Transcriptome Profile of Next Generation Sequence Data Related to Inflammation on Nasopharyngeal Carcinoma Cases in Indonesia

Sudigyo, Digdo; Rahmawati, Gisti; Setiasari, Dicka Wahyu; Poluan, Risky Hiskia; Sesotyosari, Salsabila Luthfi; Wardana, Tirta; Herawati, Cita; Heriyanto, Didik Setyo; Indrasari, Sagung Rai; Afiahayati, -; Astuti, Indwiani; Haryana, Sofia Mubarika

doi:10.31557/APJCP.2020.21.9.2763

Transcriptome Profile of Next Generation Sequence Data Related to Inflammation on Nasopharyngeal Carcinoma Cases in Indonesia

Document Type : Research Articles

Authors

¹ Study Program of Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia.

² 6Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia.

³ Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.

⁴ Department of Computer Science and Electronics, Universitas Gadjah Mada, Yogyakarta, Indonesia.

⁵ Dharmais Cancer Hospital, Jakarta, Indonesia.

⁶ Jenderal Soedirman, Central Java, Indonesia.

10.31557/APJCP.2020.21.9.2763

Abstract

Objective: Transcriptomic Profile Analysis Related to Inflammation in Nasopharyngeal Carcinoma Cases. Methods: 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. Results: 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. Conclusion: 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.

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