Identification of discriminatory gene expression of EBV-associated primary lymphoepithelioma-like carcinoma of lung by oligonucleotide microarray analysis

Abstract

Lymphoepithelioma-like carcinomas (LELC) of the lung is a distinct type of primary lung cancer constituting 5-9% of non-small cell lung cancers. LELC occurring in oriental ethnic groups are etiologically related to EBV infection and demonstrate clonal episomal EBV genomes as well as EBV marker expression in tumor cells. There is no relation with tobacco exposure but a close morphological resemblance to nasopharyngeal undifferentiated carcinomas, which is also a common EBV-related tumor in Chinese, is striking. The molecular pathways involved in lung LELC are incompletely understood. In order to identify signature molecules of LELC, we compared the expression profiles of 8 untreated, EBV-positive primary lung LELC with 9 normal lung tissues by oligonucleotide microarray analysis (HGU133A chips, Affymetrix). Verification of the differential expression of selective genes was performed using quantitative PCR (tagman probes) and immunohistochemical evaluation on a tissue microarray. The data were evaluated with the method of feature partitioning for single and pair-wise gene expression (Yap et al, 2004) which identified a discriminatory gene set of 1480 genes capable of distinguishing LELC from the normal lung tissue expression profiles with 100% accuracy. The identified gene set included a higher proportion of genes related to active cellular proliferation, mitosis, cell cycle, DNA replication and nuclear division compared to the arrayed probe set. Examples of tumor-related genes in the discriminatory gene set included those involved in EBV viral gene interaction (BS69, EBI3, EIF5A, KPNA2, MYB, p100, RECK, TAL1), cell proliferation or growth (EZH2, HMGA1, PTTG1, STK6), cell adhesion or extracellular matrix modification (EPHB2, GPI, HMMR, MMP9, MMP12, TIMP3, TNXB), apoptosis or cell survival (AVEN, BCL2, BIRC5, GG2-1), tumor suppression (DAPK1, GADD45B, PLAGL1, PPARG, RTN4), cell cycle checkpoint (CDKN1C, CGR19, WFDC1), anti-angiogenesis (ADAMTS1) and negative regulation of cell growth (CTNNAL1, DLC1, DUSP6, TGFBR2, TGFBR3, TU3A). A change of cytoskeletal expression profile was also observed with underexpression of KRT 7, SCEL and overexpression of the keratins KRT5, 6A and B, 8, 13, 15, 17, 19 as well as some basal cell or cell junction markers such as BPAG1 and KIND1. In addition, several genes related to potential resistance to drug treatment showed elevated expression (ABCE1, CTPS, RRM2, TYMS). The identified genes could contribute to a better understanding of EBV- induced carcinogenesis as well as signify new molecular targets of therapy for EBV-related tumors of the lung and other body regions. (Supported by HKSAR RGC grants 7486/03M, 7468/04M)