DNA Methylation in Ovarian Tumors-a Comparison Between Fresh Tissue and FFPE Samples

The Impact of Inherited Genetic Variation on DNA Methylation in Prostate Cancer and Benign Tissues of African American and European American Men

BACKGROUND

American men of African ancestry (AA) have higher prostate cancer incidence and mortality rates compared with American men of European ancestry (EA). Differences in genetic susceptibility mechanisms may contribute to this disparity.

METHODS

To gain insights into the regulatory mechanisms of prostate cancer susceptibility variants, we tested the association between SNPs and DNA methylation (DNAm) at nearby CpG sites across the genome in benign and cancer prostate tissue from 74 AA and 74 EA men. Genome-wide SNP data (from benign tissue) and DNAm were generated using Illumina arrays.

RESULTS

Among AA men, we identified 6,298 and 2,641 cis-methylation QTLs (meQTL; FDR of 0.05) in benign and tumor tissue, respectively, with 6,960 and 1,700 detected in EA men. We leveraged genome-wide association study (GWAS) summary statistics to identify previously reported prostate cancer GWAS signals likely to share a common causal variant with a detected meQTL. We identified nine GWAS-meQTL pairs with strong evidence of colocalization (four in EA benign, three in EA tumor, two in AA benign, and three in AA tumor). Among these colocalized GWAS-meQTL pairs, we identified colocalizing expression quantitative trait loci (eQTL) impacting four eGenes with known roles in tumorigenesis.

CONCLUSIONS

These findings highlight epigenetic regulatory mechanisms by which prostate cancer-risk SNPs can modify local DNAm and/or gene expression in prostate tissue.

IMPACT

Overall, our findings showed general consistency in the meQTL landscape of AA and EA men, but meQTLs often differ by tissue type (normal vs. cancer). Ancestry-based linkage disequilibrium differences and lack of AA representation in GWAS decrease statistical power to detect colocalization for some regions.

DNA methylation profiling identifies epigenetic signatures of early gastric cancer

Research on the DNA methylation status of gastric cancer (GC) has primarily focused on identifying invasive GC to develop biomarkers for diagnostic. However, DNA methylation in noninvasive GC remains unclear. We conducted a comprehensive DNA methylation profiling study of differentiated-type intramucosal GCs (IMCs). Illumina 850K microarrays were utilized to assess the DNA methylation profiles of formalin-fixed paraffin-embedded tissues from eight patients who were Epstein-Barr virus-negative and DNA mismatch repair proficient, including IMCs and paired adjacent nontumor mucosa. Gene expression profiling microarray data from the GEO database were analyzed via bioinformatics to identify candidate methylation genes. The final validation was conducted using quantitative real-time PCR, the TCGA methylation database, and single-sample gene set enrichment analysis (GSEA). Genome-wide DNA methylation profiling revealed a global decrease in methylation in IMCs compared with nontumor tissues. Differential methylation analysis between IMCs and nontumor tissues identified 449 differentially methylated probes, with a majority of sites showing hypomethylation in IMCs compared with nontumor tissues (66.1% vs 33.9%). Integrating two RNA-seq microarray datasets, we found one hypomethylation-upregulated gene: eEF1A2, overlapped with our DNA methylation data. The mRNA expression of eEF1A2 was higher in twenty-four IMC tissues than in their paired adjacent nontumor tissues. GSEA indicated that the functions of eEF1A2 were associated with the development of IMCs. Furthermore, TCGA data indicated that eEF1A2 is hypomethylated in advanced GC. Our study illustrates the implications of DNA methylation alterations in IMCs and suggests that aberrant hypomethylation and high mRNA expression of eEF1A2 might play a role in IMCs development.

Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels

Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.

Analysis of Competitive Endogenous Mechanism and Survival Prognosis of Serum Exosomes in Ovarian Cancer Patients Based on Sequencing Technology and Bioinformatics

Background: We determined the competitive endogenous in serum exosomes of ovarian cancer patients via sequencing technology and raw signal analysis. We performed an in-depth study of the potential mechanisms of ovarian cancer, predicted potential therapeutic targets and performed survival analysis of the potential targets.

Methods: Serum exosomes from three ovarian cancer patients were used as the experimental group, serum exosomes from three patients with uterine fibroids were used as the control group, and whole transcriptome analysis of serum exosomes was performed to identify differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in ovarian cancer. The miRcode database and miRNA target gene prediction website were used to predict the target genes. Cytoscape software was used to generate a competing endogenous RNA (ceRNA) network of competitive endogenous mechanism of serum exosomes in ovarian cancer, and the R language was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the target genes. Finally, the TCGA website was used to download clinical and expression data related to ovarian cancer, and the common potential target genes obtained previously were analyzed for survival.

Results: A total of 117 differentially expressed lncRNAs as well as 513 differentially expressed mRNAs (p < 0.05, |log2 fold change (FC)|≥ 1.0) were obtained by combining sequencing data and raw signal analysis, and 841 predicted target genes were reciprocally mapped by combining the data from the miRcode database and miRNA target gene prediction website, resulting in 11 potential target genes related to ovarian cancer (FGFR3, BMPR1B, TRIM29, FBN2, PAPPA, CCDC58, IGSF3, FBXO10, GPAM, HOXA10, and LHFPL4). Survival analysis of the above 11 target genes revealed that the survival curve was statistically significant (p < 0.05) for HOXA10 but not for the other genes. Through enrichment analysis, we found that the above target genes were mainly involved in biological processes such as regulation of transmembrane receptor protein kinase activity, structural molecule activity with elasticity, transforming growth factor-activated receptor activity, and GABA receptor binding and were mainly enriched in signaling pathways regulating stem cell pluripotency, bladder cancer, glycerolipid metabolism, central carbon metabolism of cancer, and tyrosine stimulation to EGFR in signaling pathways such as resistance to enzyme inhibitors.

Conclusions: The serum exosomal DIO3OS-hsa-miR-27a-3p-HOXA10 competitive endogenous signaling axis affects ovarian cancer development and disease survival by targeting dysregulated transcriptional pathways in cancer.

A Potential Indicator ARRDC2 Has Feasibility to Evaluate Prognosis and Immune Microenvironment in Ovarian Cancer

Background: The abnormal expression of α-arrestin protein family plays a key regulatory role in the occurrence and development of many cancers, including colorectal cancer and cervical cancer, and is inseparable from changes in the tumor immune microenvironment. However, the role of ARRDC2, an important member of this family, in the malignant biological process of ovarian cancer (OC) has not been reported, and its role in the change of the immune microenvironment is also unknown.

Methods: In this study, HPA, TCGA, GEO and other databases were used to explore the role of ARRDC2 in the prognosis assessment of ovarian cancer. Then, GO, KEGG analysis and GSEA analysis of the biological processes and cell signaling pathways that ARRDC2 may be involved in activated or inhibited. In addition, the TIMER and TISIDB database were used to conduct in-depth research on the role of ARRDC2 in the change of the immune microenvironment of ovarian cancer. The CMap database explored and screened drugs that may be used for treatment. Through cell transfection, CCK-8, Ki-67 immunofluorescence, wound healing, transwell and clone formation assay, the effect of ARRDC2 knockdown on the malignant biological behavior of OC cells were explored.

Results: There were significant differences between OC and ARRDC2 mRNA and protein levels. High ARRDC2 expression level is associated with poor overall survival and can be used as an independent prognostic factor. Interestingly, ARRDC2 expression is positively correlated with B cells, Neutrophils, Dendritic cells and CD8+ T cells, signifying that ARRDC2 may be related to infiltration of immune cells. ARRDC2 and its co-expressed genes are enriched in cell signaling pathways related to the immune system. We explored two possible drugs for the treatment of ovarian cancer. Finally, the results of in vitro experiments indicated that knockdown of ARRDC2 may inhibit malignant phenotypes such as proliferation and migration of OC cells.

Conclusion: The differentially expressed ARRDC2 may be a potential prognostic indicator and can be used as a novel biomarker for exploring the immune microenvironment of ovarian cancer.

DNA Methylation in Polycystic Ovary Syndrome：Emerging Evidence and Challenges

Polycystic ovary syndrome (PCOS) is a disease related to reproductive endocrine abnormalities in women of reproductive age, often accompanied by metabolic diseases such as hyperandrogenemia, insulin resistance and dyslipidemia. However, the etiology and mechanism of PCOS are still unclear. In recent years, more and more studies have found that epigenetic factors play an important role in PCOS. DNA methylation is the most widely studied epigenetic modification. At present, changes of DNA methylation have been found in serum, ovarian, hypothalamus, skeletal muscle, adipose tissue of PCOS patients, and these changes are closely related to insulin resistance, lipid metabolism and follicular development of PCOS. Although the current research on DNA methylation in PCOS is not in-depth, it indicated up a good direction for future research on the etiology and mechanism of PCOS. This review discussed the relationship between DNA methylation and PCOS. It is expected to help accelerate the application of DNA methylation in the diagnosis and treatment of PCOS.