes expressed in human oral squamous cell carcinoma (OSCC) cell lines. The transcriptome profiles of OSCC cell lines (H357, KB and Hep-2) and normal Human oral keratinocytes (HOK) were obtained from the high throughput RNA sequencing sequencing using Illumina Hiseq2500 platform. We obtained 10160, 10251, 10191, 10201 transcripts expressed in HOK, H357, KB, and Hep-2 respectively, which include protein coding genes (PCGs), lncRNAs, pseudogenes and others. Our results showed a set of transcripts that are dysregulated in OSCC, which might be playing some key roles in tumorigenesis process. Further in-depth analysis might provide clues for better understanding of gene function in OSCC.
2022-10-01 | GSE196688 | GEO
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