Gene expression signatures in EGFR-deleted oral squamous cell carcinoma (OSCC) cell lines
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ABSTRACT:
PROVIDER: PRJNA922911 | ENA |
REPOSITORIES: ENA
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Project description:To investigate the effect of EGFR disruption on gene expression, we generated EGFR-knockout (EGFR-KO) cell clones using CRISPR/Cas9 system with OSCC cell lines HSC-2 and HSC-3 cells. The OSCC cells were incubated for 48 h in vitro.
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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.
2025-10-07 | MSV000099414 | MassIVE
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.
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Project description:As a Class II small leucine-rich proteoglycan, fibromodulin (FMOD) plays critical roles in collagen fibrillogenesis and angiogenesis. However, the biological function of FMOD in oral squamous cell carcinoma remains unknown to date. In this study, immunohistochemistry and immunofluorescence assays identified that FMOD protein was located in cytoplasm and nucleus and was overexpressed in OSCC tissues and cell lines. Clinical analysis confirmed that FMOD overexpression showed a significant association with malignant progression (P=0.011) and lymph node metastasis (P=0.032) in OSCC patients. Moreover, loss-of-function studies verified that knockdown of FMOD significantly inhibited OSCC growth and metastasis in vitro and in vivo. Mechanismly, RNA sequencing studies further confirmed that. Knockdown of FMOD expression inhibited OSCC cell proliferation, migration, invasion, and tumor growth probably through altering transcriptome leading to active cell cycle, down-regulating Cell adhesion molecules and ECM-receptor interaction and through inhibiting EGFR-ERK and EGFR-AKT pathways.
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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.
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Project description:CNTNAP2 has two isoforms with clear evidence of expression: CNTNAP2-201 and CNTNAP2-203. Extensive research has centered on the full-length CNTNAP2-201, as a neuronal adhesion molecule, due to its association with numerous neurodevelopmental disorders, the role of CNTNAP2-203 in disease pathology has remained largely unexplored. Oral squamous cell carcinoma (OSCC) is a major malignancy in the head and neck region with high mortality and morbidity, partially due to a limited understanding of molecular mechanisms underlying its onset and progression. This study reveals that CNTNAP2-203 mRNA and protein levels are significantly elevated in OSCC tissues compared to their adjacent normal tissues, and high CNTNAP2-203 expression is closely associated with worsened clinical outcomes in OSCC patients. Functionally, CNTNAP2-203 plays a role in driving OSCC cell proliferation in vitro and tumor growth in vivo by modulating E2F1 activity. Mechanistically, CNTNAP2-203 interacts with the epidermal growth factor receptor (EGFR) and amplifies EGFR signal activities, promoting OSCC tumorigenesis through the EGFR-E2F1 axis. Notably, OSCC cells with elevated CNTNAP2-203 demonstrate increased sensitivity to Gefitinib, either alone or in combination with Cisplatin, suggesting patients with high CNTNAP2-203 levels may achieve better outcomes when treated with such regimens. Therefore, this study not only elucidates the pathogenic role of CNTNAP2-203 in OSCC but also highlights the potential of using CNTNAP2-203 as a biomarker for guiding therapeutic strategies in OSCC management.
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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
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. 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: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