5hmC Gene Signature Predicts the Treatment Response to Azacitidine with High-Dose Cytarabine and Mitoxantrone in AML

Introduction Acute myeloid leukemia (AML) is an aggressive disease with genetic and phenotypic heterogeneity that results in a highly variable response to standard chemotherapy. Azacitidine (AZA) is a hypomethylating agent (HMA) and has been investigated in combination with intensive chemotherapy as an epigenetic primer to sensitize leukemic cells to treatment. In a phase 1 trial, this regimen was safe and well-tolerated with overall response rate (CR+CRi) of 61% and complete remission rate of 41% (Cahill et al, Blood Adv 2020). Predictive biomarkers for response to this treatment strategy have not yet been identified. Since 5-hydroxymethylcytosine (5hmC) is an epigenetic biomarker in cancer, we hypothesized that Nano-5hmC-Seal sequencing technology may serve as a novel approach to identifying 5hmC profiles predictive of treatment response to epigenetic priming. Methods We performed RNA-seq gene expression and Nano-5hmC-Seal DNA profiling from peripheral blood/bone marrow samples of patients with high-risk AML to identify potential 5hmC profile biomarkers and gene expression changes (Figure 1A). Patients (n=46) were treated in a 3+3 dose-escalation scheme of AZA (37.5 mg/m 2, 50 mg/m 2, or 75 mg/m 2) on days 1-5 followed by high-dose cytarabine (3000 mg/m 2) and mitoxantrone (30 mg/m 2) (AZA-HiDAC-Mito) on day 6 and day 10 in a phase 1 trial previously reported (Cahill et al, Blood Adv 2020). We compared pre-treatment RNA-seq gene expression and 5hmC DNA profiles between responders (CR+CRi) and non-responders, as well as between pre-treatment and after 5 days of AZA for individual patients. We used an XGBoost machine learning model in Python based on a training set of patients to develop a 5hmC gene signature to predict response to AZA-HiDAC-Mito in an independent test set of patients. We compared continuous variables with two-tailed Student's t-test and used the Kaplan-Meier method with log-rank test for survival analysis. Results Thirty-three patients (72%) had adequate RNA samples for RNA-seq gene expression analysis. Eighteen responded to treatment (CR +CRi) and were enriched with gene expression patterns involved in cell-cell interaction and activation of cell cycle, while non-responders (n=15) had a higher expression of leukemic stem cell (LSC) signatures. There was no difference in gene expression profile when comparing pre-treatment samples to day 5 samples after AZA exposure. From the 5hmC profiling [n=40 (87%) patients with adequate samples], increased 5hmC in LSC genes was associated with treatment resistance to AZA-HiDAC-Mito (p=0.044). The number of differentially hydroxy-methylated genes (DhMGs) increased with higher doses of AZA exposure suggesting a dose-dependent epigenetic effect from AZA. Patients with a greater number of DhMGs following 5 days of AZA treatment had improved survival (p=0.015) (Figure 1B). Using the 5hmC-based XGBoost machine learning model comparing 5hmC profiles between responders to non-responders from a training set of patients (n=22), we developed an 11-gene 5hmC pre-treatment signature (including SKP1, WNT8A, CYP2E1, and NBPF9) to predict treatment response. The model was highly effective in predicting response to therapy, with an area under the curve (AUC) of 0.86 in an independent test set of patients (n=18) treated with AZA-HiDAC-Mito (Figure 1C). Conclusion In patients with AML treated with AZA-HiDAC-Mito, a pre-treatment LSC gene expression signature enriched with 5hmC was associated with treatment resistance. More DhMGs at day 5 appear to be a dose-dependent epigenetic effect that is induced by AZA and is associated with longer survival despite the absence of an immediate change in gene expression levels. An 11-gene 5hmC pre-treatment signature may be a predictive biomarker for AZA-HiDAC-Mito therapy and other HMA-based approaches. These findings warrant validation in a larger prospective trial. Figure 1 Figure 1. Disclosures Zhang: Bristol-Myers Squibb: Current Employment. Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. Odenike: Celgene, Incyte, AstraZeneca, Astex, NS Pharma, AbbVie, Gilead, Janssen, Oncotherapy, Agios, CTI/Baxalta, Aprea: Research Funding; AbbVie, Celgene, Impact Biomedicines, Novartis, Taiho Oncology, Takeda: Consultancy. He: Epican Genetech: Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company.

NAD Modulates DNA Methylation and Cell Differentiation

Nutritional intake impacts the human epigenome by directing epigenetic pathways in normal cell development via as yet unknown molecular mechanisms. Consequently, imbalance in the nutritional intake is able to dysregulate the epigenetic profile and drive cells towards malignant transformation. Here we present a novel epigenetic effect of the essential nutrient, NAD. We demonstrate that impairment of DNMT1 enzymatic activity by NAD-promoted ADP-ribosylation leads to demethylation and transcriptional activation of the CEBPA gene, suggesting the existence of an unknown NAD-controlled region within the locus. In addition to the molecular events, NAD- treated cells exhibit significant morphological and phenotypical changes that correspond to myeloid differentiation. Collectively, these results delineate a novel role for NAD in cell differentiation, and indicate novel nutri-epigenetic strategies to regulate and control gene expression in human cells.

Epigenome-Wide Association Study Reveals Methylation Loci Associated With Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome

<i>Objective: </i>Gestational diabetes mellitus (GDM) is associated with a future offspring risk for the development of obesity and insulin resistance in Gestational diabetes mellitus (GDM) is associated with an increased risk of obesity and insulin resistance in offspring later in life, which might be explained by epigenetic changes in response to maternal hyperglycaemic exposure. <p><i>Research Design and Methods: </i>We explored the association of GDM exposure on maternal blood and newborn cord-blood methylation of 536 mother-offspring pairs from the prospective FinnGeDi cohort, using Illumina’s methylationEPIC BeadChip 850K arrays. We assessed two hypotheses First, we tested for shared maternal and offspring epigenetic effects due to GDM exposure. Second, we tested whether GDM exposure and maternal methylation has an epigenetic effect on the offspring.</p> <p><i>Results: </i>We did not find any epigenetic marks (differentially methylated CpG probes) with shared and consistent effects between mothers and offspring. After including maternal methylation in the model, we identified a single significant (FDR = 1.38 x 10^-2) CpG at the cg22790973 probe (<i>TFCP2)</i> associated with GDM. We identified seven additional FDR-significant interactions of maternal methylation and GDM status, with the strongest association at the same cg22790973 probe (<i>TFCP2)</i>, plus cg03456133, cg24440941 (<i>H3C6</i>), cg20002843 (<i>LOC127841)</i>, cg19107264, cg11493553 located in the <i>UBE3C</i> gene and cg17065901 in <i>FAM13A, </i>both<i> </i> susceptibility genes for type 2 diabetes and BMI and cg23355087, within the <i>DLGAP2</i> gene, known to be involved in insulin resistance during pregnancy.</p> <p><i>Conclusion: </i>Our study reveals the potential complexity of the epigenetic transmission between GDM mothers and their offspring, likely determined by not only GDM exposure, but also other factors indicated by maternal epigenetic status, such as maternal metabolic history.<br> </p>

Epigenome-Wide Association Study Reveals Methylation Loci Associated With Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome

<i>Objective: </i>Gestational diabetes mellitus (GDM) is associated with a future offspring risk for the development of obesity and insulin resistance in Gestational diabetes mellitus (GDM) is associated with an increased risk of obesity and insulin resistance in offspring later in life, which might be explained by epigenetic changes in response to maternal hyperglycaemic exposure. <p><i>Research Design and Methods: </i>We explored the association of GDM exposure on maternal blood and newborn cord-blood methylation of 536 mother-offspring pairs from the prospective FinnGeDi cohort, using Illumina’s methylationEPIC BeadChip 850K arrays. We assessed two hypotheses First, we tested for shared maternal and offspring epigenetic effects due to GDM exposure. Second, we tested whether GDM exposure and maternal methylation has an epigenetic effect on the offspring.</p> <p><i>Results: </i>We did not find any epigenetic marks (differentially methylated CpG probes) with shared and consistent effects between mothers and offspring. After including maternal methylation in the model, we identified a single significant (FDR = 1.38 x 10^-2) CpG at the cg22790973 probe (<i>TFCP2)</i> associated with GDM. We identified seven additional FDR-significant interactions of maternal methylation and GDM status, with the strongest association at the same cg22790973 probe (<i>TFCP2)</i>, plus cg03456133, cg24440941 (<i>H3C6</i>), cg20002843 (<i>LOC127841)</i>, cg19107264, cg11493553 located in the <i>UBE3C</i> gene and cg17065901 in <i>FAM13A, </i>both<i> </i> susceptibility genes for type 2 diabetes and BMI and cg23355087, within the <i>DLGAP2</i> gene, known to be involved in insulin resistance during pregnancy.</p> <p><i>Conclusion: </i>Our study reveals the potential complexity of the epigenetic transmission between GDM mothers and their offspring, likely determined by not only GDM exposure, but also other factors indicated by maternal epigenetic status, such as maternal metabolic history.<br> </p>

Formation conditions of noble metal mineralization in sulfide cobalt-copper-nickel ores of Kamchatka (on the example of Annabergitovaya Schel ore occurrence)

The authors present research results, the purpose of which is to study the specifics of noble metal mineralization and its genesis in sulfide cobalt-copper-nickel ores of the Kamchatka nickel-bearing province. The paper is dedicated to one of its many ore occurrences called Annabergitovaya Schel (Annabergite Gap). The material composition of platinoid, silver, gold, bismuth and tellurium minerals, as well as sulfarsenides in the ores of this occurrence was investigated. Based on the data of mineral formation sequence and the use of geosensors, conclusions were drawn regarding the genesis of noble metal mineralization. Formation of platinoid minerals, silver and gold at the Annabergitovaya Schel ore occurrence is mainly associated with the epigenetic effect of post-ore granitoids on ore-bearing intrusion rocks of the Dukuk complex of the cortlandite-norite formation and on syngenetic ores. An early association of noble metal minerals is represented by sperrylite, irarsite, and rare unnamed phases of Pt + Ir + Te. Irarsite and Pt + Ir + Te phases were formed at the contact-metasomatic stage. Sperrylite can be assumed to be of magmatic origin. Silver sulfides and tellurides, silver and palladium bismuth tellurides, and native gold were formed at the late, hydrothermal-metasomatic, stage. The occurrence conditions of mineral parageneses, associated with noble metal mineralization, correspond to the formation of shallow-depth metasomatic rocks (5 km). Sub-developed quartz-feldspar metasomatites, associated with the formation of early platinoid arsenides and sulfarsenides, are in equilibrium with circumneutral solutions (pH of 4.5-6.5) at temperatures of 350-600 °C. Late hydrothermal association with Pd, Ag and Au minerals is close to propylites and was formed at pH values of 4.5-6.5 and temperature of 150-350 °C.

Resistance to Thyroid Hormone Beta: A Focused Review

Resistance to thyroid hormone (RTH) is a clinical syndrome defined by impaired sensitivity to thyroid hormone (TH) and its more common form is caused by mutations in the thyroid hormone receptor beta (THRB) gene, termed RTHβ. The characteristic biochemical profile is that of elevated serum TH levels in absence of thyrotropin suppression. Although most individuals are considered clinically euthyroid, there is variability in phenotypic manifestation among individuals harboring different THRB mutations and among tissue types in the same individual due in part to differential expression of the mutant TRβ protein. As a result, management is tailored to the specific symptoms of TH excess or deprivation encountered in the affected individual as currently there is no available therapy to fully correct the TRβ defect. This focused review aims to provide a concise update on RTHβ, discuss less well recognized associations with other thyroid disorders, such as thyroid dysgenesis and autoimmune thyroid disease, and summarize existing evidence and controversies regarding the phenotypic variability of the syndrome. Review of management addresses goiter, attention deficit disorder and “foggy brain”. Lastly, this work covers emerging areas of interest, such as the relevance of variants of unknown significance and novel data on the epigenetic effect resulting from intrauterine exposure to high TH levels and its transgenerational inheritance.

Genetic and Epigenetic Consequence of Early-Life Social Stress on Depression: Role of Serotonin-Associated Genes

Early-life adversity caused by poor social bonding and deprived maternal care is known to affect mental wellbeing and physical health. It is a form of chronic social stress that persists because of a negative environment, and the consequences are long-lasting on mental health. The presence of social stress during early life can have an epigenetic effect on the body, possibly resulting in many complex mental disorders, including depression in later life. Here, we review the evidence for early-life social stress-induced epigenetic changes that modulate juvenile and adult social behavior (depression and anxiety). This review has a particular emphasis on the interaction between early-life social stress and genetic variation of serotonin associate genes including the serotonin transporter gene (5-HTT; also known as SLC6A4), which are key molecules involved in depression.

Epigenetic Alteration Shaped by the Environmental Chemical Bisphenol A

Bisphenol A (BPA) is extensively used in plastic products and epoxy resins. The epigenetic response to the environmental chemical BPA was involved in multiple dysfunctional categories, such as cancer, the reproductive system, metabolism, pubertal development, peripheral arterial disease, infant and childhood growth, and neurodevelopment outcomes. In this mini-review, we described the recent progress of the epigenetic effects of the environmental chemical BPA, including DNA methylation, histone methylation, and toxic epigenomics. Notably, the histone modification changes under BPA exposure are summarized in this review. DNA methylation accompanied by transcriptional changes in key genes affected by BPA exposure is related to various processes, including neural development, cancer pathways, and generational transmission. In addition, BPA could also affect histone modifications in many species, such as humans, rats, and zebrafish. Finally, we reviewed recent studies of the toxico-epigenomics approach to reveal the epigenetic effect of BPA exposure genome-wide.

Epigenetic Neuropharmacology: Drugs Affecting the Epigenome in the Brain

This review explores how different classes of drugs, including those with therapeutic and abuse potential, alter brain functions and behavior via the epigenome. Epigenetics, in its simplest interpretation, is the study of the regulation of a genes’ transcriptional potential. The epigenome is established during development but is malleable throughout life by a wide variety of drugs, with both clinical utility and abuse potential. An epigenetic effect can be central to the drug's therapeutic or abuse potential, or it can be independent from the main effect but nevertheless produce beneficial or adverse side effects. Here, I discuss the various epigenetic effects of main pharmacological drug classes, including antidepressants, antiepileptics, and drugs of abuse.