Epigenetic and genetic alterations of the EDNRB gene in nasopharyngeal carcinoma

A computational model revealing the immune-related hub genes and key pathways involved in rheumatoid arthritis (RA)

Rheumatoid arthritis (RA) has one of the highest disability rates among inflammatory joint disorders. However, the reason and possible molecular events are still unclear. There are various treatment options available, but no complete cure. To obtain early diagnosis and successful medication in RA, it is necessary to explore gene susceptibility and pathogenic factors. The main intend of our work is to explore the immune-related hub genes with similar functions that are differentially expressed in RA patients. Three datasets such as GSE21959, GSE55457, and GSE77298, were taken to analyze the differently expressed genes (DEGs) among 55 RA and 33 control samples. We obtained 331 upregulated and 275 downregulated DEGs from three Gene Expression Omnibus (GEO) datasets using the R package. Furthermore, a protein-protein interaction network was built for upregulated and downregulated DEGs using Cytoscape. Subsequently, MCODE analysis was performed and obtained the top two modules in each DEG's upregulated and downregulated protein-protein interactions (PPIs) network. CytoNCA and cytoHubba were performed and identified overlapping DEGs. In addition, we narrowed down DEGs by filtering with immune-related genes and identified DE-IRGs. Gene ontology (GO) and KEGG pathway analysis in upregulated and downregulated DEGs were executed with the DAVID platform. Our study obtained the nine most significant DE-IRGs in RA such as CXCR4, CDK1, BUB1, BIRC5, AGTR1, EGFR, EDNRB, KALRN, and GHSR. Among them, CXCR4, CDK1, BUB1, and BIRC5 are overexpressed in RA and may contribute to the pathophysiology of the disease. Similarly, AGTR1, EGFR, EDNRB, KALRN, and GHSR are all low expressed in RA and may have a contribution to pathogenesis. GO, KEGG functional enrichment, and GeneMANIA showed that the dysregulated process of DE-IRGs causes RA development and progression. These findings may be helpful in future studies in RA diagnosis and therapy.

Endothelin: 30 Years From Discovery to Therapy

Discovered in 1987 as a potent endothelial cell-derived vasoconstrictor peptide, endothelin-1 (ET-1), the predominant member of the endothelin peptide family, is now recognized as a multifunctional peptide with cytokine-like activity contributing to almost all aspects of physiology and cell function. More than 30 000 scientific articles on endothelin were published over the past 3 decades, leading to the development and subsequent regulatory approval of a new class of therapeutics-the endothelin receptor antagonists (ERAs). This article reviews the history of the discovery of endothelin and its role in genetics, physiology, and disease. Here, we summarize the main clinical trials using ERAs and discuss the role of endothelin in cardiovascular diseases such as arterial hypertension, preecclampsia, coronary atherosclerosis, myocardial infarction in the absence of obstructive coronary artery disease (MINOCA) caused by spontaneous coronary artery dissection (SCAD), Takotsubo syndrome, and heart failure. We also discuss how endothelins contributes to diabetic kidney disease and focal segmental glomerulosclerosis, pulmonary arterial hypertension, as well as cancer, immune disorders, and allograft rejection (which all involve ET_A autoantibodies), and neurological diseases. The application of ERAs, dual endothelin receptor/angiotensin receptor antagonists (DARAs), selective ET_B agonists, novel biologics such as receptor-targeting antibodies, or immunization against ET_A receptors holds the potential to slow the progression or even reverse chronic noncommunicable diseases. Future clinical studies will show whether targeting endothelin receptors can prevent or reduce disability from disease and improve clinical outcome, quality of life, and survival in patients.

In vivo characterization of neural crest-derived fibro/adipogenic progenitor cells as a likely cellular substrate for craniofacial fibrofatty infiltrating disorders

The cellular substrate underlying aberrant craniofacial connective tissue accumulation that occurs in disorders such as congenital infiltration of the face (CILF) remain elusive. Here we analyze the in vivo properties of a recently identified population of neural crest-derived CD31-:CD45-:alpha7-:Sca1+:PDGFRa+ fibro/adipogenic progenitors (NCFAPs). In serial transplantation experiments in which NCFAPs were prospectively purified and transplanted into wild type mice, NCFAPs were found to be capable of self-renewal while keeping their adipogenic potential. NCFAPs constitute the main responsive FAP fraction following acute masseter muscle damage, surpassing the number of mesoderm-derived FAPs (MFAPs) during the regenerative response. Lastly, NCFAPs differentiate into adipocytes during muscle regeneration in response to pro-adipogenic systemic cues. Altogether our data indicate that NCFAPs are a population of stem/primitive progenitor cells primarily involved in craniofacial muscle regeneration that can cause tissue degeneration when the damage co-occurs with an obesity inducing diet.

Early progress in epigenetic regulation of endothelin pathway genes

Control of gene transcription is a major regulatory determinant for function of the endothelin pathway. Epigenetic mechanisms act on tissue-specific gene expression during development and in response to physiological stimuli. Most of the limited evidence available on epigenetic regulation of the endothelin pathway focuses on the EDN1 and EDNRB genes. Examination of whole genome databases suggests that both genes are influenced by histone modifications and DNA methylation. This interpretation is supported by studies directed at detecting epigenetic action on the two genes. The clearest illustration of epigenetic factors altering endothelin signalling is DNA methylation-associated EDNRB silencing during tumourigenesis. This review summarizes our current understanding of epigenetic regulation of the endothelin pathway genes. LINKED ARTICLES This article is part of a themed section on Endothelin. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.168.issue-1.

Screening of candidate tumor-suppressor genes in 3p21.3 and investigation of the methylation of gene promoters in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is the most common type of head and neck malignant tumor. however, its pathological mechanisms have not yet been elucidated. In the present study, we screened for candidate tumor-suppressor genes (TSGs) related to OSCC among 10 candidate genes located in 3p21.3, a region abundant with TSGs based on previous studies, using semi-quantitative reverse transcription PCR (RT-PCR). Three genes, GNAT1, SEMA3B and AXUD1, with low or no expression in OSCC tissues and the cell line TCA8113 were selected, and the promoter methylation status was further analyzed by methylation-specific PCR (MS-PCR). Hypermethylation in the promoter regions of SEMA3B was found in OSCC tissues, and a significant difference in the frequency of methylation of SEMA3B was observed between OSCC and non-cancerous tissues. Furthermore, TCA8113 cells treated with 5-Aza-Cdc started to re-express SEMA3B at a concentration of 5 µM or higher. Our study confirmed that three candidate TSGs with low expression may be involved in OSCC and that hypermethylation in promoter regions may contribute to the low expression of SEMA3B. These findings offer novel insights for clarifying the molecular mechanisms of tumorigenesis of OSCC as well as for aiding in its clinical diagnosis and therapeutic strategy.

Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer

OBJECTIVES

Cigarette smoking is the most demonstrated risk factor for the development of lung cancer, while the related genetic mechanisms are still unclear.

METHODS

The preprocessed microarray expression dataset was downloaded from Gene Expression Omnibus database. Samples were classified according to the disease state, stage and smoking state. A new computational strategy was applied for the identification and biological interpretation of new candidate genes in lung cancer and smoking by coupling a network-based approach with gene set enrichment analysis.

MEASUREMENTS

Network analysis was performed by pair-wise comparison according to the disease states (tumor or normal), smoking states (current smokers or nonsmokers or former smokers), or the disease stage (stages I-IV). The most activated metabolic pathways were identified by gene set enrichment analysis.

RESULTS

Panels of top ranked gene candidates in smoking or cancer development were identified, including genes involved in cell proliferation and drug metabolism like cytochrome P450 and WW domain containing transcription regulator 1. Semaphorin 5A and protein phosphatase 1F are the common genes represented as major hubs in both the smoking and cancer related network. Six pathways, e.g. cell cycle, DNA replication, RNA transport, protein processing in endoplasmic reticulum, vascular smooth muscle contraction and endocytosis were commonly involved in smoking and lung cancer when comparing the top ten selected pathways.

CONCLUSION

New approach of bioinformatics for biomarker identification and validation can probe into deep genetic relationships between cigarette smoking and lung cancer. Our studies indicate that disease-specific network biomarkers, interaction between genes/proteins, or cross-talking of pathways provide more specific values for the development of precision therapies for lung.

Role of DNA methylation in head and neck cancer

Head and neck cancer (HNC) is a heterogenous and complex entity including diverse anatomical sites and a variety of tumor types displaying unique characteristics and different etilogies. Both environmental and genetic factors play a role in the development of the disease, but the underlying mechanism is still far from clear. Previous studies suggest that alterations in the genes acting in cellular signal pathways may contribute to head and neck carcinogenesis. In cancer, DNA methylation patterns display specific aberrations even in the early and precancerous stages and may confer susceptibility to further genetic or epigenetic changes. Silencing of the genes by hypermethylation or induction of oncogenes by promoter hypomethylation are frequent mechanisms in different types of cancer and achieve increasing diagnostic and therapeutic importance since the changes are reversible. Therefore, methylation analysis may provide promising clinical applications, including the development of new biomarkers and prediction of the therapeutic response or prognosis. In this review, we aimed to analyze the available information indicating a role for the epigenetic changes in HNC.

Polymorphisms in the endothelin-1 and endothelin a receptor genes and survival in patients with locoregionally advanced nasopharyngeal carcinoma

PURPOSE

We aimed to investigate the prognostic role of endothelin-1 (EDN1) and endothelin A receptor (EDNRA) gene polymorphisms in patients with locoregionally advanced nasopharyngeal carcinoma (NPC).

EXPERIMENTAL DESIGN

Two hundred three consecutive patients with locoregionally advanced NPC were enrolled. Seven potentially functional polymorphisms in the EDN1 and EDNRA genes were determined by ligase detection reaction-PCR method from prospectively collected blood samples. The influence of the genetic polymorphisms on patient overall survival (OS) was analyzed using Cox proportional hazards model, Kaplan-Meier method, and the log-rank test.

RESULTS

The 5-year OS in patients with EDNRA/H323H TT, TC, and CC genotypes were 81.3%, 62.1%, and 75.0%, respectively (P = 0.004). Patients carrying the heterozygous (TC) or homozygous variant (CC) genotype in EDNRA/H323H were combined for analysis, which revealed that the 5-year OS in patients with TC/CC genotypes was significantly lower than those with the wild-type TT genotype (63.2% vs. 81.3%; P = 0.002). Multivariate analysis showed that EDNRA/H323H polymorphism (HR: 1.95; 95% CI: 1.18-3.23; P = 0.009) and N classification (HR: 1.35; 95% CI: 1.03-1.79; P = 0.03) were independent significant prognostic factors for OS in patients with locoregionally advanced NPC. In contrast, the EDN1 polymorphisms revealed no prognostic value.

CONCLUSIONS

The EDNRA/H323H polymorphism was a novel and independent prognostic marker for patients with locoregionally advanced NPC. The analysis of EDNRA/H323H polymorphism may help identify patient subgroups at high risk for poor disease outcome.

Treatment with 5-Aza-2'-deoxycytidine induces promoter demethylation of the EDNRB gene and inhibits cell proliferation in human gastric carcinoma cell line SGC-7901

AIM: To investigate the effects of 5-Aza-2'-deoxycytidine on promoter hypermethylation of the EDNRB gene and cell proliferation in human gastric carcinoma cell line SGC-7901.

METHODS: After SGC-7901 cells were treated with different concentrations (1, 2, 5, 10 μmol/L) of 5-Aza-2'-deoxycytidine, the promoter methylation status of the EDNRB gene in SGC-7901 cells was analyzed using methylation-specific polymerase chain reaction (MSP); the expression of EDNRB gene in SGC-7901 cells was detected by reverse transcription polymerase chain reaction (RT-PCR); cell proliferation was measured by MTT assay; and cell cycle distribution and apoptosis were analyzed by flow cytometry.

RESULTS: Before treatment with 5-Aza-2'-deoxycytidine, promoter hypermethylation of the EDNRB gene was detected in SGC-7901 cells. Accordingly, the expression of EDNRB mRNA was not detected in SGC-7901 cells. After treatment of cells with 5-Aza-2'-deoxycytidine for four days, promoter demethylation of the EDNRB gene was induced and EDNRB mRNA expression was detected. Treatment with 5-Aza-2'-deoxycytidine restrained the proliferation of SGC-7901 cells in a time- and dose-dependent manner. Treatment with 5-Aza-CdR induced cell cycle arrest in S phase. The apoptosis rate was significantly higher in SGC-7901 cells treated with 5 or 10 μmol/L 5-Aza-CdR than in control cells (7.13% ± 0.87%, 13.34% ± 1.12% vs 3.69% ± 0.52%, both P < 0. 05).

CONCLUSION: 5-Aza-2'-deoxycytidine can effectively induce promoter demethylation of the EDNRB gene, activate EDNRB gene expression, and inhibit cell growth in human gastric carcinoma cell line SGC-7901.

Detection of the promoter methylation status of the EDNRB gene in human gastric cancer cell line KATO III

AIM: To detect the promoter methylation status and mRNA expression of the endothelin receptor type B (EDNRB) gene in human gastric cancer cell line KATO III and to analyze their clinical significance.

METHODS: Genomic DNA and total RNA were extracted from healthy adult peripheral blood samples and KATO III cells. Bisulfite sequencing PCR and reverse transcription-PCR were performed to analyze the promoter methylation status and mRNA expression of the EDNRB gene, respectively.

RESULTS: In KATO III cells, some CG loci (≤20%) were not or lowly methylated, while some others (≥50%) were hypermethylated. In healthy adult peripheral blood samples, only one CG locus (10%) was methylated, while the others were not methylated. The promoter methylation extent of the EDNRB gene in KATO III cells was higher than that in healthy adult peripheral blood samples. The mRNA expression was inhibited significantly in KATO III cells compared with healthy adult peripheral blood samples.

CONCLUSION: EDNRB gene promoter is hypermethylated in KATO III cells. The promoter methylation of the EDNRB gene may play an important role in the pathogenesis of gastric cancer.

KIF1A and EDNRB are differentially methylated in primary HNSCC and salivary rinses

Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. In this study, we aimed to evaluate to the utility of aberrant promoter hypermethylation for detection in a panel of 10 genes (KIF1A, EDNRB, CDH4, TERT, CD44, NISCH, PAK3, VGF, MAL and FKBP4) in head and neck squamous cell carcinoma (HNSCC) via a candidate gene approach. We investigated methylation of the gene promoters by bisulfite modification and quantitative methylation-specific PCR (Q-MSP) in a preliminary study of a limited cohort of salivary rinses from healthy subjects (n = 61) and patients with HNSCC (n = 33). The methylation status of 2 selected genes (EDNRB and KIF1A) were then analyzed in 15 normal mucosa samples from a healthy population, 101 HNSCC tumors and the corresponding salivary rinses from 71 out of the 101 HNSCC patients were collected before treatment. The promoter regions of CDH4, TERT, VGF, MAL, FKBP4, NISCH and PAK3 were methylated in normal salivary rinses while no methylation of CD44 was observed in either normal salivary rinses or tumor samples. However, KIF1A and EDNRB were methylated in 98 and 97% of primary HNSCC tissues respectively and were only methylated in 2 and 6.6% of normal salivary rinses. In addition, KIF1A and EDNRB were methylated in 38 and 67.6% of salivary rinses from HNSCC patients, respectively. Promoter hypermethylation of KIF1A and EDNRB is a frequent event in primary HNSCC, and these genes are preferentially methylated in salivary rinses from HNSCC patients. KIF1A and EDNRB are potential biomarkers for HNSCC detection.

Promoter hypermethylation in Indian primary oral squamous cell carcinoma

We evaluated promoter hypermethylation of a panel of tumor suppressor genes as a means to detect epigenetic alterations in oral squamous cell carcinomas (OSCC) of Indian-origin and compare with North-American head and neck squamous cell carcinomas (HNSCC). Quantitative-methylation-specific PCR was used to investigate the promoter methylation status of DCC, EDNRB, p16(INK4a) and KIF1A in 92 OSCC, and compared to 48 paired normal tissues and 30 saliva and sera samples from healthy control subjects. Aberrant methylation of at-least one of these genes was detected in 74/92 (80.4%) OSCC; 72.8% at EDNRB, 71.7% at KIF1A, 47.8% at p16(INK4a) and 58.7% at DCC; and in 5 of 48 (10.4%) normal oral tissues. None of the saliva and sera samples from controls exhibited DNA methylation in these four target genes. Thirty-two of 72 node positive cases harbored p16(INK4a) and DCC hypermethylation (p = 0.005). Thus, promoter hypermethylation in genes analyzed herein is a common event in Indian OSCC and may represent promising markers for the molecular staging of OSCC patients. We found higher frequency of p16(INK4a) methylation (47.8%) in this Indian cohort in comparison with a North-American cohort (37.5%). In conclusion, aberrant methylation of EDNRB, KIF1A, DCC and p16(INK4a) genes is a common event in Indian OSCC, suggesting that epigenetic alterations of these genes warrant validation in larger studies for their potential use as biomarkers.

Advances in understanding the relationship between aberrant methylation of EDNRB and tumors

DNA methylation is a major epigenetic mechanism and plays an important role in the pathogenesis of tumors. The endothelin receptor B (EDNRB) gene is an important candidate tumor suppressor gene. EDNRB promoter hypermethylation has been detected in several types of tumors and may therefore be used as a useful molecular marker for tumor diagnosis. In addition, EDNRB gene methylation may also be used as a new target for tumor treatment due to the reversibility of DNA methylation.

Epigenetic dysregulation of the host cell genome in Epstein-Barr virus-associated neoplasia

Epstein-Barr virus (EBV), a human herpesvirus, is associated with a wide variety of malignant tumors. The expression of the latent viral RNAs is under strict, host-cell dependent transcriptional control. This results in an almost complete transcriptional silencing of the EBV genome in memory B-cells. In tumor cells, germinal center B-cells and lymphoblastoid cells, distinct viral latency promoters are active. Epigenetic mechanisms contribute to this strict control. In EBV-infected cells, epigenetic mechanisms also alter the expression of cellular genes, including tumor suppressor genes. In Nasopharyngeal Carcinoma, the hypermethylation of certain cellular promoters is attributed to the upregulation of DNA methyltransferases by the viral oncoprotein LMP1 (latent membrane protein 1) via JNK/AP1-signaling. The role of other viral latency products in the epigenetic dysregulation of the cellular genome remains to be established. Analysis of epigenetic alterations in EBV-associated neoplasms may result in a better understanding of their pathogenesis and may facilitate the development of new therapies.

Inactivation of LARS2, located at the commonly deleted region 3p21.3, by both epigenetic and genetic mechanisms in nasopharyngeal carcinoma

Allelic loss of chromosome 3p, including the 3p21.3 region, is found in 95-100% of primary nasopharyngeal carcinoma (NPC) biopsies, suggesting that this region should harbor some tumor suppressor genes (TSGs) closely related to NPC development. Several TSGs located at 3p21.3, such as RASSF1A, LTF and BLU, have been demonstrated to be involved in NPC development. LARS2 (leucyl-tRNA synthetase 2, mitochondrial) is another gene located in the chromosome 3 common eliminated region-1 (C3CER1) at 3p21.3. In this study, we focussed on the epigenetic and genetic alterations of LARS2 in NPC. The mRNA expression of LARS2 was detected in 36 NPC and 8 chronic nasopharyngitis (NP) tissues by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Subsequently, the mutation, allelic loss, and methylation status of LARS2 were analysed by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP), homozygous deletion (HD) analysis and methylation-specific polymerase chain reaction in primary NPC tissues. No expression or downregulation of LARS2 was observed in 78% of primary NPC tissues. No mutations, assessed by PCR-SSCP and DNA sequencing, were found in the promoter region and exon 1 of LARS2 in NPC tissues, whereas HD was detected in 28% of NPC specimens at the LARS2 locus. In addition, hypermethylation of LARS2 was found in 64% of NPC samples but only in 12.5% of NP biopsies. Our data indicate that inactivation of LARS2 by both genetic and epigenetic mechanisms may be a common and important event in the carcinogenesis of NPC.

The DLC-1 -29A/T polymorphism is not associated with nasopharyngeal carcinoma risk in Chinese population

Deleted in liver cancer-1 (DLC-1), encoding a Rho GTPase-activating protein (GAP), is considered as a promising candidate tumor suppressor gene in nasopharyngeal carcinoma (NPC). The single-nucleotide polymorphism (SNP) -29A/T upstream of ATG start codon was found when gene mutation profile of DLC-1 in NPC was analyzed. To evaluate the correlation between SNP -29A/T in the promoter region of DLC-1 gene and risk of NPC, a total of 521 samples from a Chinese population, including 320 healthy individuals and 201 NPC patients, were collected for SNP analysis by PCR-single-strand conformation polymorphism and sequencing. The differences in allele and genotype frequencies between NPC patients and controls were tested using logistic regression statistical method. No significant differences were found in allele or genotype frequencies between NPC patients and controls or among different NPC clinical stages. Hence, our data indicate that the SNP -29A/T of DLC-1 gene is not associated with NPC susceptibility.