Expression Profiling of Paraffin Embedded Lymphoepithelioma-Like Carcinoma of the Uterine Cervix Using Nanostring Arrays Reveals No Evidence of Epstein-Barr Virus Infection.
Natalie Banet, Charles Sailey, Weihua Tang, Margaret L Gulley. University of North Carolina, Chapel Hill
Background: Epstein-Barr virus (EBV) is found in nearly all lymphoepitheliomas of the nasopharynx and in a subset of lymphocyte rich undifferentiated carcinomas at other anatomic sites. Its presence in cervical cancer is unclear, and the sensitivity of EBV- Encoded RNA in situ hybridization (EBER-ISH) assays has been questioned. The Nanostring assay allows for detection of gene expression in paraffin embedded tissue without the use of reverse transcription or amplification, making it ideal for studies in which this is the only type of tissue available for analysis.
Design: We examined tumors from 16 patients with lymphoepithelioma-like carcinomas of the cervix using EBER ISH. To further explore the possiblity that EBV infection is present but EBER is not expressed, we designed an array-based assay to detect additional viral gene products. The Nanostring array targets 96 genes, 22 of which are EBV-encoded RNAs including latent and lytic gene products.
Results: In all 16 cases, we found no evidence of EBER expression. Control hybridization showed adequate RNA preservation, confirming that the EBER ISH results are truly negative. RNA was successfully extracted from all 12 of the cervical cancers and from 12 matched normal uterine tissues of the same patients. Nanostring array hybridization was successful in all 24 specimens as judged by recovery of 6 spiked RNAs and 4 housekeeping human transcripts. There was low background signal as confirmed by probing 8 non-human non-pathogen targets. Results of the array studies showed low to absent signal for all 22 virally encoded factors, confirming little if any latent or lytic EBV infection in the 12 benign and matched 12 malignant cervical tissues. Although unrelated to the aim of the study, the Proliferating Cell Nuclear Antigen (PCNA) Gene was uniformly overexpressed in all 12 cancers. This is a gene which is known to be involved in DNA replication.
Conclusions: This study shows that EBV is rarely associated with lymphoepithelioma-like carcinoma in the United States, and it also demonstrates performance characteristics of the Nanostring system for gene expression profiling.
Category: Gynecologic & Obstetrics
Tuesday, March 1, 2011 9:30 AM
Poster Session III # 219, Tuesday Morning