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Gene expression profilings of normal human oral keratinocyte (HOK) and dysplastic oral keratinocyte cell line from a heavy smoker (DOK)

ABSTRACT: In our previous study, we identified global genetic and epigenetic aberrations in the tumors of oral squamous cell carcinoma (OSCC) patients who were habitual smokers. We hypothesized that cigarette smoke might play a role in oral malignant transformation. DOK cell line is a dysplasitc oral keratinocyte derived from a heavy smoker with OSCC. The differentially expressed genes between DOK and normal human oral keratinocytes (HOK) may provide important information about OSCC carcinogenesis mediated by cigarette smoking.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54861 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA237894

REPOSITORIES: GEO

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Gene expression profilings of normal human oral keratinocyte (HOK) and dysplastic oral keratinocyte cell line from a heavy smoker (DOK)

Project description:In our previous study, we identified global genetic and epigenetic aberrations in the tumors of oral squamous cell carcinoma (OSCC) patients who were habitual smokers. We hypothesized that cigarette smoke might play a role in oral malignant transformation. DOK cell line is a dysplasitc oral keratinocyte derived from a heavy smoker with OSCC. The differentially expressed genes between DOK and normal human oral keratinocytes (HOK) may provide important information about OSCC carcinogenesis mediated by cigarette smoking. Total RNA was collected from DOK and HOK cells followed by gene expression microarray analysis.

2015-12-31 | E-GEOD-54861 | biostudies-arrayexpress

High-throughput RNA sequencing of transcriptomes expressed in Oral squamous cell carcinoma (OSCC) and human oral keratinocytes (HOK)

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

Genome-wide profiling of small RNAs in human Oral squamous cell carcinoma (OSCC) cell lines

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

Transcriptome analysis of normal oral cells and oral cancer cells treated with elemental diet (ED) Elental®

Project description:Purpose: Previously, we have reported the effectiveness of elemental diet (ED) Elental® against radiotherapy- or chemoradiotherapy- induced oral mucositis (Support Care Cancer 2016, Mol Clin Oncol 2019). However, administration of additional nutrition or ED in oral cancer patients might also provide extra nutrition for cancer cells, which could result in cancer development. At present, it is still unclear whether the beneficial effect of ED can be expected to surpass its possible harmful effect on oral cancer treatment. In the present study, we tried to clarify whether Elental® has different effects on human oral keratinocyte (HOK) cells compared to oral squamous cell carcinoma (OSCC) cells (HSC2). Method: Gene expression profiles of HOK cells and HSC2 cells treated with Elental® were generated by deep sequencing. Results: Whole transcriptome analysis data suggested that Elental® helped in the proliferation and survival of HOK through the induction of ERK. Moreover, Elental® added stress to HSC2 through the induction of endoplasmic reticulum stress response marker, BiP. Our results showed that Elental® might add stress to HSC2, and provide growth stimulation to HOK. Conclusion: Whole transcriptome analysis showed different gene expression profile between HOK cells and HSC2 cells treated with Elental®, suggesting that effects of Elental® might differ between normal oral cells and oral cancer cells.

2021-07-31 | GSE151420 | GEO

Methylation profiling of oral squamous cell carcinoma (OSCC)

Project description:According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the epigenome, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate aberrent methylation patterns are prevalent in OSCC patients with ABC risk factors. Genomic DNA was collected from tumor and non-tumor pair-wise samples. These biopsies were obtained from 40 male OSCC patients who regularly drink alcohol, chew areca nut and smoking.

2015-04-01 | E-GEOD-38532 | biostudies-arrayexpress

Methylation profiling of oral squamous cell carcinoma (OSCC)

2015-04-01 | GSE38532 | GEO

Gene expression profiling of oral squamous cell carcinoma (OSCC)

Project description:According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the transcriptom, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate several potential oncogenes and tumor suppressor genes are dysregulated in OSCC patients with ABC risk factors. Total RNA was collected from tumor and non-tumor pair-wise samples. These biopsies were obtained from 40 male OSCC patients who regularly drink alcohol, chew areca nut and smoking.

2013-05-02 | E-GEOD-37991 | biostudies-arrayexpress

Gene expression profiling of oral squamous cell carcinoma (OSCC)

Project description:According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the transcriptom, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate several potential oncogenes and tumor suppressor genes are dysregulated in OSCC patients with ABC risk factors.

2013-05-02 | GSE37991 | GEO

Affymetrix SNP array data for oral squamous cell carcinoma and oral dysplasia samples

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

Gene expression profiling of oral squamous cell carcinoma (OSCC)

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

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