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.
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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.
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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.
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