Microarray analysis of microRNAs in NPC FFPE tissue samples

Nasopharyngeal carcinoma (NPC) is a challenging cancer that is rare in the United States but shows exceptionally high incidence in Southern China, Indonesia, and Malaysia. While the hallmark of NPC is striking geographic variation, early detection and clinical management are also critical characteristics of this cancer. The etiology of NPC is complex, involving the interplay of multiple factors, including Epstein Barr Virus (EBV), which appears to play an oncogenic role. While multimodality therapy is the mainstay of treatment for NPC, the impact of this treatment is greatly influenced by the presenting tumor stage, tumor size, nodal involvement, and the histologic subtype classification. Up to 40% percent of NPC cases present at an advanced stage, likely due to its deep location in the lymphatic-rich nasopharynx and its propensity for early lymphatic spread. Recent modifications in the TNM staging schema have attempted to improve prognostic accuracy, but variations in clinical outcome are still reported in patients with the same stage and similar treatment regimens. The various molecular markers developed to monitor disease progression have also proven unreliable. Hence, there is a significant need for a new kind of prognostic biomarker for NPC. Herein different approaches were applied to a set of samples to detect NPC-related miRNAs, potential circulating biomarkers. We have optimized the extraction of total RNA from NPC Formalin-fixed, paraffin-embedded (FFPE) samples and sera from four patients and matched controls and analyzed the miRNA expression profile by microarray, qPCR and RNAseq. The microarray analysis showed that 46 miRNAs were found to be differentially and significantly expressed in carcinogenic tissue compared to healthy tissue. Twenty-three (23) microRNAs were significantly upregulated (21 human microRNAs and 2 EBV miRNAs), whereas 13 were down-regulated. A total of 8 unique samples were analyzed on Agilent human miRNA microarray (miRBase Release 16.0). Of the 8 samples, 4 are from Non-keratinizing NPC tissue. Non-NPC (normal) tissue were taken from 4 individuals that were diagnosed with NPC (2 of which were matched/paired from the NPC case).