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Using the TCGA Database to Predict and Analyze Tumor Microenvironment Genes Related to Poor Prognosis of Colon Cancer.

利用 TCGA 数据库预测和分析与结肠癌不良预后相关的肿瘤微环境基因。

  • 影响因子:2.03
  • DOI:10.12659/MSM.923707
  • 作者列表:"Chen S","Yida L","Chen B","Xiong M
  • 发表时间:2020-06-18
Abstract

:BACKGROUND Colon cancer (COAD) is a highly malignant gastrointestinal cancer. The existence of the TCGA database allows us to more easily perform gene expression profiling and data mining on colon cancer patients worldwide, and to more easily discover the correlation between genes and survival prognosis of colon cancer. Related reports show that the degree of infiltration of tumor immune cells and stromal cells in tumor microenvironment cells has a significant impact on the prognosis of cancer patients. MATERIAL AND METHODS The immune and stromal components in colon cancer can be quantitatively analyzed using relevant scores obtained by use of the ESTIMATE calculation method. To better explain the effect of relevant genes of cells associated with immunity and stroma on the survival prognosis of colon cancer, we divided the data from 191 downloaded case into high and low groups according to their scores of immunity and stroma, and identified differentially expressed genes. RESULTS The results showed that immune and stromal scores were significantly associated with survival prognosis. After performing biological function enrichment analysis and protein interaction network on the target genes, the results showed that these genes are mainly involved in inflammatory response, immune response, and chemotaxis. We then performed relevant survival prognosis analysis of these genes. CONCLUSIONS We found a number of genes that possess the properties of tumor immune microenvironment and can predict poor prognosis of colon cancer.

摘要

: 背景结肠癌 (COAD) 是一种高度恶性的胃肠道恶性肿瘤。TCGA 数据库的存在使我们能够更容易地对全球结肠癌患者进行基因表达谱分析和数据挖掘,更容易发现基因与结肠癌生存预后的相关性。相关报道显示肿瘤微环境细胞中肿瘤免疫细胞和基质细胞的浸润程度对癌症患者的预后有显著影响。材料与方法结肠癌的免疫和间质成分可以用估计计算方法得到的相关分数进行定量分析。为了更好地解释与免疫和间质相关的细胞的相关基因对结肠癌生存预后的影响,我们根据免疫和间质评分将 191 例下载病例的数据分为高低组,并鉴定差异表达基因。结果免疫和间质评分与生存预后显著相关。对目的基因进行生物功能富集分析和蛋白质相互作用网络分析后,结果表明这些基因主要参与炎症反应、免疫反应和趋化反应。然后我们对这些基因进行相关的生存预后分析。结论我们发现了许多具有肿瘤免疫微环境特性的基因,可以预测结肠癌的不良预后。

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影响因子:2.03
发表时间:2020-01-27
DOI:10.1080/09553002.2020.1721609
作者列表:["Anuja K","Kar M","Chowdhury AR","Shankar G","Padhi S","Roy S","Akhter Y","Rath AK","Banerjee B"]

METHODS::Aims: Radiotherapy is predominantly used as one of the treatment modalities to treat local tumor in colorectal cancer (CRC). Hindrance in disease treatment can be attributed to radio-tolerance of cancer stem cells (CSCs) subsistence in the tumor. Understanding the radio-resistant property of CSCs might help in the accomplishment of targeted radiotherapy treatment and increased disease-free survival. Telomeric RAP1 contributes in modulation of various transcription factors leading to aberrant cell proliferation and tumor cell migration. Therefore, we investigated the role of RAP1 in maintaining resistance phenotype and acquired stemness in radio-resistant cells.Main Methods: Characterization of HCT116 derived radio-resistant cell (HCT116RR) was performed by cell survival and DNA damage profiling. RAP1 silenced cells were investigated for DNA damage and expression of CSC markers through western blotting and Real-time PCR post-irradiation. Molecular docking and co-immunoprecipitation study were performed to investigate RAP1 and KLF4 interaction followed by RAP1 protein status profiling in CRC patient.Key findings: We established radio-resistant cells, which showed tolerance to radiotherapy and elevated expression of CSC markers along with RAP1. RAP1 silencing showed enhanced DNA damage and reduced expression of CSC markers post-irradiation. We observed strong physical interaction between RAP1 and KLF4 protein. Furthermore, higher RAP1 expression was observed in the tumor of CRC patients. Dataset analysis also revealed that high expression of RAP1 expression is associated with poor prognosis.Significance: We conclude that higher expression ofRAP1 implicates its possible role in promoting radio-resistance in CRC cells by modulating DNA damage and CSC phenotype.

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影响因子:2.69
发表时间:2020-01-18
DOI:10.1016/j.bbrc.2020.01.048
作者列表:["Li Y","Wang Z","Jin J","Zhu SX","He GQ","Li SH","Wang J","Cai Y"]

METHODS::Cancer stem-like cells are rare immortal cells within tumor, which are thought to play important roles in ionizing radiation (IR) therapy-resistance. Quercetin is a natural flavonoid with potential anti-cancer properties without significant cytotoxicity in normal tissues. In this study, we demonstrated that quercetin-IR combination treatment exhibited more dramatic anti-cancer effect than either quercetin or IR treatment alone via targeting colon cancer stem cells (CSCs) and inhibiting the Notch-1 signaling. These effects were further verified by in vivo studies which showed remarkable decrease of the CSCs markers and the expression of Notch-1 signaling proteins in human colon cancer xenografts in nude mice. Co-treatment with quercetin and low dose of radiation significantly reduced the expressions of all five proteins of γ-secretase complex in HT-29 and DLD-1 cells. In addition, ectopic expression of the Notch intracellular domain (NICD) partly reversed the inhibition effects by the combination therapy. In conclusion, our results indicated that the combination of quercetin (20 μM) and IR (5Gy) might be a promising therapeutic strategy for colon cancer treatment by targeting colon cancer stem-like cells and inhibiting the Notch-1 signaling. In future studies, we intend to further explore the potential therapeutic efficacy of the quercetin-radiation combination treatment in clinical trials.

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影响因子:2.46
发表时间:2020-01-01
DOI:10.1097/COC.0000000000000609
作者列表:["Appelt AL","Andersen RF","Lindebjerg J","Jakobsen A"]

METHODS:OBJECTIVES:Long-term prevention of metastatic disease remains a challenge in locally advanced rectal cancer, and robust pretreatment prognostic factors for metastatic progression are lacking. We hypothesized that detecting circulating tumor-specific DNA (ctDNA) based on hypermethylation of the neuropeptide Y gene (meth-ctDNA) could be a prognostic marker in the neoadjuvant setting; we examined this in a secondary, explorative analysis of a prospective trial. MATERIALS AND METHODS:Serum samples were prospectively collected in a phase III trial for locally advanced rectal cancer. Positivity for and fractional abundance of meth-ctDNA in baseline samples were estimated. Overall survival (OS) and the rate of distant metastases were compared between meth-ctDNA positive and negative patients; other prognostic factors were controlled for in multivariate Cox regression. Importance of quantitative load was examined by considering the fractional abundance of meth-ctDNA relative to total circulating DNA. RESULTS:Baseline serum samples were available for 146 patients. In total, 30 patients had presence of meth-ctDNA, with no correlation with cT (P=0.8) or cN (P=0.6) stages. Median follow-up was 10.6 years for OS and 5.1 years for freedom from distant metastases. Patients with meth-ctDNA had significantly worse 5-year OS (47% vs. 69%), even when controlling for other prognostic factors (hazard ratio=2.08; 95% confidence interval, 1.23-1.51). This seemed mainly driven by disparity in the rate of distant metastases (55% vs. 72% at 5 y, P=0.01); hazard ratio=2.20 (95% confidence interval, 1.19-4.07, P=0.01) in multivariate analysis. Increased quantitative load was highly significant for worse outcomes. CONCLUSIONS:Meth-ctDNA could be a potential prognostic marker in the neoadjuvant setting and may, if validated, identify patients at increased risk of distant metastases.

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