Xiaoling Weng

Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway

Individuals with gallbladder carcinoma (GBC), the most aggressive malignancy of the biliary tract, have a poor prognosis. Here we report the identification of somatic mutations for GBC in 57 tumor-normal pairs through a combination of exome sequencing and ultra-deep sequencing of cancer-related genes. The mutation pattern is defined by a dominant prevalence of C>T mutations at TCN sites. Genes with a significant frequency (false discovery rate (FDR) < 0.05) of non-silent mutations include TP53 (47.1%), KRAS (7.8%) and ERBB3 (11.8%). Moreover, ErbB signaling (including EGFR, ERBB2, ERBB3, ERBB4 and their downstream genes) is the most extensively mutated pathway, affecting 36.8% (21/57) of the GBC samples. Multivariate analyses further show that cases with ErbB pathway mutations have a worse outcome (P = 0.001). These findings provide insight into the somatic mutational landscape in GBC and highlight the key role of the ErbB signaling pathway in GBC pathogenesis.

The draft genome of the large yellow croaker reveals well-developed innate immunity

The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

A Genome-Wide Association Study Identifies a Locus on TERT for Mean Telomere Length in Han Chinese

Leukocyte telomere length (LTL) is a predictor of aging and a number of age-related diseases. We performed genome-wide association studies of mean LTL in 2632 individuals,with a two-stage replication in 3917 individuals from Chinese populations. To further validate our findings, we get the results of 696 samples from a cohort of European ancestry. We identified two loci associated with LTL that map in telomerase reverse transcriptase (TERT; rs2736100, P = 1.93×10−5) on chromosome 5p15.33 and near keratin 80 (KRT80; rs17653722, P = 6.96×10−6) on 12q13.13. In Chinese population each C allele of rs2736100 and T allele of rs17653722 was associated with a longer mean telomere length of 0.026 and 0.059 T/S, respectively, equivalent to about 3 and 7 years of average age-related telomere attrition. Our findings provide new insights into telomere regulatory mechanism and even pathogenesis of age-related diseases.

TERT Polymorphism rs2736100-C Is Associated with EGFR Mutation–Positive Non–Small Cell Lung Cancer

Purpose: EGF receptor (EGFR) mutation–positive (EGFRmut+) non–small cell lung cancer (NSCLC) may be a unique orphan disease. Previous studies suggested that the telomerase reverse transcriptase (TERT) gene polymorphism is associated with demographic and clinical features strongly associated with EGFR mutations, for example, adenocarcinoma histology, never-smoking history, and female gender. We aim to test the association between TERT polymorphism and EGFRmut+ NSCLC. Experimental Design: We conducted a genetic association study in Chinese patients with NSCLC (n = 714) and healthy controls (n = 2,520), between the rs2736100 polymorphism and EGFRmut+ NSCLC. We further tested the association between the EGFR mutation status and mean leukocyte telomere length (LTL). The potential function of rs2736100 in lung epithelial cells was also explored. Results: The rs2736100-C allele was significantly associated with EGFRmut+ NSCLC [OR, 1.52; 95% confidence interval (CI), 1.28–1.80; P = 1.6 × 10−6] but not EGFRmut− NSCLC (OR = 1.07, 95% CI, 0.92–1.24, P = 0.4). While patients with NSCLC as a whole have significantly longer LTL than healthy controls (P ≤ 10−13), the EGFRmut+ patients have even longer LTL than EGFRmut− patients (P = 0.008). Meanwhile, rs2736100 was significantly associated with TERT mRNA expression in both normal and tumor lung tissues. All results remained significant after controlling for age, gender, smoking status, and histology (P < 0.05 for all tests). Moreover, the rs2736100 DNA sequence has an allele-specific affinity to nuclear proteins extracted from lung epithelial cells, which led to an altered enhancer activity of the sequence in vitro. Conclusions: Our study suggests that telomerase and telomere function may be essential for carcinogenesis of EGFRmut+ NSCLC. Further investigation for the underlying mechanism is warranted. Clin Cancer Res; 21(22); 5173–80. ©2015 AACR.

Promoter hypermethylation of TERT is associated with hepatocellular carcinoma in the Han Chinese population

BACKGROUND Upstream of the transcription start site (UTSS), hypermethylation of the telomerase reverse transcriptase (TERT) gene has been shown to be associated with tumour progression and a poor prognosis in paediatric brain tumours (Castelo-Branco 2013). It has been inferred that the UTSS region of TERT is a potentially accessible biomarker for various cancers. In this study, we aimed to explore the role of TERT in hepatocellular carcinoma (HCC) and to investigate whether the UTSS region of the TERT promoter shows the same methylation pattern in HCC. METHODS We analysed the results of a methylation assay for TERT, including the UTSS region, from 125 paired HCC samples using Mass Array EpiTyper (Sequenom, San Diego, CA, USA). To determine the relationship between TERT promoter methylation status and the TERT expression level, we analysed a validation group of 12 paired HCC samples and acquired the FPKM values for the TERT gene. RESULTS Our results showed aberrant methylation of the UTSS region of the TERT promoter in HCC (mean=15.1) compared with the adjacent normal tissues (mean=6.1, P<0.00001). Furthermore, a nearly 56-fold increase in TERT expression from the hypermethylated promoter was found in HCC (P<0.05), indicating a positive relationship between TERT methylation and expression. CONCLUSIONS As hypermethylation was positively correlated with high expression of TERT in HCC, TERT is likely to be involved in the aetiology of HCC. Our findings indicate that future studies on TERT might be fruitful.

Hypermethylated Epidermal growth factor receptor (EGFR) promoter is associated with gastric cancer

Epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinases ErbB family and it is found to be overexpressed in gastric cancer. However, the mechanism of the regulation of the EGFR expression is still unknown. We used the Sequenom EpiTYPER assay to detect the methylation status of the EGFR promoter in normal and tumour tissues of 30 patients with gastric cancer. We also carried out quantitative real time PCR (qPCR) to detect the expression level of EGFR in our 30 patients. Notably, increased methylation level at EGFR promoter was found in tumour tissues than the corresponding adjacent noncancerous. In both Region I DMR and Region II DMR detected in our study, tumor tissues were significantly hypermethylated (P = 2.7743E−10 and 2.1703E−05, respectively). Region I_⊿CpG_2 was also found to be associated with the presence of distant metastasis (P = 0.0323). Furthermore, the results showed a strongly significant association between the relative EGFR expression and the EGFR methylation changes in both Region I and Region II (P = 0.0004 and 0.0001, respectively). Our findings help to indicate the hypermethylation at EGFR promoter in gastric cancer and it could be a potential epigenetic biomarker for gastric cancer status and progression.

Comparative transcriptome analysis reveals that the extracellular matrix receptor interaction contributes to the venous metastases of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common type of liver cancer in the world. Portal vein tumor thrombus (PVTT) is one of the most serious complications of HCC and is strongly correlated with a poor prognosis for HCC patients. However, the detailed mechanism of PVTT development remains to be explored. In this study, we present a large-scale transcriptome analysis, by RNA sequencing, of 11 patients diagnosed with HCC with PVTT. The dysregulated genes between HCC and PVTT suggested that the extracellular matrix receptor interaction was correlated with the venous metastases of HCC. Among all of the recurrent alternative splicing events, we identified exon 6 skipping of RPS24, which is likely to be a cancer driver. We also identified five common fusion genes between HCC and its corresponding PVTT samples, including ARID1A-GPATCH3, MDM1-NUP107, PTGES3-RARG, PRLR-TERT, and C9orf3-TMC1. All of these findings broaden our knowledge of PVTT development and may also contribute to the diagnosis and treatment of HCC patients with PVTT.

No evidence of association between variant rs2075650 in lipid metabolism-related locus APOE/TOMM40 and advanced age-related macular degeneration in Han Chinese population.

Age-related macular degeneration (AMD) is a late-onset, neurodegenerative disease. Genes related to lipid metabolism are important in AMD pathogenesis. Recently, a variant rs2075650 located in lipid metabolism-related locus APOE/TOMM40 was identified to be associated with advanced AMD and early AMD, respectively, in two genome-wide association studies with European ancestry, while no association study between rs2075650 and overall advanced AMD in Chinese population has been conducted before. We evaluated the potential effect of this variant on advanced AMD in a Han Chinese cohort with 204 advanced AMD patients and 1536 healthy controls. The results suggested that rs2075650 was neither associated with advanced AMD in allele level (P = 0.348) nor in genotype level (P = 0.890 under additive model with age and sex adjusted). In conclusion, our study did not confirm the impact of rs2075650 on advanced AMD risk, indicating that rs2075650 is unlikely a superior marker for APOE/TOMM40 susceptible region with advanced AMD in Han Chinese population.

Common variant rs10033900 near the complement factor I gene is associated with age-related macular degeneration risk in Han Chinese population.

Age-related macular degeneration (AMD) is a late-onset, neurodegenerative disease that causes visual impairment and blindness in the elderly population.1 Multiple genetic loci have been identified as contributing to AMD, including complement pathway-related genes (CFH,2, 3, 4 C2-CFB,5 C3,6, 7 CFI8), lipoprotein metabolism-related genes (APOE,9, 10, 11 LIPC,12 TIMP313) and additional loci such as VEGFA14 and ARMS2/HTRA1.15, 16 Fagerness et al8 initially reported the complement factor I (CFI) gene region associated with AMD in a Caucasian cohort (1228 cases and 825 controls), with the rs10033900 variant located in a downstream region near the CFI gene showing the most significant signal (P=6.46 × 10−8). This association signal was also confirmed by meta-analysis in a genome-wide association study (2594 cases and 4134 controls) with follow-up replication (5640 cases and 52174 controls) in the largest sample of individuals with European ancestry (P=4.1 × 10−10).14 In addition, the C allele of rs10033900 has been commonly identified as a protective allele against AMD in genetic studies.8, 14, 17, 18 However, there remains debate as to whether rs10033900 contributes to AMD susceptibility, due to contradicting evidence published in this journal.18, 19, 20 For example, Ennis et al20 confirmed the association between the CFI region and AMD susceptibility in a UK cohort, although rs10033900 showed no association with AMD. Kondo et al18 demonstrated the association of rs10033900 with the C allele in a Japanese cohort, showing the same association direction as the results of Fagerness et al.8 In contrast, Cipriani et al19 observed no association between rs10033900 and AMD in a study of two independent cohorts from England and Scotland. To investigate the reported association of rs10033900 in the Han Chinese population, we studied this locus in our cohort of 288 unrelated AMD patients and 384 healthy controls.

DNA methylation profiling in the thalamus and hippocampus of postnatal malnourished mice, including effects related to long-term potentiation

BackgroundDNA methylation has been viewed as the most highly characterized epigenetic mark for genome regulation and development. Postnatal brains appear to exhibit stimulus-induced methylation changes because of factors such as environment, lifestyle, and diet (nutrition). The purpose of this study was to examine how extensively the brain DNA methylome is regulated by nutrition in early life.ResultsBy quantifying the total amount of 5-methylcytosine (5mC) in the thalamus and the hippocampus of postnatal malnourished mice and normal mice, we found the two regions showed differences in global DNA methylation status. The methylation level in the thalamus was much higher than that in the hippocampus. Then, we used a next-generation sequencing (NGS)-based method (MSCC) to detect the whole genome methylation of the two regions in malnourished mice and normal mice. Notably, we found that in the thalamus, 500 discriminable variations existed and that approximately 60% were related to neuronal development or psychiatric diseases. Pathway analyses of the corresponding genes highlighted changes for 9 genes related to long-term potentiation (5.3-fold enrichment, P = 0.033).ConclusionsOur findings may help to indicate the genome-wide DNA methylation status of different brain regions and the effects of malnutrition on brain DNA methylation. The results also indicate that postnatal malnutrition may increase the risk of psychiatric disorders.