Bioinformatics Accelerates Drug Repositioning*

Huang, Hong; Fang, Liang; Wang, Xiong; Li, Xiaoling; Zeng, Zhaoyang; Li, Guiyuan

doi:10.3724/sp.j.1206.2011.00453

Cited by 8 publications

(8 citation statements)

References 53 publications

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“…Mining of published high-throughput data is a commonly used and low-cost method for identifying novel biomarkers and gaining insight into the biological functions of novel genes [21–23]. To identify potential novel functions of AFAP1-AS1 , we downloaded a GEP dataset, GSE12452, from the GEO database; this dataset consists of 41 samples of whole-genome GEP data, including 10 samples of non-tumor nasopharyngeal epithelial (NPE) biopsies and 31 cases of NPC [24].…”

Section: Resultsmentioning

confidence: 99%

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

et al. 2017

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Nasopharyngeal carcinoma (NPC) carries a high potential for metastasis and immune escape, with a great risk of relapse after primary treatment. Through analysis of whole genome expression profiling data in NPC samples, we found that the expression of a long non-coding RNA (lncRNA), actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1), is significantly correlated with the immune escape marker programmed death 1 (PD-1). We therefore assessed the expression of AFAP1-AS1 and PD-1 in a cohort of 96 paraffin-embedded NPC samples and confirmed that AFAP1-AS1 and PD-1 are co-expressed in infiltrating lymphocytes in NPC tissue. Moreover, patients with high expression of AFAP1-AS1 or PD-1 in infiltrating lymphocytes were more prone to distant metastasis, and NPC patients with positive expression of both AFAP1-AS1 and PD-1 had the poorest prognosis. This study suggests that AFAP1-AS1 and PD-1 may be potential therapeutic targets in NPC and that patients with co-expression of AFAP1-AS1 and PD-1 may be ideal candidates for future clinical trials of anti-PD-1 immune therapy.

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Section: Resultsmentioning

confidence: 99%

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

et al. 2017

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“…GSE9844 contain 26 cancer tissues and 12 normal adjacent tissues. Significant Analysis of Microarray (SAM) software 33-35 were used to analyze normal lingual mucous membrane and TSCC tissue samples for differences in the expression of lncRNAs in these two published TSCC dataset. The cut-off value for differentially expressed lncRNA was set at ≥ 1.5-fold or ≤ 0.67-fold change and the false discovery ratio (FDR) was < 0.05.…”

Section: Methodsmentioning

confidence: 99%

Upregulated long non-coding RNA LINC00152 expression is associated with progression and poor prognosis of tongue squamous cell carcinoma

Yu¹,

Ling²,

Guo³

et al. 2017

J. Cancer

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101

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Altered expression of long non-coding RNAs (lncRNAs) associated with human carcinogenesis and might be used as diagnosis and prognosis biomarkers. However, the expression of lncRNAs in tongue squamous cell carcinoma (TSCC) and their relevance on the diagnosis, progression and prognosis of TSCC have not been thoroughly elucidated. To discover novel TSCC-related lncRNAs, we analyzed the lncRNA expression patterns in two sets of previously published TSCC gene expression profile data (GSE30784 and GSE9844), and found that long intergenic non-coding RNA 152 (LINC00152) was significantly upregulated in TSCC samples. We then detected LINC00152 expression in two other cohorts of TSCC samples. Quantitative Real time PCR (qRT-PCR) results indicated that LINC00152 was highly expressed in 15 primary TSCC biopsies when compared with 14 adjacent non-tumor tongue squamous cell epithelium samples. The expression of LINC00152 was also measured in 182 paraffin-embedded human TSCC tissues by in situ hybridization, increased expression of LINC00152 was significantly correlated with TSCC progression, such as T stage (p = 0.009), N stage (p = 0.036), TNM stage (p = 0.017), and associated with relapse (p < 0.001), and invasion (p < 0.001). Kaplan-Meier analysis demonstrated that increased LINC00152 expression contributed to both poor overall survival (p = 0.006) and disease-free survival (p = 0.007) of TSCC patients. These findings suggest that LINC00152 might serve as a potential biomarker for early detection and prognosis prediction of TSCC.

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“…GSE30784 has 167 cancer tissues and 45 normal adjacent tissues. Significant Analysis of Microarray (SAM) [48–51] software was used to analyze the different expression of lncRNAs between normal lingual mucous membrane and TSCC tissue samples in these two published TSCC datasets. The cut-off value for differentially expressed lncRNA was set at ≥ 1.5-fold change and the false discovery ratio (FDR) was < 0.05.…”

Section: Methodsmentioning

confidence: 99%

Overexpression long non-coding RNA LINC00673 is associated with poor prognosis and promotes invasion and metastasis in tongue squamous cell carcinoma

Liu

Gong

et al. 2016

Oncotarget

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Long non-coding RNAs (lncRNAs) associated with the tumorigenesis of human cancers. However, the relevance of lncRNAs in tongue squamous cell carcinoma (TSCC) is still unclear. To discover novel TSCC-related lncRNAs, we analyzed the lncRNA expression patterns in two sets of TSCC gene expression profile data, and found that long intergenic non-coding RNA 673 (LINC00673) was significantly upregulated in TSCC samples. Then we examined LINC00673 expression in 202 TSCC tissue specimens, LINC00673 is highly expressed in a significant proportion of human TSCC biopsies and correlates with poor prognosis. Knockdown LINC00673 significantly inhibited the cell invasion and migration capability in TSCC cells. Our findings suggest that LINC00673 may play an essential role in TSCC progression and might serve as a potential biomarker for early detection and prognosis prediction of TSCC.

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Bioinformatics Accelerates Drug Repositioning*

Cited by 8 publications

References 53 publications

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

Upregulated long non-coding RNA LINC00152 expression is associated with progression and poor prognosis of tongue squamous cell carcinoma

Overexpression long non-coding RNA LINC00673 is associated with poor prognosis and promotes invasion and metastasis in tongue squamous cell carcinoma

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