Abstract
Objective:This study aims to obtain the transcriptomes profile associated with avoiding immune destruction from nasopharyngeal cancer patients in Indonesia using next-generation sequencing. Methods:The samples are divided into two types of samples; 1) biopsy of nasopharyngeal cancer tissue samples, 2) brushing tissue of people without nasopharyngeal cancer as control samples. The sequencing results were mapped (HISAT2) and quantified (HTSeq) for differential expression analysis using edgeR software. Transcripts data analyzed with Pantherdb and DAVID software to find genes related to the immune system and pathways related to immune destruction by cancer. Results:The differential expression results show that 2,046 genes that have a significant differential expression. The 90 genes expression has down-regulated and 1,956 genes expression up-regulated, there are 20 genes related to the immune system. The 20 genes related to the immune system by analyzing lionproject.net that directly related to hallmark avoiding immune destruction that genes are CXCL9/10/11. The gene expression of CXCL9/10/11 regulates PD-L1 expressions via the Jak/STAT signaling pathway. The interaction between the extracellular domain PD-1 and PD-L1 in cancer cells have avoiding immune destruction. Conclusion:The results of this study suggest that the gene expression of CXCL9/10/11 have up-regulated is related to avoiding immune destruction that can use as an early detection biomarker of nasopharyngeal cancer in Indonesian patients.
Highlights
According to data from the World Health Organization (WHO) in 2015, cancer is the first or second cause of human death in the age before 70 years in 91 countries from 172 countries (Bray et al, 2018)
This study aims to obtain the transcriptomes profile associated with avoiding immune destruction from nasopharyngeal cancer patients in Indonesia using next-generation sequencing
The 20 genes related to the immune system by analyzing lionproject.net that directly related to hallmark avoiding immune destruction that genes are CXCL9/10/11
Summary
According to data from the World Health Organization (WHO) in 2015, cancer is the first or second cause of human death in the age before 70 years in 91 countries from 172 countries (Bray et al, 2018). One key aspect of cancer research is to understand the principles and mechanisms of changes in gene expression that contribute to carcinogenesis and cancer development. In the post-genomic era, many methods for profiling gene expression have been developed, such as microarrays and next-generation sequencing, genomically, miRNA-omics, transcriptomics, proteomics and, metabolomics, to classify cancers and identify new biomarkers for prognosis and diagnosis, and as targets for therapy (Bucca et al, 2004). One strategy to identify the main patterns of expression, next-generation sequencing (NGS) has been used to explore genetic heterogeneity and gene expression through transcriptomes profiles related to cancer development. Transcriptomic data can be used as new prognostic and diagnostic markers for cancer, related to hallmark avoiding immune destruction in Indonesian nasopharyngeal cancer patients
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