Heritability Enrichment of Immunoglobulin G N-Glycosylation in Specific Tissues.

Genome-wide association studies (GWAS) have identified over 60 genetic loci associated with immunoglobulin G (IgG) N-glycosylation; however, the causal genes and their abundance in relevant tissues are uncertain. Leveraging data from GWAS summary statistics for 8,090 Europeans, and large-scale expression quantitative trait loci (eQTL) data from the genotype-tissue expression of 53 types of tissues (GTEx v7), we derived a linkage disequilibrium score for the specific expression of genes (LDSC-SEG) and conducted a transcriptome-wide association study (TWAS). We identified 55 gene associations whose predicted levels of expression were significantly associated with IgG N-glycosylation in 14 tissues. Three working scenarios, i.e., tissue-specific, pleiotropic, and coassociated, were observed for candidate genetic predisposition affecting IgG N-glycosylation traits. Furthermore, pathway enrichment showed several IgG N-glycosylation-related pathways, such as asparagine N-linked glycosylation, N-glycan biosynthesis and transport to the Golgi and subsequent modification. Through phenome-wide association studies (PheWAS), most genetic variants underlying TWAS hits were found to be correlated with health measures (height, waist-hip ratio, systolic blood pressure) and diseases, such as systemic lupus erythematosus, inflammatory bowel disease, and Parkinson's disease, which are related to IgG N-glycosylation. Our study provides an atlas of genetic regulatory loci and their target genes within functionally relevant tissues, for further studies on the mechanisms of IgG N-glycosylation and its related diseases.

Connections between metabolism and epigenetic modifications in cancer.

How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.

Spina bifida in fetus is associated with an altered pattern of DNA methylation in placenta.

Failure in closure of neural tube leads to neural tube defects (NTDs), which are among the most common symptoms of human birth defects. Although epigenetic status in placenta is linked to fetal development, the mechanism behind this remains unknown. Because of the importance of DNA methylation in gene function, we set to explore whether or not DNA methylation in human placenta is also linked to fetal NTDs. Here we show for the first time that alteration of DNA methylation in placenta is closely associated with the phenotypes of fetal spina bifida (Sb). We found that patterns of DNA methylation for genes in neurological system process were differentially altered in the Sb placenta. In particular, the transcription regulatory regions of TRIM26 and GANS were kept at the hypomethylation status in Sb placenta alone. Accordingly, the protein levels of TRIM26 and GNAS were significantly elevated only in the Sb placenta but not in the Sb-affected fetuses. In cellular model of CHO cells deficient in Dihydrofolate reductase and treated with 5-aza-2'-deoxycytidine, the protein levels of GNAS and TRIM26 were significantly higher than those in normal control cells. These findings suggested that epigenetic status of genes in placenta have profound impacts on the development of NTDs.