Transcriptome Profile of Next-Generation Sequencing Data Relate to Proliferation Aberration of Nasopharyngeal Carcinoma Patients in Indonesia
Nasopharyngeal carcinoma (NPC) is cancer that occurs in epithelial cells of nasopharynx. This cancer has unique epidemiology that is common in China, Southeast Asia, including Indonesia. This disease is strongly associated with EBV infection, genetic susceptibility, and the environment. In this study, transcriptome profiling analysis was performed using RNA-Seq technology to determine the differential expression gene relate to proliferation aberration that occurs in Indonesian NPC patients. We used 9 samples, 7 NPC samples and 2 normal samples as control. Fresh tissue of tumor samples were collected from biopsy, and normal samples were collected brushing technique. The total RNA was isolated from fresh tissue samples and brushing samples using the Rneasy® RNA Extraction Mini Kit. The cDNA library was generated using TruSeq® RNA Library Preparation Kit V2, and its concentration was determined using qPCR. The library was sequenced using the Next-Generation Sequencing (NGS) Illumina Next Seq 550 platform. The raw sequence data quality was analyzed using FastQC and interpreted using HISAT2, HTSeq, edgeR, and PANTHER. From the analysis, 25493 gene transcripts were expressed, with 1956 genes were significantly upregulated, 90 genes were significantly downregulated in NPC samples, and 23897 genes did not change the expression level significantly (P<0.05), 10 of which genes were associated with cell proliferation. These genes are involved in the regulation of cancer cell proliferation through several signaling pathways, which are apoptosis signaling pathway, IGF signaling pathway, Notch signaling pathway, and P13K signaling pathway. The results showed that there were significant changes in gene expression levels between NPC patients and normal individuals. The differential level of gene expression causes a difference in the regulation of cell proliferation. Genes that have changed the expression level play a role in regulating various pathways that lead to cell proliferation aberration in NPC cases.
Asian Pacific journal of cancer prevention: APJCP
Dicka Wahyu Setiasari, Gisti Rahmawati, Digdo Sudigyo, Risky Hiskia Poluan, Salsabila Lutfi Sesotyosari, Tirta Wardana, Sagung Rai Indrasari, Cita Herawati, Didik Setyo Heriyanto, Indwiani Astuti, Afiahayati, and Sofia Mubarika Haryana
