Specific DNA Methylation Research Articles

The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models

Taxanes are standard therapy in clinical practice for metastatic breast cancer; however, primary or acquired chemoresistance are a common cause of mortality. Breast cancer patient-derived xenografts (PDX) are powerful tools for the study of cancer biology and drug treatment response. Specific DNA methylation patterns have been associated to different breast cancer subtypes but its association with chemoresistance remains unstudied. Aiming to elucidate docetaxel resistance mechanisms, we performed genome-wide DNA methylation in breast cancer PDX models, including luminal and triple-negative breast cancer (TNBC) models sensitive to docetaxel, their matched models after emergence of chemoresistance and residual disease after short-term docetaxel treatment. We found that DNA methylation profiles from breast cancer PDX models maintain the subtype-specific methylation patterns of clinical samples. Two main DNA methylation clusters were found in TNBC PDX and remain stable during the emergence of docetaxel resistance; however, some genes/pathways were differentially methylated according to docetaxel response. A DNA methylation signature of resistance able to segregate TNBC based on chemotherapy response was identified. Transcriptomic profiling of selected sensitive/resistant pairs and integrative analysis with methylation data demonstrated correlation between some differentially methylated and expressed genes in docetaxel-resistant TNBC PDX models. Multiple gene expression changes were found after the emergence of docetaxel resistance in TNBC. DNA methylation and transcriptional changes identified between docetaxel-sensitive and -resistant TNBC PDX models or residual disease may have predictive value for chemotherapy response in TNBC. IMPLICATIONS: Subtype-specific DNA methylation patterns are maintained in breast cancer PDX models. While no global methylation changes were found, we uncovered differentially DNA methylated and expressed genes/pathways associated with the emergence of docetaxel resistance in TNBC.

Isomorphic diffuse glioma is a morphologically and molecularly distinct tumour entity with recurrent gene fusions of MYBL1 or MYB and a benign disease course.

The "isomorphic subtype of diffuse astrocytoma" was identified histologically in 2004 as a supratentorial, highly differentiated glioma with low cellularity, low proliferation and focal diffuse brain infiltration. Patients typically had seizures since childhood and all were operated on as adults. To define the position of these lesions among brain tumours, we histologically, molecularly and clinically analysed 26 histologically prototypical isomorphic diffuse gliomas. Immunohistochemically, they were GFAP-positive, MAP2-, OLIG2- and CD34-negative, nuclear ATRX-expression was retained and proliferation was low. All 24 cases sequenced were IDH-wildtype. In cluster analyses of DNA methylation data, isomorphic diffuse gliomas formed a group clearly distinct from other glial/glio-neuronal brain tumours and normal hemispheric tissue, most closely related to paediatric MYB/MYBL1-altered diffuse astrocytomas and angiocentric gliomas. Half of the isomorphic diffuse gliomas had copy number alterations of MYBL1 or MYB (13/25, 52%). Gene fusions of MYBL1 or MYB with various gene partners were identified in 11/22 (50%) and were associated with an increased RNA-expression of the respective MYB-family gene. Integrating copy number alterations and available RNA sequencing data, 20/26 (77%) of isomorphic diffuse gliomas demonstrated MYBL1 (54%) or MYB (23%) alterations. Clinically, 89% of patients were seizure-free after surgery and all had a good outcome. In summary, we here define a distinct benign tumour class belonging to the family of MYB/MYBL1-altered gliomas. Isomorphic diffuse glioma occurs both in children and adults, has a concise morphology, frequent MYBL1 and MYB alterations and a specific DNA methylation profile. As an exclusively histological diagnosis may be very challenging and as paediatric MYB/MYBL1-altered diffuse astrocytomas may have the same gene fusions, we consider DNA methylation profiling very helpful for their identification.

Adipose tissue mitochondrial dysfunction in human obesity is linked to a specific DNA methylation signature in adipose-derived stem cells

This epigenome-wide association study in stromal/stem cells (ASCs), derived from subcutaneous adipose tissue samples of lean and obese subjects, revealed a specific DNA methylation signature in adipocyte precursors associated with obesity, which has a significant impact on the metabolic phenotype and the mitochondrial function of mature adipocytes.

Specific Glioma Prognostic Subtype Distinctions Based on DNA Methylation Patterns

DNA methylation is an important regulator of gene expression and may provide an important basis for effective glioma diagnosis and therapy. Here, we explored specific prognosis subtypes based on DNA methylation status using 653 gliomas from The Cancer Genome Atlas (TCGA) database. Five subgroups were distinguished by consensus clustering using 11,637 cytosines preceding a guanosine (CpGs) that significantly influenced survival. The specific DNA methylation patterns were correlated with age, tumor stage, and prognosis. Additionally, weighted gene co-expression network analysis (WGCNA) analysis of CpG sites revealed that 11 of them could distinguish the samples into high- and low-methylation groups and could classify the prognostic information of samples after cluster analysis of the training set samples using the hierarchical clustering algorithm. Similar results were obtained from the test set and 12 glioma patients. Moreover, in vitro experiments revealed an inverse relationship between methylation level and migration ability or insensitivity to temozolomide (or radiotherapy) of glioma cells based on the final prognostic predictor. Thus, these results suggested that the model constructed in this study could provide guidance for clinicians regarding the prognosis of various epigenetic subtypes.

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.

Dynamic 3D chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of 3D genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell Chromatin Conformation Capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. To address these challenges, we have developed single-nucleus methyl-3C sequencing (sn-m3C-seq) to capture chromatin organization and DNA methylation information and robustly separate heterogeneous cell types. Applying this method to >4,200 single human brain prefrontal cortex cells, we reconstruct cell-type specific chromatin conformation maps from 14 cortical cell types. These datasets reveal the genome-wide association between cell-type specific chromatin conformation and differential DNA methylation, suggesting pervasive interactions between epigenetic processes regulating gene expression.

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer\u2019s disease

BackgroundAlzheimer’s disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs.ResultsComparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p value ≤ 0.05. Several of the affected genes are primarily associated with neuronal functions and pathologies and do not display disease-associated differences in gene expression in blood. The DNA methylation mark in ADARB2 gene was found to be differentially methylated also in the anterior hippocampus, including entorhinal cortex, of non-twin cases and controls. Targeted bisulfite pyrosequencing of the DNA methylation mark in ADARB2 gene in 62 Finnish and Swedish twin pairs revealed that, in addition to the disease status, DNA methylation of this region is influenced by gender, age, zygosity, APOE genotype, and smoking. Further analysis of 120 Swedish twin pairs indicated that this specific DNA methylation mark is not predictive for Alzheimer’s disease and becomes differentially methylated after disease onset.ConclusionsDNA methylation differences can be detected in the peripheral blood of twin pairs discordant for Alzheimer’s disease. These DNA methylation signatures may have value as disease markers and provide insights into the molecular mechanisms of pathogenesis. We found no evidence that the DNA methylation marks would be associated with gene expression in blood. Further studies are needed to elucidate the potential importance of the associated genes in neuronal functions and to validate the prognostic or diagnostic value of the individual marks or marker panels.

DNA methylation signature is prognostic of choroid plexus tumor aggressiveness

BackgroundHistological grading of choroid plexus tumors (CPTs) remains the best prognostic tool to distinguish between aggressive choroid plexus carcinoma (CPC) and the more benign choroid plexus papilloma (CPP) or atypical choroid plexus papilloma (aCPP); however, these distinctions can be challenging. Standard treatment of CPC is very aggressive and often leads to severe damage to the young child’s brain. Therefore, it is crucial to distinguish between CPC and less aggressive entities (CPP or aCPP) to avoid unnecessary exposure of the young patient to neurotoxic therapy. To better stratify CPTs, we utilized DNA methylation (DNAm) to identify prognostic epigenetic biomarkers for CPCs.MethodsWe obtained DNA methylation profiles of 34 CPTs using the HumanMethylation450 BeadChip from Illumina, and the data was analyzed using the Illumina Genome Studio analysis software. Validation of differentially methylated CpG sites chosen as biomarkers was performed using pyrosequencing analysis on additional 22 CPTs. Sensitivity testing of the CPC DNAm signature was performed on a replication cohort of 61 CPT tumors obtained from Neuropathology, University Hospital Münster, Germany.ResultsGenerated genome-wide DNAm profiles of CPTs showed significant differences in DNAm between CPCs and the CPPs or aCPPs. The prediction of clinical outcome could be improved by combining the DNAm profile with the mutational status of TP53. CPCs with homozygous TP53 mutations clustered as a group separate from those carrying a heterozygous TP53 mutation or CPCs with wild type TP53 (TP53-wt) and showed the worst survival outcome. Specific DNAm signatures for CPCs revealed AK1, PER2, and PLSCR4 as potential biomarkers for CPC that can be used to improve molecular stratification for diagnosis and treatment.ConclusionsWe demonstrate that combining specific DNAm signature for CPCs with histological approaches better differentiate aggressive tumors from those that are not life threatening. These findings have important implications for future prognostic risk prediction in clinical disease management.

Epigenetic Reprogramming of Immune Cells in Women With PCOS Impact Genes Controlling Reproductive Function.

Polycystic ovary syndrome (PCOS) is a chronic disease affecting reproductive function and whole-body metabolism. Although the etiology is unclear, emerging evidence indicates that the epigenetics may be a contributing factor. To determine the role of global and genome-wide epigenetic modifications in specific immune cells in PCOS compared with controls and whether these could be related to clinical features of PCOS. Cross-sectional study. Women with (n = 17) or without PCOS (n = 17). Recruited from the general community. Isolated peripheral blood mononuclear cells were analyzed using multicolor flow cytometry methods to determine global DNA methylation levels in a cell-specific fashion. Transcriptomic and genome-wide DNA methylation analyses were performed on T helper cells using RNA sequencing and reduced representation bisulfite sequencing. Women with PCOS had lower global DNA methylation in monocytes (P = 0.006) and in T helper (P = 0.004), T cytotoxic (P = 0.004), and B cells (P = 0.03). Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5581 differentially methylated CpG sites. Functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. However, these genes were not altered at the transcriptomic level. It was shown that PCOS is associated with global and gene-specific DNA methylation remodeling in a cell type-specific manner. Further investigation is warranted to determine whether epigenetic reprogramming of immune cells is important in determining the different phenotypes of PCOS.

Development of a body fluid identification multiplex via DNA methylation analysis.

The goal of this study is to develop an epigenetic multiplex for body fluid identification based on tissue specific DNA methylation. A series of genetic loci capable of discerning the origin of DNA as coming from saliva, blood, vaginal epithelia, or semen were used for this application. The markers - BCAS4, CG06379435, VE_8, and ZC3H12D - were amplified together and then sequenced via pyrosequencing. Methylation values for cytosine guanine dinucleotide (CpG) sites at each locus were then measured across the four markers. In total, 124 samples were collected, and bisulfite modified to convert unmethylated DNA to uracil. This converted DNA was then amplified via multiplex PCR with reverse primers containing a biotin molecule. Biotinylated PCR products were then analyzed using pyrosequencing to generate a series of pyrograms containing 18 CpG sites. The percent methylation at each CpG site was determined, and then agglomerative hierarchical cluster analysis was used to create a model to indicate sample origin. Further analysis reduced the number of CpG sites required for optimal determination of body fluid type to five. This study demonstrates an efficient multiplexed body fluid identification process utilizing DNA methylation that can be easily implemented in forensic laboratories.

DNA methylation-based classification and identification of renal cell carcinoma prognosis-subgroups

BackgroundRenal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. The combination of DNA methylation and gene expression data can improve the classification of tumor heterogeneity, by incorporating differences at the epigenetic level and clinical features.MethodsIn this study, we identified the prognostic methylation and constructed specific prognosis-subgroups based on the DNA methylation spectrum of RCC from the TCGA database.ResultsSignificant differences in DNA methylation profiles among the seven subgroups were revealed by consistent clustering using 3389 CpGs that indicated that were significant differences in prognosis. The specific DNA methylation patterns reflected differentially in the clinical index, including TNM classification, pathological grade, clinical stage, and age. In addition, 437 CpGs corresponding to 477 genes of 151 samples were identified as specific hyper/hypomethylation sites for each specific subgroup. A total of 277 and 212 genes corresponding to DNA methylation at promoter sites were enriched in transcription factor of GKLF and RREB-1, respectively. Finally, Bayesian network classifier with specific methylation sites was constructed and was used to verify the test set of prognoses into DNA methylation subgroups, which was found to be consistent with the classification results of the train set. DNA methylation-based classification can be used to identify the distinct subtypes of renal cell carcinoma.ConclusionsThis study shows that DNA methylation-based classification is highly relevant for future diagnosis and treatment of renal cell carcinoma as it identifies the prognostic value of each epigenetic subtype.

Abstract 4222: Omega-3 fatty acids produce DNA methylation changes in inflammation-related genes and pathways with implication of toll-like receptor signaling

Abstract Introduction Omega-3 polyunsaturated fatty acids (n-3 PUFA) have been studied for potential health benefits in many diseases including breast cancer. The preventive effects of n-3 PUFAs may relate in part to inhibition of chronic, low-grade inflammation. Of interest is the role of n-3 PUFAs in modulating pro-inflammatory gene expression via epigenetic factors such as DNA methylation (DNAm). Methods DNA methylation of PBMCs obtained at 0 and 6 months of n-3 PUFA supplementation was assessed via reduced representation bisulfite sequencing (RRBS). PBMC samples were obtained from women at high risk for breast cancer during a randomized clinical trial investigating the effects of different n-3 PUFA doses. The dosing arm selected for this study was 5 g of EPA+DHA/day, with baseline and 6 month samples (n=10). DNAm was quantified using Bismark from trimmed, pass filter reads and analyzed with MethylKit to determine n-3 PUFA treatment specific DNAm changes. Results Global DNAm showed no change after 6 months of n-3 PUFA treatment; however, we detected 30,974 differentially methylated CpGs (DMCs) across the genome. DMCs, both genome-wide and in gene promoters, where DNAm can regulate gene expression, were significantly enriched for hypermethylation events after treatment. Focusing the analysis on pro-inflammatory signaling mediators led to identification of candidate gene promoter DMCs involved in several inflammation-related pathways. Four pathways were significantly enriched for both DMCs and DMC hypermethylation events even when accounting for the genome-wide trend toward hypermethylated DMCs (hypergeometric test p-value < 0.001). The Toll-Like Receptor Pathway (TLR) genes harbored the most DNAm changes post n-3 PUFA treatment. Conclusion Our findings demonstrate that n-3 PUFA supplementation can result in inflammation-related changes stemming from PBMC methylome perturbation. The results suggest the TLR pathway as a potential mechanism for the anti-inflammatory effects of EPA and DHA. Functional studies are needed to confirm our current observation. Citation Format: David E. Frankhouser, Sarah Woelke, Michael Sovic, Ralf Bundschuh, Pearlly Yan, Lisa D. Yee. Omega-3 fatty acids produce DNA methylation changes in inflammation-related genes and pathways with implication of toll-like receptor signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4222.

Correlation Between Altered DNA Methylation of Intergenic Regions of ITPR3 and Development of Delayed Cerebral Ischemia in Patients with Subarachnoid Hemorrhage

Delayed cerebral ischemia (DCI) is related to the major causes of morbidity and mortality in patients following subarachnoid hemorrhage (SAH); however, little is known about the role of epigenetics in the pathogenesis of DCI. We investigated the specific DNA methylation profile that may affect the expression of inositol 1-,4-,5-trisphosphate receptor (ITPR3) responsible for cerebral vasospasm following SAH. We prospectively studied patients with SAH between March 2015 and October 2018. The degree of methylation in the distal intergenic region (IGR) located on ITPR3 and gene expression were measured using methylation-specific polymerase chain reaction (MSP) and quantitative real-time polymerase chain reaction (qPCR). To investigate the regulatory mechanims of DNA hypermethylation, we further analyzed the mRNA expression of DNA methyltransferase (DNMT1) and ten-eleven translocation enzymes (TET1, TET2, and TET3). A total of 42 patients were included in our analysis. Patients with SAH and DCI had significantly higher levels of methylation intensity of distal IGR upstream of ITPR3 than those without DCI (median, 0.941 [interquartile range (IQR), 0.857-0.984] versus (0.670 [IQR, 0.543-0.761]; P < 0.001). In addition, patients with DCI showed decreased mRNA expression of ITPR3 compared with patients without DCI (median, 0.039 [IQR, 0.030-0.045] vs. 0.047 [IQR, 0.038-0.064]; P= 0.0328). Patients with DCI had higher DNMT1 expression (P < 0.001) and lower TET1 expression (P= 0.040) than those without DCI; however, differences in TET2 and TET3 levels between the 2 groups were not statistically significant. Hypermethylation of the distal IGR located upstream of ITPR3 is related to greater DCI development in patients with SAH. Further studies of the precise mechanisms of methylation degree and DCI development using invitro and invivo models are needed.

Circadian glucocorticoid oscillations preserve a population of adult hippocampal neural stem cells in the aging brain

A decrease in adult hippocampal neurogenesis has been linked to age-related cognitive impairment. However, the mechanisms involved in this age-related reduction remain elusive. Glucocorticoid hormones (GC) are important regulators of neural stem/precursor cells (NSPC) proliferation. GC are released from the adrenal glands in ultradian secretory pulses that generate characteristic circadian oscillations. Here, we investigated the hypothesis that GC oscillations prevent NSPC activation and preserve a quiescent NSPC pool in the aging hippocampus. We found that hippocampal NSPC populations lacking expression of the glucocorticoid receptor (GR) decayed exponentially with age, while GR-positive populations decayed linearly and predominated in the hippocampus from middle age onwards. Importantly, GC oscillations controlled NSPC activation and GR knockdown reactivated NSPC proliferation in aged mice. When modeled in primary hippocampal NSPC cultures, GC oscillations control cell cycle progression and induce specific genome-wide DNA methylation profiles. GC oscillations induced lasting changes in the methylation state of a group of gene promoters associated with cell cycle regulation and the canonical Wnt signaling pathway. Finally, in a mouse model of accelerated aging, we show that disruption of GC oscillations induces lasting changes in dendritic complexity, spine numbers and morphology of newborn granule neurons. Together, these results indicate that GC oscillations preserve a population of GR-expressing NSPC during aging, preventing their activation possibly by epigenetic programming through methylation of specific gene promoters. Our observations suggest a novel mechanism mediated by GC that controls NSPC proliferation and preserves a dormant NSPC pool, possibly contributing to a neuroplasticity reserve in the aging brain.

MiR‑29 promoter and enhancer methylation identified by pyrosequencing in Burkitt lymhoma cells: Interplay between MYC and miR‑29 regulation.

Deregulation of microRNA expression plays a significant role in several cancer types including Burkitt lymphoma (BL). MicroRNA genes may be regulated through epigenetic mechanisms, such as specific histone modifications and/or DNA methylation of CpG islands in promoter regions, or by regions that are located next to microRNA genes. Given the regulatory role of MYC in miR‑29 expression, methylation as an additional mechanism for miR‑29 silencing was investigated. Methylation of miR‑29a/b/c in BL tumour samples and BL cell lines (BL41 and Raji) was assessed by pyrosequencing assay. BL cells were treated with 5‑aza‑2'‑deoxicitidine (decitabine) and evaluated for miR‑29a/b/c expression and methylation status. MYC, DNMT1 and DNMT3B protein expression were accessed by western blotting. For Epstein‑Barr virus (EBV) microRNA (miR)‑BART6 inhibition, the cells were transiently transfected with anti‑BART6‑5p. BL tumour samples and BL cell lines presented miR‑29a/b1 and miR‑29b2/c genes methylated in CpG sites located in both the promoter and enhancer regions. The treatment of BL cells with decitabine reduced methylation, induced miR‑29s expression and downregulated MYC protein levels in a dose‑dependent manner. Notably, inhibition of EBV miR‑BART6‑5p combined with decitabine enhanced miR‑29 expression in an EBV‑BL cell line. In conclusion, the miR‑29a/b1 and miR‑29b2/c genes have methylated CpG sequences at promoter and enhancer regions that may contribute to the regulation of miR‑29 expression in BL tumours. The present findings indicated interplay between MYC and miR‑29 regulation, highlighting the potential role of EBV‑miRNAs in miR‑29 regulation for BL pathogenesis.

Methylation profile of genes involved in inflammation, in the blood from pregnancies with maternal preeclampsia due to untreated gestational diabetes mellitus.

To investigate DNA methylation changes in peripheral blood from patients with gestational diabetes mellitus (GDM) and preeclampsia (PE) due to poorly treated GDM. Eighteen pregnant women participated in the study: 6 with GDM, 6 with PE, and 6 healthy controls. The promoter methylation status of genes was profiled using the Human Inflammatory Response and Autoimmunity EpiTect Methyl II Signature PCR Array profiles. The results were validated with quantitative real-time polymerase chain reaction (qRT-PCR). Fewer inflammation-related genes were significantly hypomethylated in PE cases compared to healthy subjects than in GDM cases. Some of the examined genes show different methylation patterns between GDM and PE. The epigenetic changes observed in this study indicate that GDM and PE exhibit specific DNA methylation profiles, with possible clinical applications.

S137 DNA METHYLATION DYNAMICS IDENTIFY LINEAGE‐SPECIFIC REGULATION PATTERNS OF HEMATOPOIETIC DIFFERENTIATION

Background:The classical hierarchical model of hematopoiesis has been revised based on single‐cell RNA sequencing (scRNAseq) data, which suggest a continuous rather than a step‐wise differentiation process. However, while differentiation trajectories can be inferred from scRNAseq data, it is impossible to discern whether discreet lineage commitment decisions occur at specific points along these trajectories. The existence of such commitment points could still be compatible with a step‐wise differentiation model and their characterization at the molecular level would be essential to accurately model the hematopoietic hierarchy.Aims:This study investigates DNA methylation programming in normal hematopoiesis to identify novel molecular commitment marks during hematopoietic differentiation. We hypothesized that whole genome DNA methylation analysis facilitates the identification of such molecular commitment marks due to the progressive nature of how this mark is programmed during differentiation.Methods:Using tagmentation‐based whole‐genome bisulfite sequencing, we generated a genome‐wide DNA methylation map of murine hematopoiesis. This map encompasses 26 murine hematopoietic cell populations throughout the hematopoietic hierarchy. Per cell population we sequenced at least three independent biological replicates. Differentially methylated regions (DMRs) were identified across all populations using DSS without smoothing. Multi‐tier single cell scRNAseq data were generated from murine bone marrow using the 10X Genomics Chromium Single Cell 3’ kit.Results:Across all cell populations studied, we identified 147,232 DMRs. Hierarchical clustering of these DMRs revealed co‐regulated epigenetic regions that show progressive DNA methylation programming during hematopoietic differentiation. These dynamically regulated regions can be interpreted as specific DNA methylation programs: pan‐hematopoietic‐, lineage‐ and cell type‐specific DNA methylation programs. The DNA methylation programs were strongly enriched in hematopoietic transcription factor binding sites as well as in lineage and cell type‐specific enhancer programs. To gain further insight into how the DNA methylation programming relates to regulation of gene expression, we generated a comprehensive multi‐tier single cell gene expression map of murine bone‐marrow cells. Integration of DNA methylome programs with single cell gene expression profiles revealed a strong anti‐correlation of promoter DNA methylation dynamics and cell‐state specific gene expression patterns. The progressive and lineage‐specific nature of DNA methylation programming occurring during hematopoietic differentiation allowed us to infer a phylogenetic tree of the hematopoietic system, which is solely based on DNA methylation dynamics. We demonstrated that previously defined subpopulations of common myeloid progenitors (CMPs) show distinct DNA methylation patterns: CD55+ CMPs showed megakaryocyte/erythrocyte patterns, while CD55‐ CMPs showed DNA methylation patterns compatible with granulocyte and monocyte differentiation. Furthermore, we showed that the identified DNA methylation programs are conserved across different mouse strains which underlines the broad applicability of this resource.Summary/Conclusion:We provide a novel view on the regulation of hematopoiesis based on DNA methylation dynamics which complements recent findings from scRNAseq studies. Our work provides a rich resource to investigate DNA methylation in normal as well as in abnormal hematopoiesis across a broad range of conditions and mouse strains.

Epigenetic Regulation of Vascular Diseases.

Epigenetic regulatory mechanisms, encompassing diverse molecular processes including DNA methylation, histone post-translational modifications, and noncoding RNAs, are essential to numerous processes such as cell differentiation, growth and development, environmental adaptation, aging, and disease states. In many cases, epigenetic changes occur in response to environmental cues and lifestyle factors, resulting in persistent changes in gene expression that affect vascular disease risk during the lifetime of the individual. Biological aging-a powerful cardiovascular risk factor-is partly genetically determined yet strongly influenced by traditional risk factors, reflecting epigenetic modulation. Quantification of specific DNA methylation patterns may serve as an accurate predictor of biological age-a concept known as the epigenetic clock, which could help to refine cardiovascular risk assessment. Epigenetic reprogramming of monocytes rewires cellular immune signaling and induces a metabolic shift toward aerobic glycolysis, thereby increasing innate immune responses. This form of trained epigenetic memory can be maladaptive, thus augmenting vascular inflammation. Somatic mutations in epigenetic regulatory enzymes lead to clonal hematopoiesis of indeterminate potential, a precursor of hematologic malignancies and a recently recognized cardiovascular risk factor; moreover, epigenetic regulators are increasingly being targeted in cancer therapeutics. Thus, understanding epigenetic regulatory mechanisms lies at the intersection between cancer and cardiovascular disease and is of paramount importance to the burgeoning field of cardio-oncology (Graphic Abstract).

Influence of early adversity on cortisol reactivity, SLC6A4 methylation and externalizing behavior in children of alcoholics

BackgroundChildren of parents with alcoholism face considerable stress, and often have externalizing behaviors. Early adversity is known to affect DNA methylation and the functioning of the HPA axis. We investigated the association of early adversity with cortisol reactivity, 5HTTLPR genotype, site specific DNA methylation in the SLC6A4 gene and externalizing behavior in children of alcoholics (COA), and a matched sample of control children. MethodsWe examined children of alcoholics (N = 50) and age matched control children (N = 50) for exposure to early adversity (both prenatal and postnatal), assessed their salivary cortisol reactivity and evaluated their levels of emotional and behavioral difficulty in terms of externalizing and internalizing behavior. Site-specific DNA methylation at a previously characterized SLC6A4 region was determined in salivary DNA using pyrosequencing. The 5HTTLPR region of the SLC6A4 gene was also genotyped. ResultsCOA had significantly higher experience of early adversity than control children. Cortisol reactivity was reduced in COA, and negatively correlated with early adversity. Both early adversity and cortisol reactivity correlated with externalizing behavior. SLC6A4 methylation was higher in COA, and correlated with early adversity. SLC6A4 genotype did not show association with any of the variables. ConclusionOur study provides further evidence that early adversity is associated with blunted cortisol reactivity, increased site-specific CpG DNA methylation at the SLC6A4 gene, and high externalizing behavior.

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome

BackgroundADNP syndrome is a rare Mendelian disorder characterized by global developmental delay, intellectual disability, and autism. It is caused by truncating mutations in ADNP, which is involved in chromatin regulation. We hypothesized that the disruption of chromatin regulation might result in specific DNA methylation patterns that could be used in the molecular diagnosis of ADNP syndrome.ResultsWe identified two distinct and partially opposing genomic DNA methylation episignatures in the peripheral blood samples from 22 patients with ADNP syndrome. The “epi-ADNP-1” episignature included ~ 6000 mostly hypomethylated CpGs, and the “epi-ADNP-2” episignature included ~ 1000 predominantly hypermethylated CpGs. The two signatures correlated with the locations of the ADNP mutations. Epi-ADNP-1 mutations occupy the N- and C-terminus, and epi-ADNP-2 mutations are centered on the nuclear localization signal. The episignatures were enriched for genes involved in neuronal system development and function. A classifier trained on these profiles yielded full sensitivity and specificity in detecting patients with either of the two episignatures. Applying this model to seven patients with uncertain clinical diagnosis enabled reclassification of genetic variants of uncertain significance and assigned new diagnosis when the primary clinical suspicion was not correct. When applied to a large cohort of unresolved patients with developmental delay (N = 1150), the model predicted three additional previously undiagnosed patients to have ADNP syndrome. DNA sequencing of these subjects, wherever available, identified pathogenic mutations within the gene domains predicted by the model.ConclusionsWe describe the first Mendelian condition with two distinct episignatures caused by mutations in a single gene. These highly sensitive and specific DNA methylation episignatures enable diagnosis, screening, and genetic variant classifications in ADNP syndrome.

Functional Implications of DNA Methylation in Adipose Biology.

The twin epidemics of obesity and type 2 diabetes (T2D) are a serious health, social, and economic issue. The dysregulation of adipose tissue biology is central to the development of these two metabolic disorders, as adipose tissue plays a pivotal role in regulating whole-body metabolism and energy homeostasis (1). Accumulating evidence indicates that multiple aspects of adipose biology are regulated, in part, by epigenetic mechanisms. The precise and comprehensive understanding of the epigenetic control of adipose tissue biology is crucial to identifying novel therapeutic interventions that target epigenetic issues. Here, we review the recent findings on DNA methylation events and machinery in regulating the developmental processes and metabolic function of adipocytes. We highlight the following points: 1) DNA methylation is a key epigenetic regulator of adipose development and gene regulation, 2) emerging evidence suggests that DNA methylation is involved in the transgenerational passage of obesity and other metabolic disorders, 3) DNA methylation is involved in regulating the altered transcriptional landscape of dysfunctional adipose tissue, 4) genome-wide studies reveal specific DNA methylation events that associate with obesity and T2D, and 5) the enzymatic effectors of DNA methylation have physiological functions in adipose development and metabolic function.