Dissecting the mechanism of colorectal tumorigenesis based on RNA-sequencing data

Liu, Fuguo; Ji, Fengzhi; Yu-ling, JI; Jiang, Yueping; Sun, Xue‐Guo; Lu, Yao; Zhang, Lingyun; Han, Yue; Liu, Xi-Shuang

doi:10.1016/j.yexmp.2015.01.004

Cited by 8 publications

(7 citation statements)

References 45 publications

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“…We observed in our results that the expression of COL1A2 was significantly elevated in gastric tumor tissues. In previous research, elevated COL1A2 expression has also been found in many different types of cancers, including breast cancer [22], head and neck cancer [4], and colorectal cancer [23]. We failed to observe the prognostic value of COL1A2 in the current analysis, whereas Misawa et al reported that the COL1A2 gene might serve as an important biomarker in head and neck squamous cell carcinoma [4].…”

Section: +contrasting

confidence: 69%

Elevated THBS2, COL1A2, and SPP1 Expression Levels as Predictors of Gastric Cancer Prognosis

Zhuo

Zhuang

et al. 2016

Cell Physiol Biochem

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Background/Aims:Gastric cancer (GC) is an important health problem. Classification based on molecular subtypes may help to determine the prognosis of patients with GC. Tumor invasion and metastasis are important factors affecting the prognosis of cancer. We aimed to identify genes related to tumor invasion and metastasis, which may serve as indicators of good GC prognosis. Methods:Tumor tissues and adjacent normal tissues were collected from 105 patients with primary GC who were treated by undergoing radical surgery. Samples were used for tissue microarray analysis. Identified genes with altered expression were further analyzed using the Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression levels of THBS2, COL1A2 and SPP1 were analyzed by RT-PCR, western blot and immunohistochemistry. The overall survival curves of patients with high and low expression of each gene of interest were plotted and compared. Results:Forty-three genes were identified. THBS2, COL1A2 and SPP1 were selected for further analysis. Altered expression levels of THBS2, COL1A2 and SPP1 in tumor tissues were confirmed. Patients with low THBS2 expression had a better prognosis; the expression of COL1A2 and SPP1 might not affect the prognosis of patients with GC. Conclusion:THBS2, but not COL1A2 and SPP1, may serve as an indicator of GC prognosis.

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Section: +contrasting

confidence: 69%

Elevated THBS2, COL1A2, and SPP1 Expression Levels as Predictors of Gastric Cancer Prognosis

Zhuo

Zhuang

et al. 2016

Cell Physiol Biochem

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“…RP11-273G15.2, RP3-439F8.1, RP11-286B14.1, RP11-161H23.9, LINC01579 and LY86-AS1. As to LY86-AS1, previous studies have proved its potential in several types of cancer, including myeloid cancer, colorectal cancer [34][35][36]. Our study confirmed the novel function of LY86-AS1 in GBM.…”

Section: Discussionsupporting

confidence: 83%

Systemic analysis of lncRNA and miRNA expression profiles with associated ceRNA network in glioblastoma

Sun¹,

Liu²,

Song³

et al. 2018

Oncotarget

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Glioblastoma (GBM) is the most common malignant brain tumor with high morbidity and mortality. Long and small non-coding RNA, i.e. lncRNA and miRNA in this study, play important roles in progression of complex diseases and competes with each other when regulate expression of mRNA. In this study, we conducted systemic analysis of high-throughput gene sequencing and microarray datasets to explore expression regulation patterns in GBM. Differential expression mRNAs, lncRNAs and miRNAs were obtained through comprehensively comparinged their expression profiles between GBM and adjacent non-tumor tissues. As a result, a total of 28 lncRNAs were found to be aberrantly expressed (|log2 (fold change)| > 1, corrected p-value < 0.01) and six out of them were significantly associated with GBM prognosis. The expression changes of the six lncRNAs were further validated through quantative PCR analysis. Finally, lncRNA mediated competition endogenous (ceRNA) network was constructed, which should be helpful for the understanding of lncRNA mediated ceRNA network and identification of prognosis biomarker for GBM.

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“…EXPH5 gene shares homology with Rab-GTPase and play a significant role in vesicle trafficking 42,43. The active participation of this gene has been reported in colorectal cancer 44. The differential methylation associated with the CpG site cg14033170 also holds greater significance.…”

Section: Discussionmentioning

confidence: 98%

Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis

Shilpi

Jung

et al. 2017

Cancer Inform

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INTRODUCTIONBreast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer. The effect of these SNPs on methylation is defined as methylation quantitative trait loci (meQTL).MATERIALS AND METHODSWe developed a novel method to identify prognostic gene signatures for breast cancer by integrating genomic and epigenomic data. This is based on the hypothesis that multiple sources of evidence pointing to the same gene or pathway are likely to lead to reduced false positives. We also apply random resampling to reduce overfitting noise by dividing samples into training and testing data sets. Specifically, the common samples between Illumina 450 DNA methylation, Affymetrix SNP array, and clinical data sets obtained from the Cancer Genome Atlas (TCGA) for breast invasive carcinoma (BRCA) were randomly divided into training and test models. An intensive statistical analysis based on log-rank test and Cox proportional hazard model has established a significant association between differential methylation and the stratification of breast cancer patients into high- and low-risk groups, respectively.RESULTSThe comprehensive assessment based on the conjoint effect of CpG–SNP pair has guided in delaminating the breast cancer patients into the high- and low-risk groups. In particular, the most significant association was found with respect to cg05370838–rs2230576, cg00956490–rs940453, and cg11340537–rs2640785 CpG–SNP pairs. These CpG–SNP pairs were strongly associated with differential expression of ADAM8, CREB5, and EXPH5 genes, respectively. Besides, the exclusive effect of SNPs such as rs10101376, rs140679, and rs1538146 also hold significant prognostic determinant.CONCLUSIONSThus, the analysis based on DNA methylation and SNPs have resulted in the identification of novel susceptible loci that hold prognostic relevance in breast cancer.

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Dissecting the mechanism of colorectal tumorigenesis based on RNA-sequencing data

Cited by 8 publications

References 45 publications

Elevated THBS2, COL1A2, and SPP1 Expression Levels as Predictors of Gastric Cancer Prognosis

Elevated THBS2, COL1A2, and SPP1 Expression Levels as Predictors of Gastric Cancer Prognosis

Systemic analysis of lncRNA and miRNA expression profiles with associated ceRNA network in glioblastoma

Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis

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