Study Program of Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia.
6Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia.
Asian Pac J Cancer Prev. 2020 Sep 1;21(9):2763-2769. doi: 10.31557/APJCP.2020.21.9.2763.
Transcriptomic Profile Analysis Related to Inflammation in Nasopharyngeal Carcinoma Cases.
This study used 2 control samples taken using the brushing technique and 7 cancer samples with tissue biopsy. Isolate total RNA using Rneasy® RNA Extraction Mini Kit. Measurement of total RNA concentration and purity using a fluorometer and nanodrop Qubit. Synthesis of cDNA library uses TruSeq® RNA Library Preparation Kit V2 and concentration is measured using qPCR. Sequencing samples using NGS Illumina NextSeq 550 platform engine. Quality control results of sequencing using FASTQC, and raw data processing using HISAT2. Differential analysis of gene expression (DEGs) using edgeR and pathway analysis using DAVID and PANTHER.
From the 25,493 genes that experienced a significant change in expression level (P <0.05) from DEG analysis there were 13 genes that play a role in the inflammatory process. Based on DAVID pathway analysis software, there are 8 genes detected based on the KEGG pathway database found in 2 pathways, namely Inflammatory Mediator Regulation of TRP Channels pathway with genes that play HTR2A, NGF, TRPA1, PRKCG, and ADCY8. CXCL9, CXCL10, and CXCL11 genes are found in the Toll-Like Receptor Signaling pathway. Based on PANTHER pathway analysis software, 6 genes were found, namely CXCL10, MYLK2, COL20A1, MYH2, ACTC1, and ALOX15 in the Inflammation Mediated by Chemokine and Cytokine Signaling pathways. Almost all genes found from DEGs are upregulated, except the ALOX15 gene that is downregulated.
There are 13 genes that play a role in the inflammatory process in Nasopharyngeal Carcinomafrom a sample of the Indonesian population. Genes CXCL9, CXCL10, CXCL11, MYLK2, COL20A1, MYH2, ACTC1, HTR2A, NGF, TRPA1, PRKCG, and ADCY8 have been upregulated and ALOX15 has been downregulated. These genes play a role in the Inflammation Mediated by Chemokine and Cytokine Signaling pathways, Inflammatory Mediator Regulation of TRP Channels, and Toll-Like Receptor Signaling.
分析与鼻咽癌病例炎症相关的转录组谱。
本研究使用 2 个采用刷拭技术采集的对照样本和 7 个采用组织活检采集的癌症样本。使用 Rneasy® RNA 提取试剂盒提取总 RNA。使用荧光计和纳米滴 Qubit 测量总 RNA 的浓度和纯度。使用 TruSeq® RNA 文库制备试剂盒 V2 合成 cDNA 文库，并使用 qPCR 测量浓度。使用 NGS Illumina NextSeq 550 平台发动机对样品进行测序。使用 FASTQC 对测序结果进行质量控制，使用 HISAT2 对原始数据进行处理。使用 edgeR 进行基因表达差异分析（DEGs），使用 DAVID 和 PANTHER 进行通路分析。
从差异表达基因分析（DEG）中经历表达水平显著变化（P<0.05）的 25493 个基因中，有 13 个基因在炎症过程中发挥作用。基于 DAVID 通路分析软件，在 2 个途径中检测到基于 KEGG 途径数据库的 8 个基因，即 HTR2A、NGF、TRPA1、PRKCG 和 ADCY8 的炎症介质调节 TRP 通道途径，以及 CXCL9、CXCL10 和 CXCL11 基因的 Toll 样受体信号途径。基于 PANTHER 通路分析软件，发现了 6 个基因，即趋化因子和细胞因子信号通路中的 CXCL10、MYLK2、COL20A1、MYH2、ACTC1 和 ALOX15。从 DEGs 中发现的几乎所有基因均上调，除了下调的 ALOX15 基因。
从印度尼西亚人群的样本中发现 13 个在鼻咽癌炎症过程中发挥作用的基因。基因 CXCL9、CXCL10、CXCL11、MYLK2、COL20A1、MYH2、ACTC1、HTR2A、NGF、TRPA1、PRKCG 和 ADCY8 上调，而 ALOX15 下调。这些基因在趋化因子和细胞因子信号通路、炎症介质调节 TRP 通道和 Toll 样受体信号等炎症介导的途径中发挥作用。
