Abstract 4522: Epstein-Barr virus infection suppresses the DNA repair mechanisms in nasopharyngeal epithelial cells via reduction of the H3K4me3 mark

Introduction: Epstein-Barr Virus (EBV) is an oncovirus, which contributes to development of various cancers, including nasopharyngeal carcinoma (NPC). EBV latent proteins play critical roles in modulation host cell histone modifications in order to regulate its signaling pathways. However, the role of EBV in regulation histone modifications in epithelia cell system is still not very clear. Further studies are necessary to characterize the functional role of EBV in regulating epithelial cell modifications.

Aim: in this current study, we aim to investigate the role of EBV infection in regulating a promoter and transcription activation histone marker, H3K4me3, in the host cell genome.

Methodologies: Chromatin immunoprecipitation sequencing (ChIPseq) was performed by using the next-generation sequencing approach. The ChIP reactions were prepared by utilizing the antibody targeting the H3K4me3 mark in two pairs of immortalized non-tumorigenic nasopharyngeal epithelial (NPE) cell lines, which were artificially infected with (550, 550-EBV, 361, and 361-EBV). The ChIPseq results were validated by the ChIP-QPCR and RT-QPCR.

Results: A total of 1747 genes show losses of H3K4me3 in both sets of EBV-infected NPE cell lines. Among them, 628 (36%) genes show losses of H3K4me3 in promoter regions. Interestingly, a total of 18 DNA damage repair signaling members in the base excision repair (BER), homologous recombination, non-homologous end-joining, and the mismatch repair pathways showed significant losses of H3K4me3 in EBV-infected NPE cells. Based on utilizing the DAVID annotation tool for pathway analysis, members in the BER pathway were significantly enriched (FDR = 0.0709, cut-off<0.1). The ChIPseq results were validated by ChIP- and RT-QPCR and showed significant losses of the H3K4me3 and expression of the BER members in both sets of EBV-infected NPE cell lines. The clinical significances were further confirmed by detection of significant down-regulation of the BER members in NPC paired biopsies.

Conclusion: EBV infection induces changes of host cell H3K4me3 levels and results in down-regulation of the BER members.

Acknowledgement: This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, People's Republic of China: Grant number AoE/M-06/08 to MLL and the Seed Funding Programme for Basic Research of the University of Hong Kong: Grant number 201308159003 to AKLC.

Citation Format: Maria L. Lung, Arthur KL Cheung, Wei Dai, Merrin ML Leong, George SW Tsao. Epstein-Barr virus infection suppresses the DNA repair mechanisms in nasopharyngeal epithelial cells via reduction of the H3K4me3 mark. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4522.

Abstract 125: Whole-exome sequencing identifies NF-kappaB pathway regulators frequently mutated in nasopharyngeal carcinoma

Introduction

Nasopharyngeal carcinoma (NPC) is a unique epithelial malignancy with a high prevalence in Southeast Asia. To date, the genomic abnormalities leading to the pathogenesis of NPC remain unclear. Thus, we sought to characterize the mutational landscape in NPC tumors using next-generation sequencing approaches and to identify significantly mutated genes and pathways.

Methods

124 NPC primary tumors were examined to define the mutational landscape with whole-exome sequencing (WES) and targeted re-sequencing. Mean target coverage of tumor and blood samples was 70X and 49X in WES, and 190X and 68X in targeted resequencing, respectively. Somatic SNPs and INDELs were called with MuTect and VarScan2, respectively. MutSigCV was applied to identify potential driver events in tumorigenesis. Verification rate for somatic mutations was 95%. The functional consequences of mutations in candidate genes were evaluated by the luciferase promoter, cell proliferation, and colony formation assays.

Results

The mutation rate of NPC is relatively low, with a median of 0.9 somatic mutations per megabase. Mutational signature analysis revealed two signatures in NPC, the ubiquitous signature in cancer characterized by C>T transitions predominantly occurring at NpCpG trinucleotides and the APOBEC-related signature characterized by C>G and C>T mutations at TpCpN trinucleotides, which is related to the innate immune APOBEC family of cytidine deaminases.

MutSigCV analysis identified significantly mutated genes, NFKBIA, TP53, CYLD, KMT2D, DMXL1, KMT2C, GPR144, RYR2, BOD1L1, AKAP9, and CEP192, with q values less than 0.1. Pathway and gene ontology analysis identified several pathways/terms with enriched somatic mutations including cell cycle phase transition, chromatin modification, cell death, immune response, p53 pathway, viral carcinogenesis, and the canonical NF-κB signaling pathways. TP53 is the most frequently mutated gene (7.3%, 9/124). Almost all somatic mutations fall into the DNA binding domain of TP53, including well-known hotspot and gain-of-function mutations.

Multiple loss-of-function (LOF) mutations were detected in NF-kB negative regulators, including NFKBIA (encodes IκBα protein), CYLD, and TNFAIP3. Mutations in NFKBIA were shown to alter the tumor suppressive function of IκBα.

Conclusions

In this study we detected an APOBEC-related signature in NPC. Several NF-kB negative regulators, including NFKBIA and CYLD, were mutated in a subset of NPC primary tumors, which may contribute to pathogenesis of NPC through NF-kB signaling pathway. These data provide an enhanced road map for understanding the molecular basis underlying NPC and also provide insight for exploring new therapies.

Acknowledgement

This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, People's Republic of China Grant number AoE/M006/08 to MLL.

Citation Format: Hong Zheng, Wei Dai, Arthur KL Cheung, Josephine MY Ko, Rebecca Kan, Bonnie WY Wong, Merrin ML Leong, Maria L. Lung. Whole-exome sequencing identifies NF-kappaB pathway regulators frequently mutated in nasopharyngeal carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 125.

Enhancement of luminol-based immunodot and Western blotting assays by iodophenol

The application of 4-iodophenol as a signal enhancer for luminol-based immunodot and Western blotting assays was investigated. Immunodetection of biotin-bovine serum albumin (BSA) using a rat anti-biotin antibody for immunodot binding and goat anti-biotin peroxidase conjugate for Western blotting assays was employed to demonstrate the signal enhancement attainable with 4-iodophenol. The addition of 4-iodophenol at a final working concentration of 52.2 microM to a light-emitting substrate, luminol, resulted in 3-fold and 10-fold signal enhancements for Western blotting and immunodot binding detection of biotin-BSA, respectively.

A photodetection device for luminol-based immunodot and Western blotting assays

A photodetection device permitting rapid and direct photographic recording of light emission from luminol-based immunodot and Western blotting assays is described in detail. This device permits contact exposure on Polaroid film of luminescent samples on nitrocellulose strips, and thus obviates the need for darkroom and film processing facilities. Immunodetection of mouse alpha-fetoprotein in brown fat homogenate and immunoglobulin E in nonimmune human sera employing luminol-based Western blotting and immunodot assays were used to demonstrate the versatility and operational simplicity of the detection device. The use of the detection device in combination with luminol-based immunoassays resulted in greater signal intensities and increased sensitivity over that attainable with the commonly used chromogenic substrate, 4-chloro-1-naphthol.

Luminescent detection method for immunodot, Western, and Southern blots

An anti-peroxidase-anti-biotin hybrid hybridoma rat cell line, capable of producing a bispecific monoclonal antibody, has been derived to explore its use in conjunction with a luminol immunodetection system. Luminescence was detected using x-ray film. The method was sufficiently sensitive and effective, but was less sensitive than autoradiographic methods using high-specific-activity 32P-labeled probes. Exposure times, on the other hand, were of the order of seconds rather than days. The direct binding of both peroxidase and biotin by the bispecific monoclonal antibody is simpler but less sensitive than the more conventional indirect method using a commercial peroxidase coupled with anti-rat antibody as a developing antibody.

The localization of genes for HPRT, G6PD, and alpha-GAL onto the X-chromosome of domestic pig (Sus scrofa domesticus)

Pig--mouse somatic cell hybrids were obtained from fusion of HPRT--mouse cells (RAG) and pig lymphocytes. The pig-mouse hybrids examined apparently retained on the average only 9 to 15 pig chromosomes. Seven of the hybrid clones were karyotyped to determine the pig chromosome constitution, and the same hybrid clones were tested electrophoretically for the expression of pig hypoxanthine-guanine phosphoribosyltransferase (HPRT), glucose-6-phosphate dehydrogenase (G6PD), and alpha-galactosidase (alpha-GAL) phenotypes. All five of the hybrid clones which had retained the pig X-chromosome exhibited concordant expression of pig HPRT, G6PD, and alpha-GAL enzymes. These data indicate that the genes HPRT, G6PD, and alpha-GAL are located on the X-chromosome of the domestic pig.

Assignment of superoxide dismutase (SOD-1) gene to chromosome No. 9 of domestic pig

Pig--mouse somatic cell hybrids were obtained by fusing pig lymphocytes with mouse cells of the RAG (HPTR-) line using polyethylene glycol. The expression of pig superoxide dismutase (SOD-1) activity in 11 hybrid clones as well as in the parental cells was investigated. Seven hybrid clones positive for the expression of pig SOD-1 displayed the corresponding parental RAG and pig bands of SOD-1 plus a heteropolymeric band of intermediate electrophoretic mobility. The positive and negative expression of pig SOD-1 was concordant with the retention and loss of pig chromosome No. 9, suggesting that the gene for pig SOD-1 is located on the chromosome No. 9 of the domestic pig.