Methylation of a newly identified region of the INS-IGF2 gene determines IGF2 expression in breast cancer tumors and in breast cancer cells

Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology

DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.

Translation of nutrigenomic research for personalised and precision nutrition for cancer prevention and for cancer survivors

Personalised and precision nutrition uses information on individual characteristics and responses to nutrients, foods and dietary patterns to develop targeted nutritional advice that is more effective in improving the diet and health of each individual. Moving away from the conventional 'one size fits all', such targeted intervention approaches may pave the way to better population health, including lower burden of non-communicable diseases. To date, most personalised and precision nutrition approaches have been focussed on tackling obesity and cardiometabolic diseases with limited efforts directed to cancer prevention and for cancer survivors. Advances in understanding the biological basis of cancer and of the role played by diet in cancer prevention and in survival after cancer diagnosis, mean that it is timely to test and to apply such personalised and precision nutrition approaches in the cancer area. This endeavour can take advantage of the enhanced understanding of interactions between dietary factors, individual genotype and the gut microbiome that impact on risk of, and survival after, cancer diagnosis. Translation of these basic research into public health action should include real-time acquisition of nutrigenomic and related data and use of AI-based data integration methods in systems approaches that can be scaled up using mobile devices.

Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics

Insulin is amongst the human genome's most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS-IGF2. This INS-IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS-IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3'UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with exon expression in various types of cancers. We further observed that the direction and strength of significant CpG-exon correlation tended to be consistent across different cancer contexts, indicating that some CpG-exon correlation patterns reflect fundamental biological mechanisms that transcend tissue- and cancer- types. We also discovered that CpG sites correlated with exon expressions were more likely to be associated with patient survival outcomes compared to CpG sites that did not correlate with exon expressions. Furthermore, we found that CpG sites were more strongly correlated with exon expression than expression of isoforms harboring the corresponding exons. This observation suggests that a major effect of CpG methylation on alternative splicing may be related to the inclusion or exclusion of exons, which subsequently impacts the relative usage of various isoforms. Overall, our study revealed correlation patterns between DNA methylation and alternative splicing, which provides new insights into the role of methylation in the transcriptional process.

High glucose increases IGF-2/H19 expression by changing DNA methylation in HTR8/SVneo trophoblast cells

INTRODUCTION

Gestational diabetes mellitus (GDM) is associated with many adverse outcomes of pregnancy, especially macrosomia. The aim of our study was to verify whether high glucose concentrations change the methylation levels of the insulin-like growth factor-2 (IGF-2)/H19 gene promoters to increase the expression of IGF-2, a key gene in fetal growth regulation.

METHODS

HTR8/SVneo cells were used to establish a cell model of intrauterine hyperglycemia in pregnant women with GDM. The RNA expression levels of the IGF-2/H19 genes and the methylation levels of the IGF-2/H19 gene promoter regions were measured. Methylated and unmethylated IGF-2/H19 gene promoter plasmids were transfected into HTR8/SVneo cells.

RESULTS

Among the five groups of cells, the RNA levels of IGF-2 and H19 were lowest in the 5-mM (physiological blood glucose level) group, which was statistically significant (all P < 0.05). Compared with those in the 5-mM group, two cytosine-phosphate-guanine (CpG) sites in the promoter region of the IGF-2 gene and twelve CpG sites in the promoter region of the H19 gene had statistically significant changes in methylation levels (all P < 0.05). Additionally, luciferase activity was significantly higher in cells transfected with the methylated H19 gene promoter plasmid than in control cells transfected with the unmethylated plasmid (P < 0.01), while the methylated IGF-2 gene promoter plasmid produced lower luciferase activity than the unmethylated plasmid (P < 0.01).

DISCUSSION

High glucose concentrations may increase IGF-2/H19 expression by changing the methylation levels of the IGF-2 and H19 gene promoters.