Wt Ng

Epigenetic markers for noninvasive early detection of nasopharyngeal carcinoma by methylation‐sensitive high resolution melting

Nasopharyngeal carcinoma (NPC) is a human malignancy that is closely associated with Epstein‐Barr Virus (EBV). Early diagnosis of NPC will greatly improve the overall survival. However, current EBV DNA marker detection still lacks the predictive value to perform well in high‐risk populations for early detection of NPC. Since aberrant promoter hypermethylation of tumor suppressor genes (TSGs) is widely considered to be an important epigenetic change in early carcinogenesis, this study identified a panel of methylation markers for early detection of NPC and also assessed the clinical usefulness of these markers with noninvasive plasma specimens instead of biopsies. MS‐HRM assays were carried out to assess the methylation status of a selected panel of four TSGs (RASSF1A, WIF1, DAPK1 and RARβ2) in biopsies, NP brushings and cell‐free plasma from NPC patients. High‐risk and cancer‐free groups were used as controls. DNA methylation panel showed higher sensitivity and specificity than EBV DNA marker in cell‐free plasma from NPC patients at early Stages (I and II) and in addition to the EBV DNA marker, MS‐HRM test for plasma and NP brushing DNA methylation significantly increased the detection rate at all NPC stages as well as local recurrence, using this selected four‐gene panel (p < 0.05). MS‐HRM assay on a selected gene panel has great potential to become a noninvasive and complementary test for NPC early and recurrent detection in combination with the EBV DNA test to increase the sensitivity for NPC detection at an early stage.

A novel Hsp90 inhibitor AT13387 induces senescence in EBV-positive nasopharyngeal carcinoma cells and suppresses tumor formation

BackgroundNasopharyngeal carcinoma (NPC) is an epithelial malignancy strongly associated with Epstein-Barr virus (EBV). AT13387 is a novel heat shock protein 90 (Hsp90) inhibitor, which inhibits the chaperone function of Hsp90 and reduces expression of Hsp90-dependent client oncoproteins. This study aimed to evaluate both the in vitro and in vivo antitumor effects of AT13387 in the EBV-positive NPC cell line C666-1.ResultsOur results showed that AT13387 inhibited C666-1 cell growth and induced cellular senescence with the downregulation of multiple Hsp90 client oncoproteins EGFR, AKT, CDK4, and restored the protein expression of negative cell cycle regulator p27. We also studied the ability of AT13387 to restore p27 expression by downregulation of AKT and the p27 ubiquitin mediator, Skp2, using AKT inhibitor and Skp2 siRNA. In the functional study, AT13387 inhibited cell migration with downregulation of a cell migration regulator, HDAC6, and increased the acetylation and stabilization of α-tubulin. We also examined the effect of AT13387 on putative cancer stem cells (CSC) by 3-D tumor sphere formation assay. AT13387 effectively reduced both the number and size of C666-1 tumor spheres with decreased expression of NPC CSC-like markers CD44 and SOX2. In the in vivo study, AT13387 significantly suppressed tumor formation in C666-1 NPC xenografts.ConclusionAT13387 suppressed cell growth, cell migration, tumor sphere formation and induced cellular senescence on EBV-positive NPC cell line C666-1. Also, the antitumor effect of AT13387 was demonstrated in an in vivo model. This study provided experimental evidence for the preclinical value of using AT13387 as an effective antitumor agent in treatment of NPC.

Whole-exome sequencing identifies multiple loss-of-function mutations of NF-κB pathway regulators in nasopharyngeal carcinoma.

Significance Host genetics, environmental factors, and EBV infection together contribute to nasopharyngeal carcinoma (NPC) development. A number of critical genetic and epigenetic events contributing to tumor development has been reported. However, the genomic alterations in NPC have not been completely deciphered. We used the whole-exome sequencing approach to study the somatic mutations in NPC, and an APOBEC-mediated mutagenesis signature was revealed. Importantly, multiple loss-of-function mutations in the NF-κB–negative regulators (NFKBIA, CYLD, and TNFAIP3) were discovered in NPC tumors, and we functionally confirmed that the NFKBIA loss-of-function mutations induce damaging effects on the WT proteins. Detection of these mutations emphasizes the critical role of NF-κB signaling in NPC tumorigenesis and provides perspectives for targeting this pathway in NPC treatment. Nasopharyngeal carcinoma (NPC) is an epithelial malignancy with a unique geographical distribution. The genomic abnormalities leading to NPC pathogenesis remain unclear. In total, 135 NPC tumors were examined to characterize the mutational landscape using whole-exome sequencing and targeted resequencing. An APOBEC cytidine deaminase mutagenesis signature was revealed in the somatic mutations. Noticeably, multiple loss-of-function mutations were identified in several NF-κB signaling negative regulators NFKBIA, CYLD, and TNFAIP3. Functional studies confirmed that inhibition of NFKBIA had a significant impact on NF-κB activity and NPC cell growth. The identified loss-of-function mutations in NFKBIA leading to protein truncation contributed to the altered NF-κB activity, which is critical for NPC tumorigenesis. In addition, somatic mutations were found in several cancer-relevant pathways, including cell cycle-phase transition, cell death, EBV infection, and viral carcinogenesis. These data provide an enhanced road map for understanding the molecular basis underlying NPC.

Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome‐wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high‐throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10−9), but was less obvious in other types of solid tumors except for prostate and Epstein–Barr virus (EBV)‐positive gastric cancer (FDR<10−3). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection.

Whole-exome sequencing identifies MST1R as a genetic susceptibility gene in nasopharyngeal carcinoma

Significance Nasopharyngeal carcinoma (NPC) is a valuable cancer model to study the interaction of host genetics, viral infection, and environment in tumorigenesis. Little is known about the genetic basis for the remarkably distinct geographical distribution of NPC. We used a whole-exome sequencing approach to identify the genetic alterations associated with NPC susceptibility and revealed a strong link between macrophage-stimulating 1 receptor (MST1R) and NPC early-age onset (age of ≤20 y). MST1R is critical for innate immunity and plays an important role for host defense against viral infection. We further discovered that an interaction network involved in the MST1R/14-3-3 complex was frequently deregulated by genetic alterations in NPC. Our findings provide new insights in the pathogenesis of NPC by highlighting the involvement of the MST1R-mediated signaling pathways. Multiple factors, including host genetics, environmental factors, and Epstein–Barr virus (EBV) infection, contribute to nasopharyngeal carcinoma (NPC) development. To identify genetic susceptibility genes for NPC, a whole-exome sequencing (WES) study was performed in 161 NPC cases and 895 controls of Southern Chinese descent. The gene-based burden test discovered an association between macrophage-stimulating 1 receptor (MST1R) and NPC. We identified 13 independent cases carrying the MST1R pathogenic heterozygous germ-line variants, and 53.8% of these cases were diagnosed with NPC aged at or even younger than 20 y, indicating that MST1R germ-line variants are relevant to disease early-age onset (EAO) (age of ≤20 y). In total, five MST1R missense variants were found in EAO cases but were rare in controls (EAO vs. control, 17.9% vs. 1.2%, P = 7.94 × 10−12). The validation study, including 2,160 cases and 2,433 controls, showed that the MST1R variant c.G917A:p.R306H is highly associated with NPC (odds ratio of 9.0). MST1R is predominantly expressed in the tissue-resident macrophages and is critical for innate immunity that protects organs from tissue damage and inflammation. Importantly, MST1R expression is detected in the ciliated epithelial cells in normal nasopharyngeal mucosa and plays a role in the cilia motility important for host defense. Although no somatic mutation of MST1R was identified in the sporadic NPC tumors, copy number alterations and promoter hypermethylation at MST1R were often observed. Our findings provide new insights into the pathogenesis of NPC by highlighting the involvement of the MST1R-mediated signaling pathways.

Multigene pathway-based analyses identify nasopharyngeal carcinoma risk associations for cumulative adverse effects of TERT-CLPTM1L and DNA double-strand breaks repair.

The genetic etiology of nasopharyngeal carcinoma (NPC) and mechanisms for inherited susceptibility remain unclear. To examine genetic risk factors for NPC, we hypothesized that heritable risk is attributable to cumulative effects of multiple common low‐risk variants. With the premise that individual SNPs only confer subtle effects for cancer risk, a multigenic pathway‐based approach was used to systematically examine associations between NPC genetic susceptibility with SNPs in genes in DNA repair pathways and from previously identified cancer genome‐wide association study analyses. This case–control study covers 161 genes/loci and focuses on pathway‐based analyses in 2,349 Hong Kong individuals, allowing stratification according to NPC familial status for meaningful association analysis. Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR 95% CI = 0.77, 0.68–0.88), MDS1‐EVI1 (OR 95% CI=0.79 0.69–0.89) and CCDC170 (OR 95% CI = 0.76, 0.66–0.86) conferred modest protective effects individually for NPC risk by the logistic regression analysis after multiple testing adjustment (pBonferroni < 0.05). Stratification of NPC according to familial status identified rs2380165 in BLM (OR 95% CI = 1.49, 1.20–1.86, pBonferroni < 0.05) association with family history‐positive NPC (FH+ NPC) patients. Multiple SNPs pathway‐based analysis revealed that the combined gene dosage effects for increasing numbers of unfavorable genotypes in TERT‐CLPTM1L and double‐strand break repair (DSBR) conferred elevated risk in FH+ and sporadic NPC patients (ORs per allele, 95% CIs = 1.37, 1.22–1.55, pBonferroni = 5.00 × 10−6; 1.17, 1.09–1.26, pBonferroni = 4.58 × 10−4, respectively, in TERT/NHEJ pathways). Our data suggested cumulative increased NPC risk associations with TERT‐CLPTM1L and DSBR pathways contribute to genetic susceptibility to NPC and have potential translational relevance for patient stratification and therapeutics.

IKBB tumor suppressive role in nasopharyngeal carcinoma via NF-κB–mediated signalling

Tumor suppressor genes (TSGs) play a prominent role in cancer and are important in the development of nasopharyngeal carcinoma (NPC), which is endemic in Southern China as well as Southeast Asia. Apart from TSGs, aberrant signalling pathways are also commonly associated with tumor progression. Unsurprisingly, the NF‐κB pathway is frequently associated with angiogenesis and promoting tumor growth and development. Functional complementation studies using microcell‐mediated chromosome transfer helped to identify IKBB as a putative TSG in NPC. IKBB, an inhibitor of NF‐κB, has recently been shown to be inversely associated with tumor growth and metastasis via inactivation of the NF‐κB pathway, but its suppressive role is still only poorly understood. This study takes the lead in revealing the suppressive role of IKBB in NPC. IKBB is silenced in the majority of NPC tumor tissues in all stages. Its suppressive role is substantiated by perturbation in tumor formation, cell migration and angiogenesis. Interestingly, IKBB not only affects the ‘seed’, but also influences the ‘soil’ by downregulating the transcriptional level of proangiogenic factors Rantes, Upar, IL6, and IL8. For the first time, our data establish the importance of a novel tumor suppressive IKBB gene in abrogating angiogenesis in NPC via the NF‐κB signalling pathway, which is likely mediated by crosstalk with the Akt/Gsk3β signalling pathway.

Test-retest reliability of a computer-assisted self-administered questionnaire on early life exposure in a nasopharyngeal carcinoma case-control study

We evaluated the reliability of early life nasopharyngeal carcinoma (NPC) aetiology factors in the questionnaire of an NPC case-control study in Hong Kong during 2014–2017. 140 subjects aged 18+ completed the same computer-assisted questionnaire twice, separated by at least 2 weeks. The questionnaire included most known NPC aetiology factors and the present analysis focused on early life exposure. Test-retest reliability of all the 285 questionnaire items was assessed in all subjects and in 5 subgroups defined by cases/controls, sex, time between 1st and 2nd questionnaire (2–29/≥30 weeks), education (secondary or less/postsecondary), and age (25–44/45–59/60+ years) at the first questionnaire. The reliability of items on dietary habits, body figure, skin tone and sun exposure in early life periods (age 6–12 and 13–18) was moderate-to-almost perfect, and most other items had fair-to-substantial reliability in all life periods (age 6–12, 13–18 and 19–30, and 10 years ago). Differences in reliability by strata of the 5 subgroups were only observed in a few items. This study is the first to report the reliability of an NPC questionnaire, and make the questionnaire available online. Overall, our questionnaire had acceptable reliability, suggesting that previous NPC study results on the same risk factors would have similar reliability.

Leukocyte telomere length associates with nasopharyngeal carcinoma risk and survival in Hong Kong Chinese: Role of LTL for NPC risk and survival of Stage IV patients

Telomere shortening occurs as an early event in tumorigenesis. The TERT‐CLPTM1L locus associates with nasopharyngeal carcinoma (NPC) risk. It remains unknown if leukocyte telomere length (LTL) associates with NPC risk and survival. The relative LTL (rLTL) was measured by quantitative‐PCR in 2,996 individuals comprised of 1,284 NPC cases and 1712 matched controls. The odds ratio (OR) and 95% confidence intervals (CI) were calculated by logistic regression. The hazard ratio (HR) and 95% CI were calculated by Cox regression for survival analysis with rLTL and other clinical parameters in 1,243 NPC with a minimum follow‐up period of 25 months. NPC patients had significantly shorter telomere length than controls. Shorter rLTL significantly associated with increased NPC risk, when the individuals were dichotomized into long and short telomeres based on median‐split rLTL in the control group (OR = 2.317; 95% CI = 1.989–2.700, p = 4.10 × 10−27). We observed a significant dose–response association (ptrend = 3.26 × 10−34) between rLTL and NPC risk with OR being 3.555 (95% CI = 2.853–4.429) for the individuals in the first quartile (shortest) compared with normal individuals in the fourth quartile (longest). A multivariate Cox regression analysis adjusted by age demonstrated an independent effect of rLTL on NPC survival for late‐stage NPC patients, when the individuals were categorized into suboptimal rLTL versus the medium rLTL based on a threshold set from normal (HR = 1.471, 95% CI = 1.056–2.048, p = 0.022). Shorter blood telomeres may be markers for higher susceptibility for NPC risk. Suboptimal rLTL may be a poor prognostic factor for advanced NPC patients, as it associates independently with poor survival.

Abstract 4773: Aberrant methylation at chromosome 6p as novel biomarkers for diagnosis and prognosis of nasopharyngeal carcinoma

Background: Nasopharyngeal carcinoma (NPC) has the highest incidence in Guangdong province and Hong Kong in Southern China. Early detection of NPC is necessary to improve patient survival. Although aberrant methylation at promoter region of the tumour suppressors were often reported in NPC, genome-wide methylation changes have not been comprehensively investigated. Aim: We aimed to examine the methylation profile of NPC patient tumours using a high-throughput approach to discover candidate biomarkers for early detection of NPC. Methods: We systematically analyzed methylome data in the primary tumours and matched normal adjacent tissues from 25 NPC patients collected by Area of Excellence (AoE) NPC Tissue Bank using the Illumina HumanMethylation450 BeadChip platform. Comparatively, methylome data of solid tumours including prostate cancer, invasive breast cancer, pancreatic cancer, kidney cancer, thyroid cancer, liver cancer, rectal cancer, colon cancer, head and neck cancer, lung adenocarcinoma and lung squamous cell carcinoma collected by The Cancer Genome Atlas (TCGA) were examined. A quantitative method, bisulfite pyrosequencing, was applied to evaluate the aberrant methylation in an independent NPC patient cohort. Results: In NPC, the hypermethylation pattern was more dominant than hypomethylation, where over 90% of the differentially methylated loci were hypermethylated within or close to CpG islands in tumours. The comparative methylome analysis reveals aberrant methylation at chromosome 6p frequently occurred in NPC (FDR = 1.33×10-9), but was rare in other types of solid tumours. Evident enrichment of the repressive mark H3K27me3 was found at this region, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation. Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort, and 76.9% of the early-stage NPC patients can be detected by aberrant methylation on 6p. Furthermore, aberrant methylation at this region was observed in NPC recurrent tumours and matched metastatic lymph nodes, indicating the potential use of genes in this region for prognosis. Conclusion: Our study highlights the importance of epigenetic deregulation in NPC. A novel genomic region on 6p with aberrant methylation was identified. This region contains several important genes that have great potential to be used as biomarkers for NPC early detection. The global genome-wide unbiased approach is useful to discover potential biomarkers for early diagnosis and prognosis in cancers. Acknowledgements: NPC AoE funding was provided by the Hong Kong Research Grants Council (AoE/M-06/08) to MLL and HKU Small Project Funding to WD. Citation Format: Wei Dai, Arthur Kwok Leung Cheung, Josephine Mun Yee Ko, Hong Zheng, Yue Cheng, Roger Kai Cheong Ngan, Wai Tong Ng, Anne Wing Mui Lee, Chun Chung Yau, Victor Ho Fu Lee, Maria Li Lung. Aberrant methylation at chromosome 6p as novel biomarkers for diagnosis and prognosis of nasopharyngeal carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4773. doi:10.1158/1538-7445.AM2015-4773