DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer

Prediction of disease-free survival of N1/2 non-small cell lung cancer after adjuvant chemotherapy by the biomarker RPMB

No molecular biomarkers have been proven applicable in clinical practice to identify patients who can benefit from adjuvant chemotherapy in non-small cell lung cancer (NSCLC). In this study, we established a biomarker, RPMB, short for promotor methylation burden of DNA repair genes (DRGs), to identify the subgroup of patients who might benefit from adjuvant chemotherapy in NSCLC. Methylation profiles of 828 NSCLC primary tumors and their clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. The RPMB for each patient after radical resection was calculated and its correlation with the prognosis of NSCLC was extensively investigated. DRGs of NSCLC were much more hypomethylated than the other genes (all p＜0.001). RPMB was defined as the ratio of methylated DRGs to the total number of all the DRGs. Patients with higher RPMB values tended to be nonsmokers, had adenocarcinoma, were female and had peripheral tumors. Subgroup analysis of forest plot among different clinical factors showed that high RPMB was significantly correlated to better disease-free survival (DFS) in pathologic N-positive patients after adjuvant chemotherapy (HR = 0.404, n = 62, p = 0.034). Notably, more superior DFS was exhibited in high RPMB NSCLCs with N1 nodal stage compared with those with low RPMB values (HR = 0.348, n = 47, p = 0.043). High RPMB might be used as a potential predictor to identify suitable N-positive NSCLC patients who can benefit from adjuvant chemotherapy after radical surgery.

p53 and PTEN expression evaluation with molecular evident recent criteria in laryngeal carcinoma

The prognosis of laryngeal cancer is affected by clinicopathological factors. Because of that, an effective prognostic marker is very valuable in managing the clinical process. The p53 evaluation method, used in the literature recently, was used for the first time in laryngeal cancer. We evaluated PTEN with 2 methods with the highest significance in the literature on laryngeal cancer. All demographic and histopathological data from 140 laryngeal cancers were compared with p53 and PTEN expressions and survival. p53 staining patterns were classified as wild and mutant. PTEN expression was evaluated according to the staining intensity named PTEN1 and according to the proportion of stained cells named PTEN2. In the series, 93.6% were males, and the mean survival was 38 months. 69.3% of cases were p53 mutants. PTEN loss was found to be 85.7% and 57.9%, respectively. Tumor size and thyroid cartilage invasion for PTEN1 and age for p53 were identified as independent predictive factors (P < .01). Advanced age, total laryngectomy, and extranodal spread were independent poor prognostic factors for overall survival and the presence of subglottic involvement, perineural invasion, and extranodal spread were for disease-free survival (P < .01). This is the first study in which the new p53 classification was used in laryngeal cancer, and will contribute significantly to the literature with differences from the previous evaluation patterns. Evaluation of PTEN based on staining intensity is more appropriate compared to the percentage of stained cells.

DNA methylation changes and increased mRNA expression of coagulation proteins, factor V and thrombomodulin in Fuchs endothelial corneal dystrophy

Late-onset Fuchs endothelial corneal dystrophy (FECD) is a disease affecting the corneal endothelium (CE), associated with a cytosine-thymine-guanine repeat expansion at the CTG18.1 locus in the transcription factor 4 (TCF4) gene. It is unknown whether CTG18.1 expansions affect global methylation including TCF4 gene in CE or whether global CE methylation changes at advanced age. Using genome-wide DNA methylation array, we investigated methylation in CE from FECD patients with CTG18.1 expansions and studied the methylation in healthy CE at different ages. The most revealing DNA methylation findings were analyzed by gene expression and protein analysis. 3488 CpGs had significantly altered methylation pattern in FECD though no substantial changes were found in TCF4. The most hypermethylated site was in a predicted promoter of aquaporin 1 (AQP1) gene, and the most hypomethylated site was in a predicted promoter of coagulation factor V (F5 for gene, FV for protein). In FECD, AQP1 mRNA expression was variable, while F5 gene expression showed a ~ 23-fold increase. FV protein was present in both healthy and affected CE. Further gene expression analysis of coagulation factors interacting with FV revealed a ~ 34-fold increase of thrombomodulin (THBD). THBD protein was detected only in CE from FECD patients. Additionally, we observed an age-dependent hypomethylation in elderly healthy CE.Thus, tissue-specific genome-wide and gene-specific methylation changes associated with altered gene expression were discovered in FECD. TCF4 pathological methylation in FECD because of CTG18.1 expansion was ruled out.

Gene body methylation in cancer: molecular mechanisms and clinical applications

DNA methylation is an important epigenetic mechanism that regulates gene expression. To date, most DNA methylation studies have focussed on CpG islands in the gene promoter region, and the mechanism of methylation and the regulation of gene expression after methylation have been clearly elucidated. However, genome-wide methylation studies have shown that DNA methylation is widespread not only in promoters but also in gene bodies. Gene body methylation is widely involved in the expression regulation of many genes and is closely related to the occurrence and progression of malignant tumours. This review focusses on the formation of gene body methylation patterns, its regulation of transcription, and its relationship with tumours, providing clues to explore the mechanism of gene body methylation in regulating gene transcription and its significance and application in the field of oncology.

Targeting DNA damage response as a potential therapeutic strategy for head and neck squamous cell carcinoma

Cells experience both endogenous and exogenous DNA damage daily. To maintain genome integrity and suppress tumorigenesis, individuals have evolutionarily acquired a series of repair functions, termed DNA damage response (DDR), to repair DNA damage and ensure the accurate transmission of genetic information. Defects in DNA damage repair pathways may lead to various diseases, including tumors. Accumulating evidence suggests that alterations in DDR-related genes, such as somatic or germline mutations, single nucleotide polymorphisms (SNPs), and promoter methylation, are closely related to the occurrence, development, and treatment of head and neck squamous cell carcinoma (HNSCC). Despite recent advances in surgery combined with radiotherapy, chemotherapy, or immunotherapy, there has been no substantial improvement in the survival rate of patients with HNSCC. Therefore, targeting DNA repair pathways may be a promising treatment for HNSCC. In this review, we summarized the sources of DNA damage and DNA damage repair pathways. Further, the role of DNA damage repair pathways in the development of HNSCC and the application of small molecule inhibitors targeting these pathways in the treatment of HNSCC were focused.

Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer

Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.

NLR, PLR, LMR and MWR as diagnostic and prognostic markers for laryngeal carcinoma

OBJECTIVE

To evaluate whether neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte to monocyte ratio (LMR) and monocyte-to-white blood cell ratio (MWR) can be used as diagnostic and prognostic markers for laryngeal carcinoma (LC).

METHODS

In this retrospective study, 50 patients with LC treated in the Department of Otolaryngology, Head and Neck Surgery of Beijing Tongren Hospital from August 2014 to August 2015 were enrolled in research group. In addition, 40 healthy volunteers from the same period were selected as control group. The counts of white blood cells, neutrophils, lymphocytes, monocytes and platelets in the peripheral blood of participants were measured with a blood counting instrument (Sysmex XE-2100, Sysmex Corporation, Japan), and the NLR, PLR, LMR and MWR were calculated. After that, the survival rate of patients was observed through a 5-year follow-up. The prognostic value of the above four indexes and their combination was discussed in patients with different clinical characteristics.

RESULTS

Compared with the control group, the NLR, PLR and MWR were higher and the LMR was lower in the research group. In terms of survival, patients with higher NLR, PLR and MWR and lower LMR showed a higher 5-year mortality than those with lower NLR, PLR and MWR and higher LMR, indicating that NLR, PLR and MWR were higher and LMR was lower in the survival group than in the death group. Subsequent analysis identified that NLR, PLR, LMR and MWR were closely correlated with age, alcohol drinking, smoking, clinical staging and T-staging. Clinical staging, T-staging, NLR, PLR, LMR, and MWR were confirmed as influencing factors for LC.

CONCLUSIONS

NLR, PLR, LMR, and MWR can be used as diagnostic and prognostic markers for LC and their combination has a superior diagnostic performance.

Identification and validation of prognosis-associated DNA repair gene signatures in colorectal cancer

Colorectal cancer (CRC) is the third most common malignant tumor. DNA damage plays a crucial role in tumorigenesis, and abnormal DNA repair pathways affect the occurrence and progression of CRC. In the current study, we aimed to construct a DNA repair-related gene (DRG) signature to predict the overall survival (OS) of patients with CRC patients. The differentially expressed DRGs (DE-DRGs) were analyzed using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The prognostic gene signature was identified by univariate Cox regression and least absolute shrinkage and selection operator (LASSO)-penalized Cox proportional hazards regression analysis. The predictive ability of the model was evaluated using the Kaplan–Meier curves and time-dependent receiver operating characteristic (ROC) curves. The gene set enrichment analysis (GSEA) was performed to explore the underlying biological processes and signaling pathways. ESTIMATE and CIBERSORT were implemented to estimate the tumor immune score and immune cell infiltration status between the different risk group. The half-maximal inhibitory concentration (IC50) was evaluated to representing the drug response of this signature. Nine DE-DRGs (ESCO2, AXIN2, PLK1, CDC25C, IGF1, TREX2, ALKBH2, ESR1 and MC1R) signatures was constructed to classify patients into high- and low-risk groups. The risk score was an independent prognostic indicator of OS (hazard ratio > 1, P < 0.001). The genetic alteration analysis indicated that the nine DE-DRGs in the signature were changed in 63 required samples (100%), and the major alteration was missense mutation. Function enrichment analysis revealed that the immune response and mtotic sister chromatid segregation were the main biological processes. The high-risk group had higher immune score than the low-risk group. What’s more, low-risk patients were more sensitive to selumetinib and dasatinib. The nine DE-DRGs signature was significantly associated with OS and provided a new insight for the diagnosis and treatment of CRC.

Upregulated expression of MTFR2 as a novel biomarker predicts poor prognosis in hepatocellular carcinoma by bioinformatics analysis

Aim: The authors investigated the clinical role of MTFR2 in hepatocellular carcinoma (HCC) progression. Results: MTFR2 expression and methylation were abnormal in HCC tissues, and HCC patients with increased MTFR2 expression or methylation had poor or better overall survival, respectively. In addition, increased MTFR2 expression was correlated with age, grade, cancer stage and T stage. MTFR2 was an independent predictor of dismal prognosis in HCC patients. MTFR2 was involved in HCC progression by modulating the cell cycle, homologous recombination, DNA replication, p53 signaling pathway, etc. The ten hub genes were overexpressed in HCC tissues and were linked to cancer stage and dismal prognosis in HCC patients. Conclusion: MTFR2 could be a prospective biomarker of poor prognosis in individuals with HCC.

Adipose most abundant 2 protein is a predictive marker for cisplatin sensitivity in cancers

Cisplatin (CDDP) is one of the chemotherapeutic drugs being used to treat various cancers. Although effective in many cases, as high doses of CDDP cause cytotoxic effects that may worsen patients' condition, therefore, a marker of sensitivity to CDDP is necessary to enhance the safety and efficiency of CDDP administration. This study focused on adipose most abundant 2 (APM2) to examine its potential as a marker of CDDP sensitivity. The relationship of APM2 expression with the mechanisms of CDDP resistance was examined in vitro and in vivo using hepatocellular carcinoma (HCC) cells, tissues and serum of HCC patients (n = 71) treated initially with intrahepatic arterial infusion of CDDP followed by surgical resection. The predictability of serum APM2 for CDDP sensitivity was assessed in additional 54 HCC patients and 14 gastric cancer (GC) patients. APM2 expression in CDDP-resistant HCC was significantly higher both in serum and the tissue. Bioinformatic analyses and histological analyses demonstrated upregulation of ERCC6L (DNA excision repair protein ERCC6-like) by APM2, which accounts for the degree of APM2 expression. The serum APM2 level and chemosensitivity for CDDP were assessed and cut-off value of serum APM2 for predicting the sensitivity to CDDP was determined to be 18.7 µg/mL. The value was assessed in HCC (n = 54) and GC (n = 14) patients for its predictability of CDDP sensitivity, resulted in predictive value of 77.3% and 100%, respectively. Our study demonstrated that APM2 expression is related to CDDP sensitivity and serum APM2 can be an effective biomarker of HCC and GC for determining the sensitivity to CDDP.Trial registration: This study was registered with the University Hospital Medical Information Network Clinical Trials Registry (UMIN000028487).

High-throughput sequencing profile of laryngeal cancers: analysis of co-expression and competing endogenous RNA networks of circular RNAs, long non-coding RNAs, and messenger RNAs

Background

Circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) have been recently identified as new classes of non-coding RNAs which participate in carcinogenesis and tumor progression. However, the functions of these non-coding RNAs and gene expression patterns are largely unknown.

Methods

We carried out high-throughput sequencing to analyze the differential expression of RNAs in 5 coupled laryngeal cancer (LC) and corresponding adjacent noncancerous tissues. Bioinformatics analyses were performed to predict the functions of these non-coding RNAs via co-expression, competing endogenous RNA networks and pathway enrichment analysis. The differential expression of the selected RNAs were confirmed using RT-qPCR. The CCK8, EDU, Transwell, and wound healing assays were conducted to validate the biological functions of SNHG29 in LC. Western blot assay was performed to identify the effects of SNHG29 having on the epithelial to mesenchymal transition process. Kaplan-Meier analysis was used to investigate whether the expression level of SNHG29 correlated with survival in LC patients. One-way ANOVA was used to analyze the correlation between the expression of SNHG29 and clinicopathological parameters of the included patients.

Results

Compared to normal laryngeal tissues, 31,763 non-coding RNAs were upregulated and 11,557 non-coding RNAs were downregulated in cancer tissues. SNHG29 expression was low in the LC cell lines and tissues predicting a better clinical prognosis. SNHG29 was also found to inhibit the proliferation, migration, and invasion ability of LC, exerting a suppressive role in the epithelial to mesenchymal transition process as well. SNHG29 downregulation was significantly correlated with differentiation (P=0.026), T-stage (P=0.041), lymphatic metastasis (P=0.044), and clinical stage (P=0.037). We found that the biological functions of differentially expressed transcripts included cell adhesion, biological adhesion, and migration and invasion related to adherens junction pathways.

Conclusions

Our study was the first to describe the non-coding RNA profile of LC, and suggested that dysregulated non-coding RNAs could be involved in LC tumorigenesis. SNHG29 was demonstrated to play crucial roles in inhibiting the pathogenesis and progression of LC. Our findings provide a new approach for further analyses of pathogenetic mechanisms, the detection of novel transcripts, and the identification of valuable biomarkers for this tumor.

Development and Validation of Epigenetic Signature Predict Survival for Patients with Laryngeal Squamous Cell Carcinoma

Establishing epigenetic signature to improve the accuracy of survival prediction and optimize therapeutic strategies for laryngeal squamous cell carcinoma (LSCC) by a genome-wide integrated analysis of methylation and the transcriptome. LSCC DNA methylation datasets and RNA sequencing datasets were acquired from the Cancer Genome Atlas (TCGA). MethylMix was applied to detect DNA methylation-driven genes (MDGs), which developed an epigenetic signature. The predictive accuracy and clinical value of the epigenetic signature were evaluated by receiver operating characteristic and decision curve analysis, and compared with tumor-node-metastasis (TNM) stage system. In addition, prognostic value of the epigenetic signature was validated by external Gene Expression Omnibus (GEO) database. According to five MDGs of epigenetic signature, the candidate small molecules for LSCC were screen out by the CMap database. A total of 88 DNA MDGs were identified, five of which (MAGEB2, SUSD1, ZNF382, ZNF418, and ZNF732) were chosen to construct an epigenetic signature. The epigenetic signature can effectively divide patients into high-risk and low-risk group, with the area under curve (AUC) of 0.8 (5-year overall survival [OS]) and AUC of 0.745 (3-year OS). Stratification analysis affirmed that the epigenetic signature was still a significant statistical prognostic model in subsets of patients with different clinical variables. Multivariate Cox regression analysis indicated that the efficacy of epigenetic signature appears independent of other clinicopathological characteristics. In terms of predictive capacity and clinical usefulness, the epigenetic signature was superior to traditional TNM stage. In addition, the epigenetic signature was confirmed in external LSCC cohorts from GEO. Finally, CMap matched the 10 most significant small molecules as promising therapeutic drugs to reverse the LSCC gene expression. An epigenetic signature, with five DNA MDGs, was identified and validated in LSCC patients by integrating multidimensional genomic data, which may offer novel research directions and prospects for individualized treatment of patients with LSCC.

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present MethylationToActivity (M2A), a machine learning framework that uses convolutional neural networks to infer promoter activities based on H3K4me3 and H3K27ac enrichment, from DNA methylation patterns for individual genes. Using publicly available datasets in real-world test scenarios, we demonstrate that M2A is highly accurate and robust in revealing promoter activity landscapes in various pediatric and adult cancers, including both solid and hematologic malignant neoplasms.

A four-methylated LncRNA signature predicts survival of osteosarcoma patients based on machine learning

Risk stratification using prognostic markers facilitates clinical decision-making in treatment of osteosarcoma (OS). In this study, we performed a comprehensive analysis of DNA methylation and transcriptome data from OS patients to establish an optimal methylated lncRNA signature for determining OS patient prognosis. The original OS datasets were downloaded from the the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Univariate, Lasso, and machine learning algorithm-iterative Lasso Cox regression analyses were used to establish a methylated lncRNA signature that significantly correlated with OS patient survival. The validity of this signature was verified by the Kaplan-Meier curves, Receiver Operating Characteristic (ROC) curves. We established a four-methylated lncRNA signature that can predict OS patient survival (verified in independent cohort [GSE39055]). Kaplan-Meier analysis showed that the signature can distinguish between the survival of high- and low-risk patients. ROC analysis corroborated this finding and revealed that the signature had higher prediction accuracy than known biomarkers. Kaplan-Meier analysis of the clinical subgroup showed that the signature's prognostic ability was independent of clinicopathological factors. The four-methylated lncRNA signature is an independent prognostic biomarker of OS.

Discovery and validation of the prognostic value of the lncRNAs encoding snoRNAs in patients with clear cell renal cell carcinoma

Some lncRNAs can encode small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which have exerted certain predictive values for the prognosis of some cancer patients. In this study, using RNA-seq and survival data in TCGA-KIRC, we examined the expression profile of 20 SNHGs and explored their prognostic values in ccRCC. Results showed that SNHG1, GAS5, SNHG3-8, SNHG11, SNHG12, SNHG15-17, SNHG20, SNHG22 and SNHG25 were significantly upregulated in ccRCC tissues compared with adjacent normal tissues. After adjustment for confounding factors, the multivariate analysis confirmed that increased SNHG3 expression was independently associated with shorter OS, while increased SNHG15 expression was an independent predictor of shorter RFS. Using the methylation data, the methylation status of 2 CpG sites (cg07807470 and cg15161854) and 2 CpG sites (cg00953154 and cg16459265) were negatively correlated with SNHG3 and SNHG15 expression, respectively. Moreover, low methylation levels of the 4 CpG sites were significantly associated with shorter OS. Furthermore, we validated the expression patterns, methylation status and prognostic value of SNHG3 and SNHG15 using clinical ccRCC samples. Taken together, SNHG3 and SNHG15 might be valuable prognostic markers in ccRCC, and DNA hypomethylation might play an important role in elevated SNHG3 and SNHG15 transcription in ccRCC.

Methylation‑driven genes PMPCAP1, SOWAHC and ZNF454 as potential prognostic biomarkers in lung squamous cell carcinoma

Of the different types of lung cancer, lung squamous cell cancer (LUSC) has the second highest rates of morbidity and mortality, which have been increasing in recent years. Epigenetic abnormalities may serve as potential biomarkers and diagnostic and/or therapeutic targets, which may help to monitor and improve the prognosis of patients with cancer. In the present study, data were obtained from The Cancer Genome Atlas database and survival and joint survival analyses were conducted using the R MethylMix package. Peptidase, mitochondrial processing a subunit pseudogene 1 (PMPCAP1), sosondowah ankyrin repeat domain family member C (SOWAHC) and zinc finger protein (ZNF) 454 were identified as independent prognosis‑related hub methylation‑driven genes (MDGs). Of these three genes, PMPCAP1 and SOWAHC, characterized by hypomethylation and high expression levels, were associated with poor prognosis in patients with LUSC, whilst ZNF454 was associated with an improved prognosis. In addition, pathway enrichment analysis suggested that PMPCAP1, SOWAHC and ZNF454 were primarily involved in gene expression or transcription pathways. Furthermore, 5, 1 and 10 key methylation sites of PMPCAP1, SOWAHC and ZNF454, respectively, were confirmed to be significantly relevant to gene expression, establishing a basis for further investigation into the mechanisms and more precise targets of these 3 genes. In conclusion, the MDGs PMPCAP1, SOWAHC and ZNF454 may be potential prognostic biomarkers of LUSC for guiding diagnosis and therapy options, as well as providing a theoretical basis for further investigation.

Epigenetic Signaling and RNA Regulation in Cardiovascular Diseases

RNA epigenetics is perhaps the most recent field of interest for translational epigeneticists. RNA modifications create such an extensive network of epigenetically driven combinations whose role in physiology and pathophysiology is still far from being elucidated. Not surprisingly, some of the players determining changes in RNA structure are in common with those involved in DNA and chromatin structure regulation, while other molecules seem very specific to RNA. It is envisaged, then, that new small molecules, acting selectively on RNA epigenetic changes, will be reported soon, opening new therapeutic interventions based on the correction of the RNA epigenetic landscape. In this review, we shall summarize some aspects of RNA epigenetics limited to those in which the potential clinical translatability to cardiovascular disease is emerging.

CCT α is a novel biomarker for diagnosis of laryngeal squamous cell cancer

Choline phosphate-based delivery systems can target the acidic tumor microenvironment. In this study, we set out to evaluate the diagnostic value of Choline phosphate cytidylyltransferase-α (CCTα) in laryngeal squamous cell cancer (LSCC). The expression of CCTα was detected using immunohistochemistry in 50 LSCC patients’ tissues and 16 vocal polyps as control group. Then, clinical data was collected and we used receiver operating characteristic curve (ROC) to estimate the potential of CCTα as diagnostic biomarker. We found CCTα levels to be significantly high in the tissues derived from LSCC patients, (p < 0.001). Further, we observed a positive correlation of CCTα with tumor size (p < 0.001), TNM stage (p < 0.001), lymph node metastasis (p < 0.001) as well as the grade of LSCC malignancy (p < 0.001). Furthermore, AUC was determined to be 0.939 by ROC, and the optimal cutoff value 3.100, with 76.0% sensitivity and 100% specificity. We also found an epigenetic basis of CCTα over-expression in LSCC tissues with significantly reduced methylation of CCTα in LSCC tissues, compared to vocal polyps (p < 0.001). These results support epigenetically-induced over-expression of CCTα as a potential diagnostic marker for LSCC.