Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma.

Aim: Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). Materials & methods: least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. Results: A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. Conclusion: The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.

Hypomethylation of Thyroid Peroxidase as a Biomarker for Hepatocellular Carcinoma with Tumor Thrombosis.

OBJECTIVE: Thyroid hormones (THs) regulate multiple physiological activities in the liver, including cellular metabolism, differentiation, and cell growth, and play important roles in the pathogenesis of hepatocellular carcinoma (HCC). Thyroid peroxidase (TPO) is a key molecule involved in the THs synthesis and signaling pathway. As an epigenetic modification, DNA methylation has a critical role in tumorigenesis with diagnostic potential. However, the connection between THs and DNA methylation has been rarely investigated. METHODS: The methylation of key TH-related genes was analyzed by in-house epigenome-wide scanning, and we further analyzed the methylation levels of the TPO promotor in 164 sample pairs of HCC and adjacent non-cancerous tissues by Sequenom EpiTYPER assays, and evaluated their clinical implications. RESULTS: We identified that the methylation of the TPO promoter was downregulated in the HCC tissues (P<0.0001) with a mean difference ranging from 18.5% to 22.3%. This methylation pattern correlated with several clinical factors, including a multi-satellite tumor, fibrous capsule, and the presence of tumor thrombus. The receiver operator characteristic (ROC) curve analysis further confirmed that the percent methylated reference (PMR) values for TPO were predictive of the tumor [the area under the curve (AUC) ranged from 0.755 to 0.818] and the thrombosis in the HCC patients (the AUC ranged from 0.706 to 0.777). CONCLUSION: These findings demonstrated that epigenetic alterations of TPO, as indicated by the PMR values, were a potential biomarker for HCC patients with tumor thrombosis.

Hypomethylation status of miR-657 promoter region as biomarker for diagnosis of hepatocellular carcinoma: a retrospective study.

Background: The purpose of our study was to evaluate whether the methylation status of the miR-657 promoter region could be used as a biomarker for diagnosis of hepatocellular carcinoma (HCC), so as to find alternative biomarkers of early HCC detection. Methods: Cancerous and paired adjacent noncancerous tissues were collected from 160 patients who had been diagnosed with HCC by histopathology and received surgery. The methylation status of the miR-657 promoter region was measured using a MassARRAY Analyzer 4. Receiver operator characteristic (ROC) curve analysis was used to assess the effectiveness of miR-657 promoter region methylation status as a biomarker for diagnosis of HCC. Results: The mean methylation level of the miR-657 promoter region was significantly lower in cancerous tissues than in normal tissues of HCC patients (48.91%:67.04%, P<0.0001). ROC curve analysis revealed that the mean methylation level of the miR-657 promoter region could distinguish cancerous tissues from paired normal tissues of HCC patients (area under the curve: 0.847, P<0.001). Using 59.50% as the optimal cut-off, the sensitivity was 95.50% and the specificity was 70.01%. Conclusions: Methylation levels of the miR-657 promoter region were decreased in HCC patients and could be used as alternative and supplementary biomarkers for diagnosis of HCC.

A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.

ARID4A plays an important role in regulating gene expression and cell proliferation. ARID4A belongs to the AT-rich interaction domain (ARID)-containing family, and a PWWP domain immediately precedes its ARID region. The molecular mechanism and structural basis of ARID4A are largely unknown. Whole-exome sequencing (WES) revealed that a novel heterozygous missense variant, ARID4A c.1231 C > G (p.His411Asp), was associated with schizophrenia (SCZ) in this study. We determined the crystal structure of the PWWP-ARID tandem at 2.05 Å, revealing an unexpected mode in which ARID4A assembles with its PWWP and ARID from a structural and functional supramodule. Our results further showed that compared with the wild type, the p.His411Asp ARID mutant protein adopts a less compact conformation and exhibits a weaker dsDNA-binding ability. The p.His411Asp mutation decreased the number of cells that were arrested in the G0-G1 phase and caused more cells to progress to the G2-M phase. In addition, the missense mutation promoted the proliferation of HEK293T cells. In conclusion, our data provide evidence that ARID4A p.His411Asp could cause a conformational change in the ARID4A ARID domain, influence the DNA binding function, and subsequently disturb the cell cycle arrest in the G1 phase. ARID4A is likely a susceptibility gene for SCZ; thus, these findings provide new insight into the role of ARID4A in psychiatric disorders.

Disturbed mitochondrial acetylation in accordance with the availability of acetyl groups in hepatocellular carcinoma.

As an essential post-translational modification, acetylation participates in various cellular processes and shows aberrances during tumorigenesis. Owing to its modification substrate, acetyl-CoA, acetylation is postulated as a depot for acetyl groups and evolve to build a connection between epigenetics and metabolism. Here we depict a distinct acetylome atlas of hepatocellular carcinoma from the perspectives of both protein acetylation and acetyl-CoA metabolism. We found that tumor acetylome demonstrated a compartment-dependent alteration that the acetylation level of mitochondrial proteins tended to be decreased while nuclear proteins were highly acetylated. In addition, elevated expression of ATP-citrate synthase (ACLY) was observed in tumors, which would facilitate histone acetylation by transporting mitochondrial acetyl coenzyme A to the nucleus. A hypothetical model of the oncogenic acetylome was proposed that growing demands for histone acetylation in tumor cells would drive the relocalization of acetyl-CoA to the nucleus, which may contribute to the global deacetylation of mitochondrial proteins to support the nuclear acetyl-CoA pool in an ACLY-dependent manner. Our findings are thought-provoking on the potential linkage between epigenetics and metabolism in the progression of tumorigenesis.

The Preoperative Prognostic Nutritional Index in Hepatocellular Carcinoma After Curative Hepatectomy: A Retrospective Cohort Study and Meta-Analysis.

OBJECTIVE: Conflicting results existed about the role of prognostic nutritional index (PNI) for hepatocellular carcinoma (HCC) patients who received curative hepatectomy. The aim of this study is to identify the predictive capacity of PNI for survival after hepatectomy. METHODS: Preoperative PNI, neutrophil-to-lymphocyte ratio (NLR), tumor feature and clinical information of 187 patients with HCC from Sir Run Run Shaw hospital were evaluated. We also conducted a meta-analysis of seven cohort studies. RESULTS: Our study showed that HCC patients with a low PNI of <45 had a poor recurrence-free survival (RFS) rate (hazard ratio [HR] 1.762, 95% confidence interval [CI] 1.066-2.911, p = 0.027, respectively). The 5-year OS and RFS rates of the high PNI (≥45) vs low PNI (<45) were 76.7% vs 50.1% (p = 0.001) and 47.0% vs 28.9% (p = 0.001), respectively. In HCC TNM I patients (n = 144), a low PNI remained an independent prognostic factor of OS and RFS (HR 2.305, 95% CI 1.008-5.268, p = 0.048; HR 2.122, 95% CI 1.149-3.920, p = 0.016). The 5-year OS and RFS rates of the high PNI vs low PNI were 81.3% vs 62.4% (p = 0.041) and 53.4% vs 45.6% (p = 0.013), respectively. In the pooled analysis, the data showed that a low PNI was significantly associated with poor OS and RFS (HR 2.27, 95% CI 1.03-4.07, p < 0.001 and HR 1.68, 95% CI 1.45-1.94, p < 0.001, respectively). CONCLUSIONS: The preoperative PNI was an independent prognostic factor for OS and RFS rates in HCC patients who received hepatectomy.

Epigenome-wide DNA methylation profiling of portal vein tumor thrombosis (PVTT) tissues in hepatocellular carcinoma patients.

Aberrant methylation is a hallmark of hepatocellular carcinoma and plays an important role in tumor initiation and progression. However, the epigenome-wide methylation patterns of portal vein tumor thrombosis (PVTTs) have not been fully explored. Here, we performed epigenome-wide DNA methylation of adjacent normal tissues (ANTs), paired tumor tissues and paired PVTTs using an Infinium HumanMethylation450 array (n = 11) and conducted the Sequenom EpiTYPER assays to confirm the aberrantly methylated genes. MTS and apoptosis assay were used to assess the synergistic effect of two drugs on the HCC cell lines. We found the mean global methylation levels of HCC tissues and PVTTs were significantly lower than ANTs (P < 0.01). A total of 864 differentially methylated CpG sites annotated in 532 genes were identified between HCC tissues and paired PVTTs (|mean methylation difference|>10%, P < 0.005). The pathway analysis based on hypermethylated genes in PVTT tissues was interestingly enriched in regulation of actin cytoskeleton pathway (P = 4.48E-5). We found 23 genes whose methylation levels were gradually alternated in HCC tissues and PVTTs. Aberrant methylation status of TNFRSF10A, ZC3H3 and SLC9A3R2 were confirmed in a validation cohort (n = 48). The functional experiments demonstrated the combination of decitabine (DAC) and tumor necrosis factor-related apoptosis-inducing ligand (rh-TRAIL) could synergistically suppress the proliferation and induce apoptosis in SK-Hep-1 and Huh7 cell lines. Together, our findings indicated that DNA methylation plays an important role in the PVTT formation through regulating the metastasis-related pathways. The combination of DAC and rh-TRAIL might be a promising treatment strategy for HCC.

CSF1R methylation is a key regulatory mechanism of tumor-associated macrophages in hepatocellular carcinoma.

Tumor-associated macrophages (TAMs) are important in tumor microenvironments and are closely associated with cancer occurrence, metastasis and progression. Colony stimulating factor 1 receptor (CSF1R) serves a crucial role in TAM formation. Whether CSF1R expression is regulated by DNA methylation in hepatocellular carcinoma (HCC) has not been fully elucidated. In the current study, HCC and adjacent non-cancerous tissue (ANT) samples were collected from 160 patients with HCC. CSF1R methylation levels were analyzed using a Mass ARRAY Analyzer to establish the potential impact of CSF1R methylation alternations on HCC clinicopathological characteristics. The mean methylation level of the CSF1R promoter (chr 5:149492491-149492958) was demonstrated to be significantly higher in ANTs compared with HCC tissues (65.3±7.5% vs. 57.3±14.4%, respectively; P<0.0001). CSF1R also exhibited decreased expression in HCC tissues compared with ANTs (P=0.0026). However, CSF1R expression was negatively correlated with CSF1R methylation levels in ANTs (r>0.4; P<0.0001). Further analysis indicated that patients with diabetes exhibited lower methylation levels in ANTs compared with HCC tissues (P=0.0062). Furthermore, CSF1R hypomethylation in ANTs was associated with a larger number of tumors (P=0.0332), larger tumor size (P=0.0494) and higher tumor grade (P=0.0244). Therefore, methylation alternation of the CSF1R promoter region analyzed in the present study was a key regulatory mechanism on CSF1R expression and ANT hypomethylation indicated poor clinicopathological characteristics of HCC. CSF1R may be a potential immunological therapeutic target for HCC.

Promoter aberrant methylation status of ADRA1A is associated with hepatocellular carcinoma.

The aim of our study was to explore the relationship between the methylation status of the alpha-1A adrenergic receptor (ADRA1A) gene and hepatocellular carcinoma (HCC). We combined our in-house data-set with the Cancer Genome Atlas (TCGA) data-set to screen and identify the methylation status and expression of adrenergic receptor (AR) genes in HCC. Immunohistochemistry and western blot were performed to assess the expression of ADRA1A in HCC cell lines and tissues. We further evaluated the methylation levels of the ADRA1A promoter region in 160 HCC patients using the Sequenom MassARRAY® platform and investigated the association between methylation of ADRA1A and clinical characteristics. The expression levels of ADRA1A mRNA and protein were significantly decreased in HCC tissues. Compared with that in paired normal tissues, the mean methylation level of the ADRA1A promoter region was significantly increased in tumour tissues from 160 HCC patients (25.2% vs. 17.0%, P < 0.0001). We found that a DNA methyltransferase inhibitor (decitabine) could increase the expression of ADRA1A mRNA in HCC cell lines. Moreover, hypermethylation of the ADRA1A gene in HCC samples was associated with clinical characteristics, including alcohol intake (P = 0.0097) and alpha-fetoprotein (P = 0.0411). Receiver operator characteristic (ROC) curve analysis demonstrated that the mean methylation levels of ADRA1A could discriminate between HCC tissues and adjacent non-cancerous tissues (AUC = 0.700, P < 0.0001). mRNA sequencing indicated that the main enriched pathways were pathways in cancer, cytokine-cytokine receptor interaction and metabolic pathways (P < 0.01). ADRA1A gene hypermethylation might contribute to HCC initiation and is a promising biomarker for the diagnosis of HCC.

Genetic And Epigenetic Regulation Of E-Cadherin Signaling In Human Hepatocellular Carcinoma.

E-cadherin is well known as a growth and invasion suppressor and belongs to the large cadherin family. Loss of E-cadherin is widely known as the hallmark of epithelial-to-mesenchymal transition (EMT) with the involvement of transcription factors such as Snail, Slug, Twist and Zeb1/2. Tumor cells undergoing EMT could migrate to distant sites and become metastases. Recently, numerous studies have revealed how the expression of E-cadherin is regulated by different kinds of genetic and epigenetic alteration, which are implicated in several crucial transcription factors and pathways. E-cadherin signaling plays an important role in hepatocellular carcinoma (HCC) initiation and progression considering the highly mutated frequency of CTNNB1 (27%). Combining the data from The Cancer Genome Atlas (TCGA) database and previous studies, we have summarized the roles of gene mutations, chromosome instability, DNA methylation, histone modifications and non-coding RNA in E-cadherin in HCC. In this review, we discuss the current understanding of the relationship between these modifications and HCC. Perspectives on E-cadherin-related research in HCC are provided.

Overexpression of zinc finger protein 384 (ZNF 384), a poor prognostic predictor, promotes cell growth by upregulating the expression of Cyclin D1 in Hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a highly heterogeneous, multigene-driven malignant tumor. ZNF384 is an overexpressed gene with a high frequency of alteration in HCC, but research on the function of ZNF384 in HCC is lacking. In this study, the expression level of ZNF384 in HCC was analyzed through immunohistochemical (IHC) staining, Western blot analysis and qRT-PCR. We also generated ZNF384 knockdown and knockout HCC cell lines using short hairpin RNA (shRNA) and CRISPR/Cas9 systems. MTS, colony formation, and 5-ethynyl-20-deoxyuridine (EdU) assays; flow cytometry; and a xenograft mouse model were used to evaluate the effects of ZNF384 on cell proliferation. Western blot analysis, a dual luciferase reporter assay and a ChIP assay were performed to explore the potential mechanism. We found that overexpression of ZNF384 in HCC and elevated expression of ZNF384 in HCC tissues was significantly correlated with tumor recurrence (P = 0.0097). Kaplan-Meier survival analysis revealed that high expression levels of ZNF384 were correlated with poor overall survival (P = 0.0386). Downregulation of ZNF384 expression suppressed HCC cell proliferation by inhibiting the expression of Cyclin D1. These findings suggest that ZNF384 tends to act as an oncogene in the development of HCC. ZNF384 promotes the proliferation of HCC cells by directly upregulating the expression of Cyclin D1 and might serve as a prognostic predictive factor for HCC patients.

Aberrant methylation status of SPG20 promoter in hepatocellular carcinoma: A potential tumor metastasis biomarker.

PURPOSE: The aim of this study is to analyze the methylation levels of SPG20 promotor region and explore the association between the methylation levels and clinical features in hepatocellular carcinoma (HCC). MATERIALS AND METHODS: We collected paired of HCC and adjacent non-cancerous tissues (ANT) from 160 HCC patients and analyze the methylation levels through MassARRAY Analyzer 4. The statistical calculations were performed using SPSS version 22.0. Real-time-quantification PCR was performed to assess expression levels of SPG20 in HCC cell lines. Wound healing assay and transwell assay was used to measure cell migration capacity. RESULT: We found that mean methylation level of SPG20 in tumor tissues was significantly higher than that in ANT (7.3% vs. 16.2%, P<0.0013). There was a significantly negative correlation between expression level and methylation level of SPG20 (P<0.01). In addition, the methylation levels in HCC were correlated with age and HBV infection. Meanwhile, micro-satellite tumors (P = 0.016) and tumor number (P = 0.018) was found significantly associated with increased methylation levels of several CpG sites and the mean levels of SPG20 promotor in ANT. In addtion, the capacity of cell migration was significantly enhanced in SPG20 knock-down HCC cells. CONCLUSION: The hypermethylation status of SPG20 gene promoter is significantly associated with intra-hepatic metastasis and contribute to HCC metastasis.

Identification of the Germline Mutation Profile in Esophageal Squamous Cell Carcinoma by Whole Exome Sequencing.

Background: Esophageal squamous cell carcinoma (ESCC) is associated with poor prognosis and occurs with high frequency in China. The germline mutation profile in ESCC remains unclear, and therefore, the discovery of oncogenic alterations in ESCC is urgently needed. This study investigates the germline mutation profile and reveals associations among genotype-environment interactions in ESCC. Methods: Whole exome sequencing and follow-up analysis were performed in 77 matched tumor-normal ESCC specimens to examine the germline profiles. Additionally, associations among genotype-environment interactions were investigated. Results: We identified 84 pathogenic/likely pathogenic mutations and 51 rare variants of uncertain significance (VUS). Twenty VUS with InterVar evidence of a score of moderate pathogenicity (PM) 2/PM2+ supporting pathogenicity (PP) 1 were found to have pathogenic significance. CYP21A2 was the most frequently mutated gene, and the p.Gln319* variant was identified in 6.5% (5/77) of patients. The TP53 p.V197E mutation, located within the DNA binding domain, was found in 1.3% (1/77) of patients. In total, the 11.7% (9/77) of individuals with homologous recombination (HR) VUS were more likely to have well-differentiated tumors than those without (P = 0.003). The degree of lymph node metastasis was correlated with homologous recombination deficiency (HRD) and VUS group (P < 0.05). Moreover, the 10.4% (8/77) of individuals with mismatch repair (MMR) VUS had a higher tumor mutational burden (TMB), although the correlation was not significant. Conclusions: Our study identified the germline mutation profiles in ESCC, providing novel insights into the molecular pathogenesis of this disease. Our results may also serve as a useful resource for the exploration of the underlying mechanism of ESCC and may provide information for the prevention, diagnosis and risk management of ESCC.

Preoperative C-reactive protein/albumin ratio to predict mortality and recurrence of patients with hepatocellular carcinoma after curative resection.

BACKGROUND & OBJECTIVES: Recent studies have shown that the C-reactive protein-to-albumin ratio (CAR) can predict the mortality in patients with hepatocellular carcinoma (HCC). The aim of the present study was to investigate the utility of preoperative CAR for predicting postoperative overall and tumor free survival among HCC patients after radical surgery. METHODS: Preoperative neutrophil-to-lymphocyte ratio (NLR), clinicopathological parameters, laboratory data and patient demographics of 187 patients with HCC receiving initial radical liver resection from Sir Run Run Shaw hospital were evaluated. Multivariate analyses were performed to identify clinical characteristics associated with overall survival (OS) and tumor free survival (TFS). Subsequently, the prognostic value of CAR was evaluated using the area under the curve (AUC) compared with other systemic inflammation-based prognostic scores. RESULTS: Multivariate analysis revealed that the tumor number [hazard ratio (HR)=2.668; p=0.018] was independently associated with OS. While, the CRP/Alb ratio [HR=0.477; p=0.006] and the tumor number [HR=2.458; p=0.006] were significantly associated with TFS. The AUC values of the CRP/Alb ratio (6 months: 0.868; 12 months: 0.787; 36 months: 0.680) were higher than those of the GPS, mGPS and NLR at all time points in OS. CONCLUSION: Preoperative CRP/Alb ratio is an independent prognostic marker with tumor free survival in patients with HCC after curative resection and the prognostic ability was comparable to other applied inflammation-based prognostic scores in both overall and tumor-free survival, especially at the early stage.

The association between methylation patterns of DNAH17 and clinicopathological factors in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is a malignancy with poor prognosis. Complex genetic and epigenetic alterations are the two primary causes of HCC. The aim of the study was mainly to explore the correlation between the methylation status of DNAH17 and HCC. METHODS: We evaluated the methylation levels of DNAH17 in 163 HCC samples and their paired normal tissue using Sequenom EpiTYPER assays and performed the TaqMan copy number assay to assess the copy number status of DNAH17 in HCC samples. RESULTS: The mean methylation levels were significantly decreased in the tumor tissues compared to the paired normal tissues in both selected regions of DNAH17 (amplicon 1:58.7% vs 84.5%, P < 0.0001; amplicon 2:69.9% vs 84.5%, P = 0.0060). Contrarily，both RNA-seq and immunohistochemistry indicated the expression of DNAH17 was increased in tumor tissues (P < 0.05). DNMT inhibitor decitabine treatment could increase the expression of DNAH17 in HCC cell lines. DNAH17 gene amplification always companied with hypomethylation status. Moreover, hypomethylation status was associated with several clinical characteristics, such as male patients, higher AFP values, higher age of onset, fibrous capsules, tumor necrosis, liver cirrhosis, and tumor thrombus (P < 0.05). Receiver operator characteristic (ROC) curve analysis demonstrated the methylation levels of DNAH17 could efficiently predict the existence of the fibrous capsule (AUC = 0.695) and tumor thrombus (AUC = 0.806). CONCLUSIONS: These findings suggested that aberrant methylation of DNAH17 was associated with comprehensive HCC clinicopathological factors and could be a promising biomarker for tumor thrombosis in HCC patients.

SPINK1, PRSS1, CTRC, and CFTR Genotypes Influence Disease Onset and Clinical Outcomes in Chronic Pancreatitis.

OBJECTIVES: Rare pathogenic variants in the SPINK1, PRSS1, CTRC, and CFTR genes have been strongly associated with a risk of developing chronic pancreatitis (CP). However, their potential impact on the age of disease onset and clinical outcomes, as well as their potential interactions with environmental risk factors, remain unclear. These issues are addressed here in a large Chinese CP cohort. METHODS: We performed targeted next-generation sequencing of the four CP-associated genes in 1061 Han Chinese CP patients and 1196 controls. To evaluate gene-environment interactions, the patients were divided into three subgroups, idiopathic CP (ICP; n = 715), alcoholic CP (ACP; n = 206), and smoking-associated CP (SCP; n = 140). The potential impact of rare pathogenic variants on the age of onset of CP and clinical outcomes was evaluated using the Kaplan-Meier model. RESULTS: We identified rare pathogenic genotypes involving the SPINK1, PRSS1, CTRC, and/or CFTR genes in 535 (50.42%) CP patients but in only 71 (5.94%) controls (odds ratio = 16.12; P < 0.001). Mutation-positive patients had significantly earlier median ages at disease onset and at diagnosis of pancreatic stones, diabetes mellitus and steatorrhea than mutation-negative ICP patients. Pathogenic genotypes were present in 57.1, 39.8, and 32.1% of the ICP, ACP, and SCP patients, respectively, and influenced age at disease onset and clinical outcomes in all subgroups. CONCLUSIONS: We provide evidence that rare pathogenic variants in the SPINK1, PRSS1, CTRC, and CFTR genes significantly influence the age of onset and clinical outcomes of CP. Extensive gene-environment interactions were also identified.

Methylation patterns of RASA3 associated with clinicopathological factors in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the sixth most common tumor worldwide. The relationship between the gene methylation accumulation and HCC has been widely studied. In our study, we used the Sequenom EpiTYPER assay to investigate the methylation levels of the RASA3 in 164 HCC samples and paired adjacent non-cancerous tissues, and the association between methylation level and clinicopathological features. The methylation level of the RASA3 in HCC samples was found significantly lower than that in the adjacent non-cancerous tissues (P<0.0001). Moreover, the hypomethylation of RASA3 in HCC samples was connected with the presence of tumornecrosis (P=0.029) and alcohol intake (P=0.002). Furthermore, it was found that the expression of RASA3 was significantly decreased in tumor tissues (P=0.0053), which was also correlated with the methylation levels of RASA3 gene. Thus, RASA3 hypomethylation is a common feature in HCC, and may be a potential mechanism for HCC development, and serves as a useful biomarker for the early detection, especially in alcohol-associated HCCs.

Polymorphisms in CYP450 Genes and the Therapeutic Effect of Atorvastatin on Ischemic Stroke: A Retrospective Cohort Study in Chinese Population.

PURPOSE: Ischemic stroke (IS) is one of the most common neurologic diseases and is the main cause of death and disability in the Chinese population. This retrospective cohort study was performed to elucidate the relationship between single nucleotide polymorphisms (SNPs) in cytochrome P450 genes and the therapeutic effect of atorvastatin. METHODS: A total of 192 cases of IS were enrolled in the study. All patients were treated with atorvastatin, and their lipid levels and proportions were measured. Six SNPs in 4 cytochrome P450 genes (CYP2C19, CYP2D6, CYP3A4, and CYP4F2) related to drug metabolism were selected to be genotyped and analyzed. FINDINGS: Data were analyzed for 192 patients (sex, male/female, 122/70; mean age, 69.81 [9.35] years; Hypertension, 163[84.90%]; Cigarette smoking, 34[17.71%]). Among the 192 patients with IS treated with atorvastatin, it was found that the G allele of rs1065852 (CYP2D6) had a better effect on lowering of ΔLDL (P < 0.001), ΔLDL/LDL (P < 0.001), Δ(LDL/HDL) (P < 0.001), and Δ(LDL/HDL)/(LDL/HDL) (P < 0.001). We also found that rs2242480 (CYP3A4) showed marginal association with ΔLDL (P = 0.049) under the dominant model. In addition, rs2242480 and rs1065852 exhibited cumulative effects on the lipid-lowering (ΔLDL, ΔLDL/LDL, and Δ[LDL/HDL]) efficacy of atorvastatin (P < 0.001). IMPLICATIONS: The results suggest that CYP2D6 and CYP3A4 affect treatment with atorvastatin in patients with IS.

Duplication of the extrahepatic bile duct: A case report and review of the literatures.

RATIONALE: Duplication of the extrahepatic bile duct is an extremely rare congenital anomaly of the biliary system. PATIENT CONCERNS: A 44-year-old woman presented with a history of continuous upper abdominal pain and vomiting. DIAGNOSES: Magnetic resonance cholangiopancreatography (MRCP) disclosed diffuse dilatation of the intrahepatic and extrahepatic bile ducts. Endoscopic retrograde cholangiopancreatography (ERCP) showed the presence of two extrahepatic bile ducts with calculus at the distal end of the CBD. INTERVENTIONS: Laparoscopic cholecystectomy (LC) was performed after an ERCP. Choledochoscopy, performed during the operation, showed duplicated common bile duct and the cystic duct was seen opening at the right side of the extrahepatic duct. OUTCOMES: The patient was doing well after 6 months of follow-up. LESSONS: We reported a case of a double common duct with choledocholithiasis and gallstone. This rare anomaly may lead to cholangitis, common bile duct injury during surgery, malignancy occurrence, and should be treated with extreme care.

Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations.

Esophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients. Applying a robust computational strategy that adjusts for both technical and biological confounding factors, we find that TP53, EP300, and NFE2L2 show higher mutational frequencies in Asian patients. Moreover, NFE2L2 mutations correlate with the allele status of a nearby high-Fst SNP, suggesting their potential interaction. Our study provides insights into the molecular basis underlying the striking racial disparities of this disease, and represents a general computational framework for such a cross-population comparison.