Gene expression analysis of laryngeal squamous cell carcinoma

Plaça, Jéssica Rodrigues; Bueno, Rafaela de Barros e Lima; Pinheiro, Daniel Guariz; Panepucci, Rodrigo Alexandre; Araújo, Luíza Ferreira de; Mamede, Rui Celso Martins; Figueiredo, David Livingstone Alves; Silva, Wilson A.

doi:10.1016/j.gdata.2015.04.024

Cited by 10 publications

(10 citation statements)

References 7 publications

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“…A common malignancy found in the head and neck tumor is laryngeal squamous cell carcinoma (LSCC) [1,2], with 151,000 new cases diagnosed worldwide [3] each year and 90,000 associated deaths [4,5]. LSCC usually affects men over 50-60 years of age [6] and is strongly related with tobacco smoking and alcohol use [7].…”

Section: Introductionmentioning

confidence: 99%

Combined Effect of HPV and Several Gene SNPs in Laryngeal Cancer

Stumbrytė-Kaminskienė

Gudlevičienė

Dabkevičienė

et al. 2020

Medicina

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Background and objectives: Laryngeal squamous cell carcinoma (LSCC) is one of the most common head and neck tumors. The molecular mechanism of LSCC remains unclear. The aim of this study was to evaluate the prevalence of Human papillomavirus (HPV) and single nucleotide polymorphisms (SNPs) of TP53, MDM2, MDM4, MTHFR, CASP8, and CCR5 genes in LSCC, and to assess their correlations with patient survival. Materials and Methods: 49 LSCC patients were enrolled in this study. PCR and qRT-PCR were used to detect, identify, and quantify HPV. SNPs were genotyped using PCR and PCR-RFLP. Results: By analyzing the interactions of the SNPs of the genes with clinical parameters, the majority of patients with lymph node status (N1,2) were identified as carriers of MDM2 T/G, CASP8 ins/del, CCR5 wt/wt SNP. Cluster analysis showed that patients with MDM2 T/T SNP survive longer than patients identified as CASP8 ins/ins, MTHFR C/C, and MDM4 A/A variant carriers; meanwhile, LSCC patients with MDM2 T/T polymorphic variant had the best survival. Multivariate analysis showed that HPV-positive patients without metastasis in regional lymph nodes (N0) and harboring CASP8 ins/del variant had the best survival. Meanwhile, HPV-negative patients with identified metastasis in lymph nodes (N1 and N2) and CASP8 ins/del variant had poor survival. Conclusions: This finding suggests patients survival prognosis and tumor behavior are different according HPV status, SNP variants, and clinical characteristics of the LSCC.

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Section: Introductionmentioning

confidence: 99%

Combined Effect of HPV and Several Gene SNPs in Laryngeal Cancer

Stumbrytė-Kaminskienė

Gudlevičienė

Dabkevičienė

et al. 2020

Medicina

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“…The expressions at 0 hr were used as control. Log2 ≥ 1 means that the gene expression was upregulated, while log2 ≤ −1 was assumed as downregulated (Plaça et al., ). Compared with R. solanacearum GMI1000 genome, the expression of some genes was obviously changed in S. tuberosum root secretions.…”

Section: Resultsmentioning

confidence: 99%

“…Data were normalized using the “Quantile” method in Gene Spring GX software, and then, a log2 transformation was conducted. The differential gene screening criterion was Log2≧1.0 or Log2≦−1 (Plaça et al., ).…”

Section: Methodsmentioning

confidence: 99%

Gene expression profile of Ralstonia Solanacearum for the rhizosphere ecological niche of Solanum tuberosum

Duan

Luo

Kong

et al. 2017

Journal of Phytopathology

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Plant root secretion can be regarded as signal molecules, which exerts impact on microorganisms in the rhizosphere ecological niche. We obtained gene expression profile of Ralstonia solanacearumPO41 under the root secretions environment of Solanum tuberosum at the time points of 8 hrs, 16 hrs and 24 hrs, respectively, after infection with RNA microarray technology. Bioinformatics tools of differential genes expression analysis, GO functional analysis, cluster analysis and pathway analysis were conducted to find out the pathogenic genes and other related genes. We found that the virulence factors of R. solanacearum mainly focused on the output pathways of toxic protein (Sec pathway, Tat pathway and type III secretion system (T3SS)), the aggregation and transfer of exopolysaccharides and the chemotactic movement and adhesion of flagellum in the potato root secretion ecological niche, while the virulence factors in the atypical output pathway mainly distributed in Sec (secB, secDF, yidc) and Tat (tatA, tatC) pathways to promote the output of folded and unfolded toxic proteins. The fliIATPase was obviously upregulated 8 hrs postinoculation, suggesting that type III secretion system was only active at the early stage of PO41 infection. The upregulated expression of phosphoglucomutase and epimerase showed that the virulence factor of exopolysaccharides (EPS) was synthesized at the early stage of R. solanacearum infection. Chemotactic receptor and motor protein were obviously upregulated within 24 hrs postinoculation. Our study revealed that R. solanacearumPO41 had already colonized to the roots within 24 hrs with the stimulating of root secretion. Some pathogenic genes were upregulated during this period.

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“…Microarray data. The expression profile with the accession number GSE59102 (12) was downloaded from the public Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) database. The data set comprised 29 cancer and 13 margin samples (control) from patients undergoing surgical ablation of LSCC.…”

Section: Methodsmentioning

confidence: 99%

“…A recent study included patients with LSCC in different tumor stages to clarify new biomarkers that had driven the progression of LSCC. Based on their finding that HOXC8 and HOXD11 were essential for FADU cell expansion, the HOX family members were suggested to be correlated with the development of LSCC (12). However, alterations of the specific genes expressed in the early and late stage of LSCC were rarely involved.…”

Section: Introductionmentioning

confidence: 99%

Identification of biomarkers with a tumor stage-dependent expression and exploration of the mechanism involved in laryngeal squamous cell carcinoma

Hui

Yang

et al. 2015

Oncology Reports

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The aim of this study was to identify biomarkers with a tumor stage-dependent expression manner and explore the regulatory mechanisms of laryngeal squamous cell carcinoma (LSCC) progression. Microarray data GSE59102 was used for differential analysis using a limma package. Enrichment analyses were performed for the differentially expressed genes (DEGs) between tumor tissues and normal tissues at different stages. A co-expressed network involving the overlapped DEGs in two stages was established based on Pearson's correlation coefficients. Furthermore, for the tumor stage‑dependent expressed DEGs, a protein‑protein interaction (PPI) network was constructed by mapping the genes using the STRING database. Transcription factors (TFs), oncogenes and tumor‑associated genes (TSGs) among the DEGs were predicted, following a search of the TRANSFAC, tumor-associated gene (TAG) and TSG databases. The CDT database was used to identify LSCC‑associated genes. In total, 696 DEGs from early stage and control samples and 622 DEGs from advanced sttage and control samples were selected, which were mainly enriched in the cell cycle pathway. In the co-expressed network, BUB1, TTK, E2F1 and CEP55 were prominent, with E2F1 being predicted as a TSG and CEP55 as an oncogene. The HOX family members were predicted as TFs. MMP1, MMP9, MMP3 and PLAU were the most evident nodes in the PPI network, where MMP3 was connected with MMP1. The ADH family was correlated with LSCC. Several biomarkers with tumor stage-dependent expression were identified including MMP1, MMP3, MMP9, PLAU and ADHs. Additionally, the dysregulated cell cycle pathway involving BUB1, TTK, E2F1 and CEP55, and the mediation of MMP1 by MMP3 as well as the predicted TF HOX, may all play significant roles in LSCC progression.

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Gene expression analysis of laryngeal squamous cell carcinoma

Cited by 10 publications

References 7 publications

Combined Effect of HPV and Several Gene SNPs in Laryngeal Cancer

Combined Effect of HPV and Several Gene SNPs in Laryngeal Cancer

Gene expression profile of Ralstonia Solanacearum for the rhizosphere ecological niche of Solanum tuberosum

Identification of biomarkers with a tumor stage-dependent expression and exploration of the mechanism involved in laryngeal squamous cell carcinoma

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