Using Illumina Infinium HumanMethylation 450K BeadChip to explore genome‑wide DNA methylation profiles in a human hepatocellular carcinoma cell line

Development of a Codetection System Based on STRs and Biofluid-Specific CpG Markers

The detection of body fluids in biological stains at crime scenes and their association with donors is increasingly important for the validity of evidence in case investigations and prosecutions. While autosomal short tandem repeats (STR) and DNA methylation markers can effectively analyze personal identification and body fluid origin, there is currently no integrated system for simultaneous STR typing (subsource level) and biofluid identification (source level). This study has developed a codetection system based on DNA methylation markers (cytosine-phosphate-guanine [CpG]) and an STR amplification system for simultaneous personal identification and biofluid origin determination using capillary electrophoresis. This system integrates a 7-plex amplification system, comprising 5 biofluid-specific CpG markers (cg05261336 for semen, cg04011671 for peripheral blood, cg09107912 for saliva, cg15988970 for vaginal secretion, and cg18069290 for menstrual blood) and 2 control markers, with a 20-plex STR amplification system. The combined system successfully distinguished five types of body fluids from single sources (peripheral blood, semen, saliva, menstrual blood, and vaginal secretion) and generated DNA methylation profiles in mixed samples of two to four body fluids in varying proportions. The cumulative discrimination power for personal identification was calculated to be 1-3.5120 × 10-25. Additionally, semen and vaginal secretion with 0.1 ng DNA input or kept at room temperature for 5 months could still be efficiently identified. This study provides a promising method for simultaneously identifying body fluids and their donors in forensic science.

Genome-Wide Scan for Copy Number Variations in Chinese Merino Sheep Based on Ovine High-Density 600K SNP Arrays

Sheep are a vital species in the global agricultural economy, providing essential resources such as meat, milk, and wool. Merino sheep (Junken type) are a key breed of fine wool sheep in China. However, research on fine wool traits has largely overlooked the role of SNPs and their association with phenotypes. Copy number variations (CNVs) have emerged as one of the most important sources of genetic variation, influencing phenotypic traits by altering gene expression and dosage. To generate a comprehensive CNVR map of the ovine genome, we conducted genome-wide CNV detection using genotyping data from 285 fine wool sheep. This analysis revealed 656 CNVRs, including 628 on autosomes and 28 on the X chromosome, covering a total of 43.9 Mbs of the sheep genome. The proportion of CNVRs varied across chromosomes, from 0.45% on chromosome 26 to 3.72% on chromosome 10. Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses highlighted significantly enriched GO terms, including odorant binding, ATP binding, and sulfuric ester hydrolase activity. The KEGG analysis identified involvement in pathways such as neuroactive ligand-receptor interaction, axon guidance, ECM-receptor interaction, the one-carbon pool by folate, and focal adhesion (p < 0.05). To validate these CNVRs, we performed quantitative real-time PCR experiments to verify copy number predictions made by PennCNV software (v1.0.5). Out of 11 selected CNVRs with predicted gain, loss, or gain-loss statuses, 8 (IDs 68, 156, 201, 284, 307, 352, 411, 601) were successfully confirmed. This study marks a significant step forward in mapping CNVs in the ovine genome and offers a valuable resource for future research on genetic variation in sheep.

The Relevance of SOCS1 Methylation and Epigenetic Therapy in Diverse Cell Populations of Hepatocellular Carcinoma

The suppressor of cytokine signaling 1 (SOCS1) is a tumor suppressor gene found to be hypermethylated in cancers. It is involved in the oncogenic transformation of cirrhotic liver tissues. Here, we investigated the clinical relevance of SOCS1 methylation and modulation upon epigenetic therapy in diverse cellular populations of hepatocellular carcinoma (HCC). HCC clinical specimens were evaluated for SOCS1 methylation and mRNA expression. The effect of 5-Azacytidine (5-AZA), a demethylation agent, was assessed in different subtypes of HCC cells. We demonstrated that the presence of SOCS1 methylation was significantly higher in HCC compared to peri-HCC and non-tumoral tissues (52% vs. 13% vs. 14%, respectively, p < 0.001). In vitro treatment with a non-toxic concentration of 5-AZA significantly reduced DNMT1 protein expression for stromal subtype lines (83%, 73%, and 79%, for HLE, HLF, and JHH6, respectively, p < 0.01) compared to cancer stem cell (CSC) lines (17% and 10%, for HepG2 and Huh7, respectively), with the strongest reduction in non-tumoral IHH cells (93%, p < 0.001). 5-AZA modulated the SOCS1 expression in different extents among the cells. It was restored in CSC HCC HepG2 and Huh7 more efficiently than sorafenib. This study indicated the relevance of SOCS1 methylation in HCC and how cellular heterogeneity influences the response to epigenetic therapy.

Identification of Methylation-Regulated Differentially Expressed Genes and Related Pathways in Hepatocellular Carcinoma: A Study Based on TCGA Database and Bioinformatics Analysis

Background

In recent years, DNA methylation modification has been shown to be a critical mechanism in the field of epigenetics.

Methods

Hepatocellular carcinoma (HCC) data were obtained from The Cancer Genome Atlas project, including RNA expression profiles, Illumina Human Methylation 450K BeadChip data, clinical information, and pathological features. Then, differentially expressed genes (DEGs) and differentially methylated genes were identified using R software. Methylation-regulated DEGs (MeDEGs) were further analyzed using Spearman’s correlation analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the DAVID database and ClueGO in Cytoscape software. Kaplan–Meier survival analysis explored the relationship between methylation, expression of MeDEGs, and survival time. Gene set enrichment analysis (GSEA) was conducted to predict the function of prognosis-related MeDEGs.

Results

A total of nine up-regulated and 72 down-regulated MeDEGs were identified. GO and KEGG pathway analyses results indicated that multiple cancer-related terms were enriched. Kaplan–Meier survival analysis showed that the methylation status of four MeDEGs (CTF1, FZD8, PDK4, and ZNF334) was negatively associated with overall survival. Moreover, the methylation status of CDF1 and PDK4 was identified as an independent prognostic factor. According to GSEA, hypermethylation of prognosis-related MeDEGs was enriched in pathways that included “Spliceosome”, “Cell cycle”, “RNA degradation”, “RNA polymerase”, “DNA replication”, “Mismatch repair”, “Base excision repair”, “Nucleotide excision repair”, “Homologous recombination”, “Protein export”, and “Pyrimidine metabolism”.

Conclusions

Aberrant DNA methylation plays a critical role in malignant progression of HCC. Prognosis-related MeDEGs identified in this research may be potential biomarkers and targets in diagnosis and treatment.

Epigenetic silencing of MEIS2 in prostate cancer recurrence

Background

Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, resulting in overdiagnosis and overtreatment of clinically insignificant tumors. Thus, to improve the management of PC, novel biomarkers are urgently needed.

Results

In this study, we integrated genome-wide methylome (Illumina 450K DNA methylation array (450K)) and RNA sequencing (RNAseq) data performed in a discovery set of 27 PC and 15 adjacent normal (AN) prostate tissue samples to identify candidate driver genes involved in PC development and/or progression. We found significant enrichment for homeobox genes among the most aberrantly methylated and transcriptionally dysregulated genes in PC. Specifically, homeobox gene MEIS2 (Myeloid Ecotropic viral Insertion Site 2) was significantly hypermethylated (p < 0.0001, Mann-Whitney test) and transcriptionally downregulated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue in our discovery sample set, which was also confirmed in an independent validation set including > 500 PC and AN tissue samples in total (TCGA cohort analyzed by 450K and RNAseq). Furthermore, in three independent radical prostatectomy (RP) cohorts (n > 700 patients in total), low MEIS2 transcriptional expression was significantly associated with poor biochemical recurrence (BCR) free survival (p = 0.0084, 0.0001, and 0.0191, respectively; log-rank test). Next, we analyzed another RP cohort consisting of > 200 PC, AN, and benign prostatic hyperplasia (BPH) samples by quantitative methylation-specific PCR (qMSP) and found that MEIS2 was significantly hypermethylated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue samples (AN and BPH) with an AUC > 0.84. Moreover, in this cohort, aberrant MEIS2 hypermethylation was significantly associated with post-operative BCR (p = 0.0068, log-rank test), which was subsequently confirmed (p = 0.0067; log-rank test) in the independent TCGA validation cohort (497 RP patients; 450K data).

Conclusions

To the best of our knowledge, this is the first study to investigate, demonstrate, and independently validate a prognostic biomarker potential for MEIS2 at the transcriptional expression level and at the DNA methylation level in PC.