Epigenetic Treatment Research Articles

Predictive molecular tumor response through circulating DNA (cDNA) measurements and correlation with established prognostic markers in a series of solid tumors treated with multitargeted epigenetic therapy (MTET).

e13015 Background: Epigenetic dysregulation of certain genes contribute to the progression of cancers. Plasma ctDNA concentrations can reflect these altered genes and have been shown to correlate well with tumor burden. Methods: We planned to assess the correlation value of c DNA on known factors for prediction of overall survival (OS), recognized as surrogates for survival. Ten( 10) genes of interest, namely NOTCH1, FGF2, MYC, RB1, ATM, MET, BRCA1, BRCA2, ATM and, VHL, were selected as being highly influenced by epigenetic control. We included 54 patients with reported cDNA on the genes of interest for this study evaluating the predictive impact of early changes in cDNA in response to multitargeted epigenetic treatment and the patient survival. There were 12 cases with NOTCH1 mutations, 20 cases with MYC mutations, 5 cases with RB1, 15 cases with BRCA1 or BRCA2 mutations, 26 cases with FGF2 mutations, 18 cases with MET mutations, 2 with VHL mutations and 2 cases with ATM mutations, for a total of 100 data points. Tests for statistical significance were completed using the Fisher Exact probability test calculator found at vassarstats.net/tab2x2.html. Significance level was set at α = .05. Results: There was statistically significant (p-value: .046) correlation on the response of the allele frequency of the observed NOTCH1 alteration with similar response in the angiogenesis biomarkers (Plasma VEGF) and presence of circulating tumor cells. There was a significant correlation (p-value: .014) between a decrease in AF of the observed MYC alteration and biomarker/imaging response on follow-up. In the group of 26 identified with FGF2 mutations, 22 saw cDNA alteration fraction(AF) reduction post therapy. 16/26 of them had either c Myc or NOTCH1 alterations. Also 8 /18 cases with c Met alterations shared NOTCH1 or Myc alteration. This represents a statistically significant (p-value: .0001) correlation on the response of the allele frequency of the observed FGFR2 alteration with the response of other biomarkers. Conclusions: There were a number of significant correlations observed between early changes in cDNA allele fractions of specific genes and the later observations of established prognostic markers. We conclude that changes in cDNA mutated allele fractions observed in liquid biopsy may provide an early useful independent prognostic marker for tumors carrying epigenetically influenced targets and their alterations.

Epigenetic treatment combinations to effectively target cisplatin-resistant germ cell tumors: past, present, and future considerations.

Type II germ cell tumors represent the most common solid malignancy in men aged 15-45years. Despite high cure rates of >90% over all stages, 10-15% of advanced patients develop treatment resistance and potentially succumb to their disease. Treatment of refractory germ cell tumors remains unsatisfactory, and new approaches are needed to further improve outcomes. With this narrative review, we highlight epigenetic mechanisms related to resistance to standard systemic treatment, which may act as promising targets for novel combined epigenetic treatment approaches. A comprehensive literature search of PubMed and MEDLINE was conducted to identify original and review articles on resistance mechanisms and/or epigenetic treatment of germ cell tumors invitro and invivo. Review articles were hand-searched to identify additional articles. Distinct epigenetic phenomena have been linked to chemotherapy resistance in germ cell tumors, among which DNA hypermethylation, histone acetylation, and bromodomain proteins appear as promising targets for therapeutic exploitation. Inhibitors of key regulators, for example DNA methyltransferases (e.g. decitabine, guadecitabine), histone deacetylases (e.g. romidepsin), and bromodomain proteins (e.g. JQ1) decreased cell viability, triggered apoptosis, and growth arrest. Additionally, these epigenetic drugs induced differentiation and led to loss of pluripotency and re-sensitization towards cisplatin in cell lines and animal models. Epigenetic treatments hold promise to (i) reduce the treatment burden of and (ii) overcome resistance to standard cisplatin-based chemotherapy. Combined approaches may enhance activity, while the ideal target and treatment combination of epigenetic drugs, either with another epigenetic agent or conventional cytotoxic agents need to be defined. Epigenetic (combination) treatment for germ cell tumors should be further explored in pre-clinical and clinical research for its potential to further improve germ cell tumor treatment.

Acetylation of CCAR2 Establishes a BET/BRD9 Acetyl Switch in Response to Combined Deacetylase and Bromodomain Inhibition.

There continues to be interest in targeting epigenetic "readers, writers, and erasers" for the treatment of cancer and other pathologies. However, a mechanistic understanding is frequently lacking for the synergy observed when combining deacetylase and bromodomain inhibitors. Here we identify cell cycle and apoptosis regulator 2 (CCAR2) as an early target for acetylation in colon cancer cells treated with sulforaphane. N-terminal acetylation of CCAR2 diminished its interactions with histone deacetylase 3 and β-catenin, interfering with Wnt coactivator functions of CCAR2, including in cells harboring genetically encoded CCAR2 acetylation. Protein domain arrays and pull-down assays identified acetyl "reader" proteins that recognized CCAR2 acetylation sites, including BRD9 and members of the bromodomain and extraterminal domain (BET) family. Treatment with the BET inhibitor JQ1 synergized with sulforaphane in colon cancer cells and suppressed tumor development effectively in a preclinical model of colorectal cancer. Studies with sulforaphane+JQ1 in combination implicated a BET/BRD9 acetyl switch and a shift in the pool of acetyl "reader" proteins in favor of BRD9-regulated target genes. SIGNIFICANCE: These results highlight the competition that exists among the "readers" of acetylated histone and nonhistone proteins and provide a mechanistic basis for potential new therapeutic avenues involving epigenetic combination treatments.

Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity

Leukemia, specifically acute myeloid leukemia (AML), is a common malignancy that can be differentiated into multiple subtypes based on leukemogenic history and etiology. Although genetic aberrations, particularly cytogenetic abnormalities and mutations in known oncogenes, play an integral role in AML development, epigenetic processes have been shown as a significant and sometimes independent dynamic in AML pathophysiology. Here, we summarize how tumors evolve and describe AML through an epigenetic lens, including discussions on recent discoveries that include prognostics from epialleles, changes in RNA function for hematopoietic stem cells and the epitranscriptome, and novel epigenetic treatment options. We further describe the limitations of treatment in the context of the high degree of heterogeneity that characterizes acute myeloid leukemia.

MEK1/2 as a Therapeutic Target in Sickle Cell Disease

Identification of novel therapeutic targets has improved diagnostics and treatment of many diseases. Many innovative treatment strategies have been developed based on the newly identified biomarkers and key molecules. Most of the research focused on ways to manipulate signaling pathways by activating or suppressing them, validate new therapeutic targets for treatment, and epigenetic treatment of diseases. With the identification of aberrations in multiple growth pathways, the focus then shifted to the small molecules involved in these pathways for targeted therapy. In this communication/short review, we highlight the importance of identification of abnormal activation of the mitogen-activated protein kinase (MAPK), ERK1/2, and its upstream mediator MEK1/2, in erythrocytes in patients with sickle cell disease (SCD) critical for the adhesive interactions of these cells with the endothelium, and leukocytes promoting circulatory obstruction leading to tissue ischemia and infraction. We also discuss how targeting this signaling cascade with MEK1/2 inhibitors can reverse acute vasoocclusive crises in SCD.

Direct modulation of the bone marrow mesenchymal stromal cell compartment by azacitidine enhances healthy hematopoiesis

AbstractMesenchymal stromal cells (MSCs) are crucial components of the bone marrow (BM) microenvironment essential for regulating self-renewal, survival, and differentiation of hematopoietic stem/progenitor cells (HSPCs) in the stem cell niche. MSCs are functionally altered in myelodysplastic syndromes (MDS) and exhibit an altered methylome compared with MSCs from healthy controls, thus contributing to disease progression. To determine whether MSCs are amenable to epigenetic therapy and if this affects their function, we examined growth, differentiation, and HSPC-supporting capacity of ex vivo–expanded MSCs from MDS patients in comparison with age-matched healthy controls after direct treatment in vitro with the hypomethylating agent azacitidine (AZA). Strikingly, we find that AZA exerts a direct effect on healthy as well as MDS-derived MSCs such that they favor support of healthy over malignant clonal HSPC expansion in coculture experiments. RNA-sequencing analyses of MSCs identified stromal networks regulated by AZA. Notably, these comprise distinct molecular pathways crucial for HSPC support, foremost extracellular matrix molecules (including collagens) and interferon pathway components. Our study demonstrates that the hypomethylating agent AZA exerts its antileukemic activity in part through a direct effect on the HSPC-supporting BM niche and provides proof of concept for the therapeutic potential of epigenetic treatment of diseased MSCs. In addition, our comprehensive data set of AZA-sensitive gene networks represents a valuable framework to guide future development of targeted epigenetic niche therapy in myeloid malignancies such as MDS and acute myeloid leukemia.

Effect of Combined Epigenetic Treatments and Ectopic NIS Expression on Undifferentiated Thyroid Cancer Cells.

Poorly differentiated (PDTC) and anaplastic thyroid (ATC) cancer cells are characterized by the acquisition of epigenetic abnormalities, leading to the silencing of both the sodium iodide co-transporter and the Coxsackie adenovirus receptor. As aberrant histone acetylation and DNA methylation represent epigenetic mechanisms involved in neoplastic transformation, our study investigated the anticancer properties of epigenetic modifiers in thyroid carcinoma. The cytotoxicity and gene expression modulation of histone deacetylase and DNA methyltransferase inhibitors were evaluated in both PDTC and ATC. Epigenetic treatments were cytotoxic to tumor thyrocytes and restored sodium iodide co-transporter and Coxsackie adenovirus receptor, expression as well as radioiodine uptake, in PDTC but not in ATC. However, ectopic expression sodium iodide co-transporter re-activated radioiodine incorporation in ATC. The ability of epigenetic treatments to interfere with tumor proliferation and induce Coxsackie adenovirus receptor expression, coupled with the ability of ectopic sodium iodide co-transporter to restore radioiodine uptake, raise the possibility that these therapeutic approaches may provide clinical benefit to patients with thyroid carcinoma refractory to radioiodine treatment.

Whole Genome Bisulfite Sequencing (WGBS) Robustly Measures the Pharmacodynamic Effect of Decitabine/Vorinostat Epigenetic Treatment in Relapsed Pediatric ALL Demonstrating Potent Hypomethylation Associated with Upregulation of PRC2 and TP53 Targets

▪IntroductionEpigenetic alterations are prevalent in ALL and have been implicated as determinants of chemotherapy resistance and relapse. Epigenetics modulating drugs, such as DNA methyltransferase and HDAC inhibitors, are of interest as a potential means of enhancing chemotherapy sensitivity and improving clinical outcomes. Interpretation of clinical responses in trials of epigenetic drugs has been hampered by lack of precision in assessing the pharmacodynamic effects of the drugs. In the context of a clinical trial testing the epigenetic modulators decitabine (10-15 mg/m2) and vorinostat (180 mg/m2) (D/V) given for one week prior to reinduction with multiagent chemotherapy in young (age 1 - 21 years) patients with relapsed ALL, we assessed genome-wide cytosine methylation with single base-pair resolution using WGBS.MethodsDNA was isolated from leukemia specimens (marrow or blood) obtained before and after 1 week of treatment with D/V from N=10 patients (20 paired samples). For N=6 of these patients (12 paired samples), RNA was also isolated. WGBS at 30X coverage and RNA-seq were performed on the DNA and RNA samples, respectively. We used a custom WGBS analysis pipeline to trim reads (TrimGalore), align to hg19 genome (Bismark/bowtie2), remove PCR duplicates and repeats, call B allele frequency at SNPs, and call methylation states at CpG sites. We used rsem, STAR and EBSeq for RNA-seq alignment and differential gene expression calls between pre- and post- treatment samples. 16 million CpGs were segmented into 1.3 million segments based on pre/post D/V methylation change (HaarSeg/R). We plotted 5 quintiles of gene expression (N=22,522 genes), from most expressed (Q1) to unexpressed (Q5), and linked to associated promoter CpG segment methylation (deepTools, Fig.1). Gene set enrichment analysis (GSEA/MSigDB) was performed on genes ranked in order by greatest promoter hypomethylation, highest significance of differential gene expression, and highest gene log2 fold overexpression post- treatment to create an “epigenetically activated” ranked gene list.ResultsWGBS showed case-specific areas of leukemia-associated allelic imbalance in each pair of samples, confirming that pre/post DV methylation differences are specific to leukemic blast population. D/V treatment reduced CpG segment methylation by 12.4% on average (range: 5.1-20.7%). Drug-induced hypomethylation was equally distributed (not specific to exon, intron, intergenic, promoter, or enhancer regions). In the 6 cases with paired RNA-seq data, we found a strong correlation between promoter methylation and gene expression in pre-treatment samples, and this correlation was maintained in the hypomethylated post-treatment samples. One of these cases, with global methylation decreased by 12.9%, is shown in Fig.1. GSEA on these 6 cases combined showed that 75/4169 gene sets (including targets of PRC2 and TP53, H3K27ME3- and H3K4ME3- bound, FDR<25%, p<0.01) were overrepresented in the “epigenetically activated” ranked gene list. In 4/6 cases we detected hypomethylated segments at the CD19 promoter and an associated 1.05- to 5.13- fold CD19 upregulation.ConclusionsWith high resolution, we observed base-pair specific reduction in CpG methylation after epigenetic modulation with decitabine and vorinostat across the genome in all cases, although the pharmacodynamic effect varied by as much as 15.6% between patients. The drug-induced activation of PRC2 targets suggests that epigenetic treatment of relapsed ALL may induce differentiation, and the activation of TP53 targets suggests that epigenetic treatment can reactivate tumor suppressor genes to suppress cell proliferation. Furthermore, epigenetic activation of CD19 expression suggests that epigenetic pre-treatment can potentially sensitize cells to CD19-targeted immunotherapies. Integrated WGBS/RNA-seq represents a powerful tool for pharmacodynamic evaluation of epigenetic therapy.Figure 1. D/V treatment reduced average CpG segment methylation by 12.9% in case T0300. Methylation of gene promoters, defined as ±3kb from the transcription start site (TSS), showed strong correlation with expression of 22,522 genes ranked and split into quintiles in order of upregulated (Q1) to downregulated (Q4-Q5) (A, B). Hypomethylation was equally distributed across promoter regions and gene bodies (TSS-TES, scaled transcription start-end sites) (C, D). DisclosuresBurke:AMGEN: Speakers Bureau; JAZZ: Speakers Bureau; Shire: Speakers Bureau.

Phase 1 Studies Assessing the Safety and Clinical Activity of Multiple Doses of a NKG2D-Based CAR-T Therapy, Cyad-01, in Acute Myeloid Leukemia

Introduction:CYAD-01 is a chimeric antigen receptor T-cell (CAR-T) product based on the receptor NKG2D which demonstrated anti-tumor efficacy through different mechanisms of action in numerous preclinical models. A comprehensive clinical program was developed with the aim to define the optimal CYAD-01 treatment in acute myeloid leukemia (AML).Methods:The ongoing Phase I THINK trial (NCT03018405) evaluates multiple CYAD-01 injections in 2 parallel cohorts: one in patients (pt) with metastatic solid tumors and the other one in relapsing/refractory hematological malignancies. The dose escalation segment of the study evaluates 3 dose levels (DL; 3x108, 1x109 and 3x109 cells per injection) of one cycle of 3 CYAD-01 administration at 2 weeks apart. As of July 30, 2018, 12 pts in the THINK hematological cohort (8 AML, 3 MM and 1 MDS) have been enrolled at the 3 DLs without prior preconditioning. No dose-limiting toxicity occurred. We evidenced promising anti-leukemic activity with 42% ORR in r/r AML with 5/7 pts having clinical benefit. Based on the initial data generated into the THINK study, two additional Phase I clinical trials have been developed to evaluate 3 DLs (1x108, 3x108 and 1x109 cells per injection) post preconditioning regimen or in association with standard of care (SoC).The DEPLETHINK study (NCT03466320) aims at evaluating the CYAD-01 treatment administered after a cyclophosphamide and fludarabine preconditioning regimen to r/r AML patients. The preconditioning chemotherapy should (i) favor the expansion and engraftment of CYAD-01, (ii) increase NKG2D ligand expression on tumor cells and (iii) help to overcome the strong immunosuppressive microenvironment.The EPITHINK study (EudraCT 2018-000745-39) aims at assessing the safety of the CYAD-01 treatment administered concurrently with SoC 5-azacytidine treatment in treatment-naïve AML pts ineligible for intensive treatment. Similar to the preconditioning treatment, the epigenetic treatment could contribute to favor engraftment of CYAD-01 cells and increase target antigen expression while better controlling the disease progression of patients early in the treatment.Results:Description of the study design and preliminary clinical data from the first cohorts of the EPITHINK and DEPLETHINK studies will be presented. The preliminary data in term of CYAD-01 engraftment kinetics, NKG2D ligand expression (including blasts and soluble ligands), and the kinetics of cytokine induction will be correlated with the concurrent treatment (preconditioning or epigenetic treatment) versus the stand alone therapeutic approach.Conclusions:We have demonstrated the feasibility and safety of multiple injections of CYAD-01 without preconditioning chemotherapy (THINK). Preliminary safety, activity and correlative science data will be presented according a prior preconditioning (DEPLETHINK) and concurrent administration with SoC epigenetic treatment (EPITHINK). DisclosuresSallman:Celgene: Research Funding, Speakers Bureau. Kerre:BMS: Consultancy; Celgene: Consultancy, Research Funding; Celyad: Consultancy. Wang:Novartis: Speakers Bureau; Amgen: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Jazz: Speakers Bureau; Novartis: Speakers Bureau; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Jazz: Speakers Bureau. Selleslag:Kiadis Pharma: Other: Financial support for study-related issues. Beguin:Kiadis Pharma: Consultancy. Al-Homsi:Celyad: Membership on an entity's Board of Directors or advisory committees. Dekker:Celyad: Employment. Breman:Celyad: Employment. Sotiropoulou:Celyad: Employment. Snykers:Celyad: Employment. Braun:Celyad: Employment. Lonez:Celyad: Employment. Verma:Celyad: Employment. Lehmann:Celyad: Employment, Honoraria, Patents & Royalties; GSK: Patents & Royalties. Davila:Celyad: Consultancy, Membership on an entity's Board of Directors or advisory committees.

Epigenetic Drug Treatment Induces Presentation of New Class of Non-Exonic, Cryptic Neoantigens in Acute Myeloid Leukemia Cells

Acute myeloid leukemia (AML) is an aggressive hematological malignancy with a 5-year overall survival rate of less than 30% which causes over 10,000 deaths per year in the United States. Treatment options for this disease increasingly include epigenetic drugs, such as hypomethylating agents (e.g. decitabine) or histone deacetylase (HDAC) inhibitors (e.g. pracinostat) which can function via direct cytotoxic mechanisms and also through altered differentiation of AML blasts; immunomodulatory effects like reactivation and presentation of cancer testis antigens in context of human leukocyte antigen (HLA) complexes have been reported as well, which may result in clearance of cells via the adaptive immune system. However, the landscape of immunogenic T cell epitopes induced by these drugs might be even broader than reported since standard analyses only consider exonic protein sequences and do not take into account typically untranslated genomic regions.Recently, it has been shown that single and combination treatment of decitabine and pracinostat can induce cryptic transcription start sites in generally epigenetically repressed solitary long-terminal repeats (LTRs) of the LTR12C family which give rise to novel mRNAs and resulting protein variants. We hypothesized that the intronic parts of these gene products might provide a source of cryptic T cell epitopes with high immunogenic potential, which are induced through epigenetic drug treatment.To test this hypothesis, we treated 5 different AML cell lines (HL-60, U937, OCI-AML02, MOLM13, AML14) with (1) DMSO, (2) 500 nM decitabine or (3) a combination of 500 nM decitabine and 100 nM pracinostat for 72 hours to induce transcription of non-annotated transcription start sites. Subsequently, HLA class I complexes were immunopurified and peptides presented by these complexes isolated and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The activation of silenced genes by epigenetic drug treatment with either decitabine alone or the combination treatment yielded increases of about two-fold in the identified unique HLA ligands. This increase in peptide identifications also led to improved detection of cancer testis antigen-derived epitopes, as has been reported before. Intriguingly, by adding LTR12C derived sequences stretching from the published GATA2 specific binding site until the next genomic exon to the peptide search analyses we were able to identify several cryptic peptides from 4 out of 5 AML cell lines derived from these usually untranscribed genomic regions. The identifications were exclusively dependent on previous treatment with either decitabine alone or in combination with pracinostat. Though the immunogenicity of these HLA ligands has not been determined yet, we assume that due to their genetically repressed state in untreated cells, these new peptide sequences represent a new class of neoepitopes, with potential to be novel targets of existing T cells within patients or after augmentation by other immunotherapies.In summary, we demonstrated for the first time the induced presentation of epitopes from normally untranscribed LTR12C regions through epigenetic drug treatment and therefore provide a previously undescribed source of potential targets for immunotherapy in AML. DisclosuresScheinberg:Eureka: Consultancy; Ensyce: Consultancy.

The Combination of PARP Inhibitors and DNMT Inhibitors Modulates Immune Activity and Suggests a Role for Immune Therapy in AML

Acute myeloid leukemia (AML) is a genetically heterogeneous disease where malignant clonal proliferation of immature myeloid cells in the bone marrow leads to disruption of normal hematopoiesis and bone marrow failure. Most treatment improvements have consisted of limited chemotherapeutic interventions, and morbidity and mortality remain unacceptably high. While patients unfit for intensive chemotherapy have the options of epigenetic treatments with DNA methyltransferase inhibitors (DNMTis), and the preclinical research underpinning these treatments is robust and promising, clinical response rates have been poor. Therefore, we have derived a unique treatment strategy combining poly-ADP ribose polymerase inhibitors (PARPis) with DNMTis, and we have previously demonstrated efficacy of this combination in AML in both in vitroand in vivomodels. This combination increases the amount and retention time of PARP1 at laser-induced DNA damage sites, increases DNA DSBs and tumor cytotoxicity, blunts cell self-renewal, and leads to strong anti-tumor responses. These results form the basis for our ongoing Phase I/II clinical trial of this combination therapy in patients with relapsed/refractory AML.To identify molecular pathways underpinning this combination, genome-wide expression microarray analysis was performed on RNA extracted from multiple BRCA-intact sporadic AML cell lines treated with single agents or drug combination. Interestingly, combination drug treatment, more than either single treatment alone, up regulated genes in immune response pathways, including interferons, natural killer cell-mediated cytotoxicity and Toll-like receptor signaling pathway genes. In both AML cell lines (N=10) and primary samples (N=8), we used qPCR to validate these expression increases, with particular focus on interferon type 1-inducible genes, including IFI6, IFI27, IFI30, IRF7, ISG15, and OASL. These interferon-inducible genes were similarly increased in selected AML clinical trial samples post combination treatment. Interferon stimulation studies showed that treatment of multiple cell lines with IFN-β similarly up regulates our genes of interest, and suggests that the immune system plays a pivotal role in mediating the effects of our combination treatment.To functionally validate this immune involvement in vivo, we use an immune competent mouse model that spontaneously develops AML. The bone marrow cells collected from leukemic FLT3/ITD;NHD13 mice are transplanted into sublethally irradiated syngeneic recipients where they undergo clonal leukemic expansion and expression of specific surface markers (CD45.1 vs CD45.2) allow for the tracking of both host and transplanted blood cells. After validating that our combination treatment increases survival and reduces tumor burden in this in vivo model, we isolated mononuclear cells from spleens and livers and found that mice in the combination therapy group had increased T cell populations with increased PD1, CD28 and 4-1BB expression. Tal single agent and combination therapy treated mice also had decreased myeloid-derived suppressor cells and increased antigen presenting cells, specifically dendritic cells, monocytes and macrophages. Finally, upon ex vivo stimulation, T cells from mice receiving combination therapy produced significantly more IFN-γ and GM-CSF than mice from other treatment groups.These results indicate that our combination therapy results in immune activation, and suggest the potential to target the immune system in order to induce anti-tumor effects, enhance efficacy of our combination treatment and improve clinical outcomes in AML. DisclosuresLapidus:KinaRx, LLC: Other: Founder and Scientific Advisor.

Network assessment of demethylation treatment in melanoma: Differential transcriptome-methylome and antigen profile signatures.

BackgroundIn melanoma, like in other cancers, both genetic alterations and epigenetic underlie the metastatic process. These effects are usually measured by changes in both methylome and transcriptome profiles, whose cross-correlation remains uncertain. We aimed to assess at systems scale the significance of epigenetic treatment in melanoma cells with different metastatic potential.Methods and findingsTreatment by DAC demethylation with 5-Aza-2’-deoxycytidine of two melanoma cell lines endowed with different metastatic potential, SKMEL-2 and HS294T, was performed and high-throughput coupled RNA-Seq and RRBS-Seq experiments delivered differential profiles (DiP) of both transcriptomes and methylomes. Methylation levels measured at both TSS and gene body were studied to inspect correlated patterns with wide-spectrum transcript abundance levels quantified in both protein coding and non-coding RNA (ncRNA) regions. The DiP were then mapped onto standard bio-annotation sources (pathways, biological processes) and network configurations were obtained. The prioritized associations for target identification purposes were expected to elucidate the reprogramming dynamics induced by the epigenetic therapy. The interactomic connectivity maps of each cell line were formed to support the analysis of epigenetically re-activated genes. i.e. those supposedly silenced by melanoma. In particular, modular protein interaction networks (PIN) were used, evidencing a limited number of shared annotations, with an example being MAPK13 (cascade of cellular responses evoked by extracellular stimuli). This gene is also a target associated to the PANDAR ncRNA, therapeutically relevant because of its aberrant expression observed in various cancers. Overall, the non-metastatic SKMEL-2 map reveals post-treatment re-activation of a richer pathway landscape, involving cadherins and integrins as signatures of cell adhesion and proliferation. Relatively more lncRNAs were also annotated, indicating more complex regulation patterns in view of target identification. Finally, the antigen maps matched to DiP display other differential signatures with respect to the metastatic potential of the cell lines. In particular, as demethylated melanomas show connected targets that grow with the increased metastatic potential, also the potential target actionability seems to depend to some degree on the metastatic state. However, caution is required when assessing the direct influence of re-activated genes over the identified targets. In light of the stronger treatment effects observed in non-metastatic conditions, some limitations likely refer to in silico data integration tools and resources available for the analysis of tumor antigens.ConclusionDemethylation treatment strongly affects early melanoma progression by re-activating many genes. This evidence suggests that the efficacy of this type of therapeutic intervention is potentially high at the pre-metastatic stages. The biomarkers that can be assessed through antigens seem informative depending on the metastatic conditions, and networks help to elucidate the assessment of possible targets actionability.

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation.

DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2'-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi.Transcriptome analyses revealed that a combined treatment with DAC and the HDACi panobinostat or valproic acid affected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative methylome and transcriptome analyses showed that a massive downregulation of genes, including oncogenes (e.g., MYC) and epigenetic modifiers (e.g., KDM2B, SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatments, and for a better understanding of responses in trials where this approach is clinically tested.

Potential Epigenetic-Based Therapeutic Targets for Glioma.

Glioma is characterized by a high recurrence rate, short survival times, high rates of mortality and treatment difficulties. Surgery, chemotherapy and radiation (RT) are the standard treatments, but outcomes rarely improve even after treatment. With the advancement of molecular pathology, recent studies have found that the development of glioma is closely related to various epigenetic phenomena, including DNA methylation, abnormal microRNA (miRNA), chromatin remodeling and histone modifications. Owing to the reversibility of epigenetic modifications, the proteins and genes that regulate these changes have become new targets in the treatment of glioma. In this review, we present a summary of the potential therapeutic targets of glioma and related effective treating drugs from the four aspects mentioned above. We further illustrate how epigenetic mechanisms dynamically regulate the pathogenesis and discuss the challenges of glioma treatment. Currently, among the epigenetic treatments, DNA methyltransferase (DNMT) inhibitors and histone deacetylase inhibitors (HDACIs) can be used for the treatment of tumors, either individually or in combination. In the treatment of glioma, only HDACIs remain a good option and they provide new directions for the treatment. Due to the complicated pathogenesis of glioma, epigenetic applications to glioma clinical treatment are still limited.

Epigenetic inhibitor treatment reduces proliferation via induction of apoptosis in a human typical bronchial carcinoid cell line

Epigenetic inhibitor treatment reduces proliferation via induction of apoptosis in a human typical bronchial carcinoid cell line

Modification effect of fenofibrate therapy, a longitudinal epigenomic-wide methylation study of triglycerides levels in the GOLDN study

BackgroundIdentification of interactions between epigenetic factors and treatments might lead to personalized intervention of diseases. This paper aims to examine the modification effect of fenofibrate therapy on the association of methylation levels and fasting blood triglycerides (TG), and the related biological pathways among methylation sites.ResultsMixed-effects models were employed to assess pre- and posttreatment associations and drug modification effects simultaneously. Five cytosine-phosphate-guanine (CpG) sites were found to be associated with TG levels before and after the fenofibrate therapy: cg00574958, cg17058475, and cg01082498 on CPT1A gene, chromosome 11; cg03725309 on SARS, chromosome 1; and cg06500161 on ABCG1, chromosome 21. In addition, fenofibrate therapy modified the methylation levels on the following 4 CpG sites: cg20015535 (gene EGLN1, chromosome 1); cg24870738 (gene RNF220, chromosome 1); cg06891775 (gene LOC283050, chromosome 10); and cg00607630 (gene USP7, chromosome 16). Further, gene set enrichment analysis (GSEA) identified cancer- and metabolism-related pathways that were associated with TG-related CpG sites.ConclusionsWe identified modification effects of fenofibrate on the associations between blood TG levels and several CpG sites. Pathway enrichment analysis indicated the alternations in some metabolism and cancer-related pathways. Our findings have important implications for future research in pharmacoepigenetics and personalized medicine.

Acetylation state of RelA modulated by epigenetic drugs prolongs survival and induces a neuroprotective effect on ALS murine model

Dysregulation in acetylation homeostasis has been implicated in the pathogenesis of the amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. It is known that the acetylation of transcriptional factors regulates their activity. The acetylation state of NF-kB RelA has been found to dictate the neuroprotective versus the neurotoxic effect of p50/RelA. Here we showed that the pro-apoptotic acetylation mode of RelA, involving a general lysine deacetylation of the subunit with the exclusion of the lysine 310, is evident in the lumbar spinal cord of SOD1(G93A) mice, a murine model of ALS. The administration of the HDAC inhibitor MS-275 and the AMPK/sirtuin 1 activator resveratrol restored the normal RelA acetylation in SOD1(G93A) mice. The SOD1(G93A) mice displayed a 3 weeks delay of the disease onset, associated with improvement of motor performance, and 2 weeks increase of lifespan. The epigenetic treatment rescued the lumbar motor neurons affected in SOD1(G93A) mice, accompanied by increased levels of protein products of NF-kB-target genes, Bcl-xL and brain-derived neurotrophic factor. In conclusion, we here demonstrate that MS-275 and resveratrol restore the acetylation state of RelA in the spinal cord, delaying the onset and increasing the lifespan of SOD1(G93A) mice.

Sonoporation by microbubbles as gene therapy approach against liver cancer.

IntroductionAn innovative method, known as sonoporation, was used to induce the expression of silenced genes, such as (but not restricted to) TRAIL and p53, in liver cancer cells (HepG2). The principal aim of the present study was the re-activation of silenced apoptotic pathways in liver cancer models, by using diagnostic synovial microbubble as plasmid gene delivery tools in combination with epigenetic treatments.Material and methodsHepG2 cells were used as a liver cancer model. Microbubbles (Sonovue®) were chosen as gene deliver system in combination with the sonoporation approach. Plasmid pEGFP-TRAIL and pEGFP-p53 were selected and propagated in Escherichia coli grown in LB broth, in order to obtain the necessary amount.ResultsSonoporation was induced by using transducer (Sonitron 2000) and, among the several conditions tested, 3 MHz, 51% Duty Cycle, and 5 W/cm2, 30 s resulted as the best parameters. Data collected showed a dose dependent effect in terms of output energy. A transfection efficacy of 30 – 50% was achieved and recombinant gene expression induced apoptotic effects. In order to increase efficacy, we used the histone deacetylase inhibitor (HDACi, entinostat) MS-275, able to activate TRAIL and thus inducing a stronger pro-apoptotic effect in combination with TRAIL-gene re-expression.ConclusionFor the first time, it was shown the possibility to induce the exogenous expression of the pro-apoptotic gene TRAIL and p53 in a liver cancer HepG2 cells via a sonoporation procedure. The epigenetic treatment using HDACi was able to increase the pro-apoptotic effects of the gene therapy.

3161 - Curcumin as a Novel Epigenetic Treatment Approach for GFI1-Associated MDS/AML

3161 - Curcumin as a Novel Epigenetic Treatment Approach for GFI1-Associated MDS/AML

Epigenetic treatment of multiple myeloma mediates tumor intrinsic and extrinsic immunomodulatory effects

ABSTRACTImmune evasion is an important driver of disease progression in the plasma cell malignancy multiple myeloma. Recent work highlights the potential of epigenetic modulating agents as tool to enhance anti-tumor immunity. The immune modulating effects of the combination of a DNA methyltransferase inhibitor and a histone deacetylase inhibitor in multiple myeloma is insufficiently characterized. Therefore, we used the murine immunocompetent 5T33MM model to investigate hallmarks of immunogenic cell death as well as alterations in the immune cell constitution in the bone marrow of diseased mice in response to the DNA methyltransferase inhibitor decitabine and the histone deacetylase inhibitor quisinostat. Vaccination of mice with 5T33 cells treated with epigenetic compounds delayed tumor development upon a subsequent tumor challenge. In vitro, epigenetic treatment induced ecto-calreticulin and CD47, as well as a type I interferon response. Moreover, treated 5T33vt cells triggered dendritic cell maturation. The combination of decitabine and quisinostat in vivo resulted in combinatory anti-myeloma effects. In vivo, epigenetic treatment increased tumoral ecto-calreticulin and decreased CD47 and PD-L1 expression, increased dendritic cell maturation and reduced CD11b positive cells. Moreover, epigenetic treatment induced a temporal increase in presence of CD8-positive and CD4-positive T cells with naive and memory-like phenotypes based on CD62L and CD44 expression levels, and reduced expression of exhaustion markers PD-1 and TIM3. In conclusion, a combination of a DNA methyltransferase inhibitor and a histone deacetylase inhibitor increased the immunogenicity of myeloma cells and altered the immune cell constitution in the bone marrow of myeloma-bearing mice.