The Function of the Metals in Regulating Epigenetics During Parkinson’s Disease

Parkinson’s means Parkinson’s disease, a chronic degenerative disease of central nervous system. The main area which is affected by this disease is motor system. Since it firstly founded by James Parkinson in his 1817 publication, nowadays, people still have lots of questions about this disease. This review mainly summarizes the epigenetics of Parkinson’s. DNA methylation is one of the epigenetic mechanisms of Parkinson’s. During the development of disease, global hypomethylation, and hypermethylation happen in different areas of patients. Another epigenetic mechanism is histone modification. People believe that some metals can induce Parkinson’s disease by modulating epigenetic mechanisms. This review summarizes the relationships between different metals and Parkinson’s disease. However, the specific roles of most metals in epigenetics are still unknown, which need further research.

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.

Molecular Profiling of Decitabine Response in MDS and AML Patients

The underlying molecular effects of decitabine treatment in MDS and AML patients are poorly understood. To systematically uncover the global genomic and transcriptomic alterations induced by decitabine in vivo, we evaluated a series of primary bone marrowf samples from patients treated with decitabine 20 mg/m2 on days 1-10 in 28 day cycles (NCT01687400). Samples were evaluated with: bulk-RNA sequencing (Day 0 & 10, n=29), single-cell RNA sequencing (Day 0 & 10, n=4), whole-genome bisulfite sequencing (WGBS, Day 0, 10, & 28, n=29), and exome sequencing (Day 0 & 28 n=44). Cases were selected for RNA-Seq and WGBS based on adequate sample availability, and founding clone mutations that were present in at least 75% of the cells in each sample on day 0. As expected, interpatient heterogeneity dominated global transcriptional variance across the bulk-RNA sequencing dataset, due to the unique mutational and cellular heterogeneity of each sample. We identified 638 significantly differentially expressed genes (DEGs) between day 0 and day 10. MSigDB-geneset analysis identified significant pathway enrichment of the day 10 upregulated genesets for myeloid maturation, immune activation, and cell cycle regulation, while down-regulated genesets were enriched for erythroid pathways, oxidative phosphorylation, cellular senescence, and metabolic processes (FDR < 0.05). Upregulated genes were strongly associated with increased expression in external datasets of flow-sorted mature myeloid cells (i.e. Bloodspot), whereas downregulated genes correlated with decreased expression in mature populations, further suggesting that decitabine induces myeloid maturation in AML and MDS patients. Application of the Telescope computational pipeline identified increased overall expression of endogenous retroviruses (ERVs) at day 10 (p < 0.01). Interpatient heterogeneity was again evident, and ERV activation was limited to 18 ERV families (FDR <0.05), which included HERVH, HERV3, HERV9, HERV30, LTR19, and HERVE. Across the dataset, overall ERV expression did not correlate significantly with GSEA-identified transcriptional signatures of inflammatory response or interferon signatures, although rare outlier cases could be identified with strong correlations (but only borderline significance). No clinical features were significantly associated with RNA-Seq transcriptional signatures (response, survival, TP53 mutation status, blast counts, ERV family activation, etc.). Single-cell RNA sequencing analysis detected induction of interferon signatures and inhibition of erythroid signatures by decitabine within subsets of predominantly malignant bone marrow cells (CD3e-CD19-), corroborating the findings from bulk-RNA sequencing. Whole-genome bisulfite sequencing analysis revealed global hypomethylation at day 10, with incomplete re-methylation by day 28 in nearly all cases. Hypomethylation and remethylation patterns were uniform across the genome, and indifferent to local genomic context. Similar hypomethylation signatures were noted at promoters, transcriptional start sites, DNase I hypersensitivity sites, CCCTC binding factor (CTCF) sites, and transcription factor binding sites, suggesting that decitabine-induced hypomethylation effects were not modified by local genomic contexts, and were not consistently associated with transcriptional changes. Of the 44 cases evaluated with serial exomes, 21 had an absolute reduction in bone marrow blasts of at least 10% on day 28, and could be evaluated for differentiation effects. Of these, all but one exhibited greater morphologic blast clearance than founding clone clearance, suggesting the persistence of malignant cells that no longer displayed blast morphology, consistent with decitabine-induced maturation of malignant cells. In summary, this study provides insights into in vivo mechanisms of decitabine activity in AML and MDS patients, which includes global hypomethylation, myeloid maturation, induction of an inflammatory response, activation of specific ERV families, and strong interpatient heterogeneity. However, no specific transcriptional or epigenetic biomarkers emerged that could serve as effective predictors of decitabine responses. Disclosures Welch: ArcherDx: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees; Notable labs: Research Funding; Janssen research: Research Funding.

Analysis of retrotransposon subfamily DNA methylation reveals novel early epigenetic changes in chronic lymphocytic leukemia

Retrotransposons such as LINE-1 and Alu comprise >25% of the human genome. While global hypomethylation of these elements has been widely reported in solid tumours, their epigenetic dysregulation is yet to be characterised in chronic lymphocytic leukaemia, and there has been scant consideration of their evolutionary history that mediates sensitivity to hypomethylation. Here, we developed an approach for locus- and evolutionary subfamily-specific analysis of retrotransposons using the Illumina Infinium Human Methylation 450K microarray platform, which we applied to publicly-available datasets from chronic lymphocytic leukaemia and other haematological malignancies. We identified 9,797 microarray probes mapping to 117 LINE-1 subfamilies and 13,130 mapping to 37 Alu subfamilies. Of these, 10,782 were differentially methylated (PFDR<0.05) in chronic lymphocytic leukaemia patients (n=139) compared with healthy individuals (n=14), with enrichment at enhancers (p=0.002). Differential methylation was associated with evolutionary age of LINE-1 (r2=0.31, p=0.003) and Alu (r2=0.74, p=0.002) elements, with greater hypomethylation of older subfamilies (L1M, AluJ). Locus-specific hypomethylation was associated with differential expression of proximal genes, including DCLK2, HK1, ILRUN, TANK, TBCD, TNFRSF1B and TXNRD2, with higher expression of DCLK2 and TNFRSF1B associated with reduced patient survival. Hypomethylation at nine loci was highly frequent in chronic lymphocytic leukaemia (>90% patients) but not observed in healthy individuals or other leukaemias, and was detectable in blood samples taken prior to chronic lymphocytic leukaemia diagnosis in 9 of 82 individuals from the Melbourne Collaborative Cohort Study. Our results demonstrate differential methylation of retrotransposons in chronic lymphocytic leukaemia by their evolutionary heritage that modulates expression of proximal genes.

Molecular Scoring of Hepatocellular Carcinoma for Predicting Metastatic Recurrence and Requirements of Systemic Chemotherapy

Hepatocellular carcinoma (HCC) causes one of the most frequent cancer-related deaths; an HCC subset shows rapid progression that affects survival. We clarify molecular features of aggressive HCC, and establish a molecular scoring system that predicts metastasis after curative treatment. In total, 125 HCCs were examined for TP53, CTNNB1, and TERT promoter mutation, methylation of 8 tumor suppressor genes, and 3 repetitive DNA sequences to estimate promoter hypermethylation and global hypomethylation. A fractional allelic loss (FAL) was calculated to represent chromosomal instability through microsatellite analysis. Molecular subclasses were determined using corresponding and hierarchical clustering analyses. Next, twenty-five HCC patients who underwent liver transplantation were analyzed for associations between molecular characteristics and metastatic recurrence; survival analyses were validated using a publicly available dataset of 376 HCC cases from the Cancer Genome Atlas (TCGA). An HCC subtype characterized by TP53 mutation, high FAL, and global hypomethylation was associated with aggressive tumor characteristics, like vascular invasion; CTNNB1 mutation was a feature of the less-progressive phenotype. A number of molecular risk factors, including TP53 mutation, high FAL, significant global hypomethylation, and absence of CTNNB1 mutation, were noted to predict shorter recurrence-free survival in patients who underwent liver transplantation (p = 0.0090 by log-rank test). These findings were validated in a cohort of resected HCC cases from TCGA (p = 0.0076). We concluded that molecular risks determined by common genetic and epigenetic alterations could predict metastatic recurrence after curative treatments, and could be a marker for considering systemic therapy for HCC patients.

Assessment of Global Methylation in Paraffin Embedded Prostatic Tissues and Cell Lines Using Flow Cytometry

Background. The aim of this study is to measure global 5-methylcystosine (5MeC) methylation in paraffin embedded prostatic tissues and cell lines using flow cytometry. Methods. Cell/nuclei suspension from 10 cases of benign prostatic hyperplasia (BPH), 10 cases of prostatic adenocarcinoma, and two prostatic cell lines (PNT1A and LNCaP) were prepared using modified heat pretreatment technique. 5MeC global methylation was assessed by flow cytometry of cell/nuclei suspension and immunostaining of tissue sections. Results. Higher percentage of positively stained cells (PPSC) and mean channel fluorescence (MCF) were detected in PNT1A cell line and BPH cell/nuclei suspensions as compared to LNCaP cell lines and adenocarcinoma cell/nuclei suspensions. Lower scores of 5MeC immunostaining were observed in all prostate adenocarcinoma tissue sections as compared to BPH sections indicating global hypomethylation in prostate adenocarcinoma. Two distinctive populations of cells were detected in histograms generated from most of the BPH cell/nuclei suspensions. Conclusion. The study developed a novel technique that could measure 5MeC global methylation in paraffin embedded prostatic tissues. This represents a rapid and objective assessment of methylation and when combined with tissue micro-dissection and cell sorting, this technique could be applied to larger tissue samples such as post radical prostatectomy and transurethral resected specimens.