DNA demethylation of neuronal cell death genes in depression

Background: DNA methylation may play a role in the etiology of neuropsychiatric disorders through abnormal genomic methylation patterns regulating genes involved in brain development or physiology. In this study we explored the DNA methylation profile of depression in the prefrontal cortex because converging evidence from brain imaging and postmortem studies has implicated this region in depression neuropathology. Materials and methods: In order to better understand both the wild type genomic DNA methylation patterns and aberrant methylation events occurring in disease states we profiled DNA methylation patterns in human postmortem brains of 12 depressed and non-psychiatric controls using the methylation mapping and paired-end sequencing (Methyl-MAPS) method. Methyl-MAPS is an enzymatic-base method that can delineate the methylation status of greater than 80% of CpG sites genome-wide (Xin et al., doi: 10.4161/epi.6.11.17876). Overall, these data represent relatively unbiased coverage of the genome, including CpG-rich domains such as CpG islands and repetitive elements. Results and conclusions: Comparative analysis of DNA methylation patterns among depressed cases and controls revealed little variation at the transcription start sites (TSS) across all RefSeq annotated genes, but significant variations were detected proximal to the TSS (referred to as “CpG island shores”). We observed statistically significant methylation loss in CpG island shores in depressed cases compared to controls. These findings were replicated in purified neuronal cell populations. Using an independent sample of depressed cases and matched non-psychiatric controls, we isolated neuronal nuclei from the dorsal prefrontal cortex of 11 depressed cases and 11 controls. Due to limited quantities of neuronal DNA typically obtained from isolation of nuclei using fluorescence-activated cell sorting, we used the Illumina HumanMethylation450 BeadChip. DNA methylation differences in CpG island shores revealed that, of the CpG dinucleotides with significant methylation differences, >95% showed loss of methylation in depressed brains. The underlying mechanism involved in the loss of methylation in depression psychopathology is unclear. However, the global 5-hydroxymethylcytosine levels in neuronal DNA from the same sample specimens also showed a loss of hydroxymethylation in depressed brains compared to controls. Although these data were not statistically significant, they revealed an important trend in loss of hydroxymethylation and the possible mechanism for DNA demethylation in brains of depressed patients. Gene ontology analysis of genes with significant methylation differences (primarily loss of methylation) in depressed vs. controls identified a number of cellular functions. Of note, the fourth most significant gene set identified was involved in programmed cell death and 74% of the genes in this set were associated with neuronal cell death. These changes in methylation dynamics suggest a possible mechanism linking neuronal cell death associated with oxidative stress and inflammation in the depressed brain

The dynamics of human bone marrow adipose tissue in response to feeding and fasting

The administration of a high fat content diet (HFD) is an accelerating factor for metabolic syndrome, impaired glucose tolerance, and early type 2 diabetes. The present study aims to assess the impact of a high fat diet or acute weight gain on human marrow adipose tissue. Adipose tissues secrete numerous active substances termed adipokines, including adiponectin, leptin, resistin, interleukin-6 (IL-6), etc. Adipokines physiologically regulate development, metabolism, eating behavior, fat storage, insulin sensitivity, hemostasis, blood pressure, immunity, and inflammation. Our objective is to determine the effect of HFD on adipokines from marrow adipose tissue, as well as, the effect of HFD on resistin, TNF?, RCAN2 and SEMA3E/PLXND1 gene expression. Marrow serum, peripheral blood serum as well as marrow adipocytes from healthy adult human who underwent either 10 days of fasting or 10 days of HFD, were collected according to published protocols. To analyze the expression of resistin, IL-6, TNF? and adiponectin in human serum from marrow and peripheral blood, we used DuoSet ELISA kit (R&D systems) respectively. To analyze the gene expression of resistin, TNF?, RCAN2 and SEMA3E/PLXND1 on marrow adipocytes, qRT-PCR were performed. All primers were synthesized by Integrated DNA Technologies (Coralville, IA). Results were normalized to GAPDH and all samples were run in duplicate. Our results show that in paired aspirates, resistin increased markedly with a HFD, but not with fasting, and not in the circulation, without significant changes on adiponectin neither IL-6 levels. Resistin is a cytokine produced in WAT (adipocytes in rodents, macrophages in human) and is thought to mediate type 2 diabetes mellitus (T2DM) and cardiovascular disease and to mark macrophage activation and TLR4 signaling. In our previous studies with mouse models, PLXND1 is highly expressed on marrow stromal cells and has been linked to adiposity and type 2 diabetes. Also, inhibition of the SEMA3E(ligand)/PLXND1(receptor) axis markedly reduced adipose tissue inflammation and improved systemic insulin resistance in mouse model. PLXND1 also was one of the most highly expressed genes in a MSCs from a mouse with high marrow adiposity and consistent with our findings noted in human volunteers. RCAN2, one of the three main regulators of calcineurin, is located 43.7 Mb on mouse chromosome 17 and in a QTL study of marrow fat from DO strains, that region gave the highest LOD score. Our data show that expression of SEMA3E/PLXND1, RCAN2 and TNF? were increased on marrow adipocytes from the HFD volunteers. Also we identified up-regulation of the macrophage gene marker, EMR-1 (homologous to F4/80 in mice), suggestive of an inflammatory response in the marrow of normal volunteers on a HFD but not fasting. The bone microenviroment can be modulated by various factors including aging, obesity, and inflammation. Stress signal could be modulated by SEMA3E/PLXND1 axis as a chemoattractant for macrophages, provoking adipose tissue inflammation, and also by RCAN2, through calcineurin activity, which is indispensable for osteoclast differentiation, creating less bone resorption and impaired normal bone homeostasis. Further analysis are needed to understanding the immune response in the context of marrow adiposity in humans and mouse models