Profiling miRNAs in nasopharyngeal carcinoma FFPE tissue by microarray and Next Generation Sequencing.
Nasopharyngeal carcinoma (NPC) is a non-lymphomatous, squamous-cell carcinoma that occurs in the epithelial lining of the nasopharynx. Nasopharyngeal carcinoma has a geographically well-defined distribution worldwide, with the highest prevalence in China, Southeast Asia, and Northern Africa. Symptoms of nascent NPC may be unapparent or trivial, with diagnosis based on the histopathology of biopsied tissue following endoscopy of the nasopharynx. The tumor node metastasis (TNM) staging system is the benchmark for the prognosis of NPC and guides treatment strategy. However, there is a consensus that the TNM system is not sufficiently specific for the prognosis of NPC, as it does not reflect the biological heterogeneity of this tumor, making another biomarker for the detection of NPC a priority. We have previously reported on different approaches for microRNA (miRNA) biomarker discovery for Formalin Fixed Paraffin Embedded (FFPE) NPC tissue samples by both a targeted (microarray) and an untargeted (small RNA-Seq) discovery platform. Both miRNA discovery platforms produced similar results, narrowing the miRNA signature to 1-5% of the known mature human miRNAs, with untargeted (small RNA-Seq approach) having the advantage of indicating "unknown" miRNAs associated with NPC. Both miRNA profiles strongly associated with NPC, providing two potential discovery platforms for biomarker signatures for NPC. Herein, we provide a detailed description of the methods that we used to interrogate FFPE samples to discover biomarkers for NPC.
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Jin
J
Peng
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Yanjun
Y
Feng
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Gabriel
G
Rinaldi
Department of Epidemiology and Biostatistics, The George Washington University School of Public Health and Health Services, Washington DC 20037, USA.
Paul
P
Levine
Department of Pathology, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Samantha
S
Easley
Department of Pathology, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Elizabeth
E
Martinez
Department of Epidemiology and Biostatistics, The George Washington University School of Public Health and Health Services, Washington DC 20037, USA.
Salman
S
Hashmi
Medical Faculty Associates, The George Washington University, Washington DC 20037, USA.
Nader
N
Sadeghi
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Paul J
PJ
Brindley
School of Biomedical Sciences, Faculty of Medicine and Biomedical Sciences, University of Queensland, Brisbane, Australia ; Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
Jason P
JP
Mulvenna
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Jeffrey M
JM
Bethony
Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington DC, USA ; Research Center for Neglected Diseases of Poverty, School of Medicine and Health Science, George Washington University, Washington DC, USA.
Jordan L
JL
Plieskatt
Biomarker; Microarray; Nasopharyngeal carcinoma; RNA-Seq; miRNA