Use Of DNA Methyltransferase Inhibitors Research Articles

PD-1 Overexpression in Sézary Syndrome Is Epigenetically Regulated

PD-1 Overexpression in Sézary Syndrome Is Epigenetically Regulated

Abstract 2110: Platinum-inducedBRCA1 promoter DNA hypermethylation and altered metabolic profile promotes chemoresistance in ovarian cancer

Abstract High grade serous ovarian cancer (HGSOC) is the most common and aggressive type of ovarian cancer (OC). Platinum resistance is a common occurrence in HGSOC leading to tumor relapse and patient mortality. Multiple mechanisms contribute to platinum resistance in OC, including enrichment of ovarian cancer stem cells (OCSCs), which is observed in relapsed tumors. Platinum treatment activates the DNA damage response (DDR) and the DNA repair protein BRCA1 is an OC susceptibility factor. In our study, we demonstrate that platinum treatment induces a decrease in BRCA1 levels that leads to an increase in activity of ALDH, an OCSC marker. In a parallel pathway that is associated with G2/M arrest, platinum treatment also induces an increase in NAMPT expression and NAD+ levels, the cofactor required for ALDH activity. BRCA1 is repressed through platinum-induced promoter DNA hypermethylation. Importantly, combination of platinum with decitabine, a DNA methyltransferase (DNMT) inhibitor, prevents the platinum-induced increase in OCSCs. This study uniquely provides preclinical support for the use of DNMT inhibitors in the neoadjuvant setting in combination with platinum treatment for OC patients. Citation Format: Riddhi Sood, Sikai Xiao, Shruthi Sriramkumar, Christiane Hassel, Kenneth Nephew, Heather O'Hagan. Platinum-inducedBRCA1 promoter DNA hypermethylation and altered metabolic profile promotes chemoresistance in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2110.

DIPG-12. TARGETING EPIGENETIC MODIFIERS TO INDUCE IMMUNE SIGNALING IN DIPG

DIPG is a universally fatal pediatric brainstem tumor with no effective therapy. Recent work has shown that over 80% of DIPG cases harbor the H3K27M mutation leading to global loss of the repressive H3K27 trimethylation mark, global DNA hypomethylation, and a distinct gene expression signature. We sought to exploit epigenetic vulnerabilities in DIPG through the use of DNA methyltransferase inhibitors and histone deacetylase (HDAC) inhibitors. We find that treatment with low-dose 5-aza-2’-deoxycytidine (decitabine), alone and in combination with HDAC inhibitors, elicits profound genome-wide demethylation in DIPG patient-derived neurosphere cell lines, impairs proliferation, and induces apoptosis. We show that this treatment induces immune activation, with induction of type I interferon signaling, increased expression of major histocompatibility complexes, and expression of tumor antigens. These results suggest that the immunogenicity of DIPG may be modulated by epigenetic therapies, suggesting the possibility of novel combination approaches to immunotherapy of DIPG in the future.

Abstract 4126: DNA methyltransferase inhibitors target a YES1-YAP1 signaling axis in childhood rhabdomyosarcoma

Abstract We have previously shown that the SRC family kinase (SFK) member, YES1, is highly expressed and rapidly activated upon IGF-1R blockade in rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children and adolescents. YAP1 (YES-associated protein) is also highly expressed in human RMS tumors where it functions as an oncoprotein when the upstream Hippo tumor suppressor pathway is silenced, driving cell growth and survival. Thus far, efforts to pharmacologically inhibit YAP1 have been unsuccessful. One activator of the Hippo pathway, RASSF1a, is epigenetically silenced in many cancer types including sarcomas. Here we show a loss of RASSF1a expression in RMS cell lines via promoter methylation. Treatment with DNA methyltransferase inhibitors (DNMTis) can re-activate RASSF1a expression, resulting in YAP phosphorylation and inactivation. DNMTi treatment also significantly inhibits RMS cell growth, which can be rescued by overexpression of a constitutively active YAPS127A. In the alveolar variant (aRMS) in particular, DNMTis increase apoptosis and decrease both YES1 expression and activation. This suggests DNMTi treatment can inhibit both YAP1 and YES1 signaling. To further investigate the connection between YES1 and YAP1 we performed proximity ligation assays and discovered that YES1 and YAP1 interact in the nucleus of RMS cell lines. Furthermore, dasatinib treatment, a known SFK inhibitor, prevents YAP1 nuclear accumulation suggesting a role for YES1 in regulating YAP1 cellular localization. YAP1 is also tyrosine phosphorylated, which may be one way YES1 regulates YAP1. Lastly, cells expressing a constitutively active YAPS127A have increased activation of SFK suggesting a positive feedback loop whereby YAP1 activity can further activate YES1 through an unknown mechanism. These data uncover a signaling axis between the YES1 and YAP1 oncoproteins in RMS and suggest an alternative way to silence YES1 and YAP1 through use of DNMTis. We will further analyze this signaling through shRNA knockdown of YES1 and evaluate combination treatment of a DNMTi and dasatinib in vitro and in vivo. Citation Format: Katherine Slemmons, Choh Yeung, Josh Baumgart, Amy McCalla-Martin, Lee Helman. DNA methyltransferase inhibitors target a YES1-YAP1 signaling axis in childhood rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4126.

Abstract IA14: Targeting human endogenous retroviruses for epigenetic therapy

Abstract Vitamin C deficiency is found in patients with cancer and might complicate various therapy paradigms. Here we show how this deficiency may influence the use of DNA methyltransferase inhibitors (DNMTis) for treatment of hematological neoplasias. In vitro, when vitamin C is added at physiological levels to low doses of the DNMTi 5-aza-2'-deoxycytidine (5-aza-CdR), there is a synergistic inhibition of cancer-cell proliferation and increased apoptosis. These effects are associated with enhanced immune signals including increased expression of bidirectionally transcribed endogenous retrovirus (ERV) transcripts, increased cytosolic dsRNA, and activation of an IFN-inducing cellular response. This synergistic effect is likely the result of both passive DNA demethylation by DNMTi and active conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) enzymes at LTR regions of ERVs, because vitamin C acts as a cofactor for TET proteins. In addition, TET2 knockout reduces the synergy between the two compounds. Furthermore, we show that many patients with hematological neoplasia are markedly vitamin C deficient. Thus, our data suggest that correction of vitamin C deficiency in patients with hematological and other cancers may improve responses to epigenetic therapy with DNMTis. Citation Format: Peter A. Jones. Targeting human endogenous retroviruses for epigenetic therapy [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA14.

Vitamin C increases viral mimicry induced by 5-aza-2′-deoxycytidine

Vitamin C deficiency is found in patients with cancer and might complicate various therapy paradigms. Here we show how this deficiency may influence the use of DNA methyltransferase inhibitors (DNMTis) for treatment of hematological neoplasias. In vitro, when vitamin C is added at physiological levels to low doses of the DNMTi 5-aza-2'-deoxycytidine (5-aza-CdR), there is a synergistic inhibition of cancer-cell proliferation and increased apoptosis. These effects are associated with enhanced immune signals including increased expression of bidirectionally transcribed endogenous retrovirus (ERV) transcripts, increased cytosolic dsRNA, and activation of an IFN-inducing cellular response. This synergistic effect is likely the result of both passive DNA demethylation by DNMTi and active conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) enzymes at LTR regions of ERVs, because vitamin C acts as a cofactor for TET proteins. In addition, TET2 knockout reduces the synergy between the two compounds. Furthermore, we show that many patients with hematological neoplasia are markedly vitamin C deficient. Thus, our data suggest that correction of vitamin C deficiency in patients with hematological and other cancers may improve responses to epigenetic therapy with DNMTis.

Epigenetic modulating agents as a new therapeutic approach in multiple myeloma.

Multiple myeloma (MM) is an incurable B-cell malignancy. Therefore, new targets and drugs are urgently needed to improve patient outcome. Epigenetic aberrations play a crucial role in development and progression in cancer, including MM. To target these aberrations, epigenetic modulating agents, such as DNA methyltransferase inhibitors (DNMTi) and histone deacetylase inhibitors (HDACi), are under intense investigation in solid and hematological cancers. A clinical benefit of the use of these agents as single agents and in combination regimens has been suggested based on numerous studies in pre-clinical tumor models, including MM models. The mechanisms of action are not yet fully understood but appear to involve a combination of true epigenetic changes and cytotoxic actions. In addition, the interactions with the BM niche are also affected by epigenetic modulating agents that will further determine the in vivo efficacy and thus patient outcome. A better understanding of the molecular events underlying the anti-tumor activity of the epigenetic drugs will lead to more rational drug combinations. This review focuses on the involvement of epigenetic changes in MM pathogenesis and how the use of DNMTi and HDACi affect the myeloma tumor itself and its interactions with the microenvironment.

Abstract 4624: Identification of novel DNA methylation markers to track patient's response to DNA demethylation agents.

Abstract The successful use of DNA methyltransferase inhibitors (DNMTis) in Myelodysplastic Syndromes (MDS) therapy has brought epigenetic drugs to the forefront of cancer management. However it has been difficult to find a consistent association between patients’ outcome and DNA methylation changes. This could be attributed to a variety of factors including the choice of DNA methylation markers to track the response to treatment. LINE-1 methylation changes are widely studied as a marker predictive of genome-wide DNA methylation changes; however recent reports have shown that its methylation levels are variable across tissues. In addition, we have found that LINE-1 remethylation after DNMTis withdrawal occurs faster than that of other regions, suggesting that LINE-1 methylation changes might not reflect the overall demethylation effects of DNMTis. Thus, it is imperative to find more sensitive DNA methylation markers to accurately track the methylation change that occurs after DNMTi treatment. Ideally, such markers could be applied to various tumor types and to samples collected by invasive and non-invasive methods. To find improved DNA methylation markers, we took advantage of the well-established Infinium DNA methylation platform and found 1429 probes, which were consistently methylated in both normal/tumor bladder tissue samples as well as white blood cells from healthy donors. The remethylation pattern of those 1439 probes was investigated in the T24 bladder cancer and HL60 leukemia cell lines treated with 5-Aza-CdR for 24 hours. Probe consensus clustering yielded a group of 79 probes that significantly responded to the demethylation treatment and remained demethylated beyond 30 days. In silico analysis of the DNA methylation patterns of the top two probes show consistent hypermethylation in both normal and tumor samples. As a proof of principle, we tested the DNA demethylation levels of these two markers in urine sediments from 7 MDS patients treated with Azacitidine using pyrosequencing. Our results showed that the two markers were significantly demethylated; in contrast, LINE-1 methylation showed no clear decreasing trend. Demethylation of these two markers was also observed in peripheral blood samples from MDS patients treated with Azacitidine. We are in the process of testing more samples to find the association between marker demethylation and patient's outcome. In summary, we have identified and validated two DNA methylation markers, which unlike LINE-1, show consistent demethylation in response to the DNMTi treatment irrespective of the type of sample tested. The wider range of demethylation provided by these markers may offer a more accurate representation of the patient's response to treatment. Citation Format: Xiaojing Yang, Han Han, Marianne B. Treppendahl, Yvonne C. Tsai, Casey O'Connell, Dan Weisenberger, Fides Lay, Kirsten Grønbæk, Gangning Liang, Peter A. Jones. Identification of novel DNA methylation markers to track patient's response to DNA demethylation agents. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4624. doi:10.1158/1538-7445.AM2013-4624

Retrospective Comparison of Azacitidine and Decitabine in the Treatment of Myleodysplastic Syndrome,

Abstract 3809 Introduction:Two DNA methyltransferase inhibitors, azacitidine and decitabine, are currently approved for the treatment of myleodysplastic syndrome (MDS) according to the results of several Phase II and III trials, which have demonstrated the efficacy of the agents. Despite widespread clinical use of DNA methyltransferase inhibitors, one of important practical issues is which drug should be chosen. In this retrospective study, we tried to compare azacitidine and decitabine for the treatment of MDS in regards to treatment response, toxicities, and survival. Methods: Between September 2006 and October 2010, a total of 149 patients were treated with either azacitidine (n=75) or decitabine (n=74) for MDS defined by the WHO classification and chronic myelomonocytic leukemia (CMML) in 3 Korean institutes; all are included in this analysis. Azacitidine 75 mg/m2/day was administered as a subcutaneous injection for 7 consecutive days and decitabine 20 mg/m2/day as a 1-hour intravenous infusion for 5 consecutive days. Both agents were repeated every 4 weeks. Treatment response was evaluated using modified International Working Group response criteria. Results: Median age of the patients, 100 males and 49 females, was 60 years (range, 23–83). WHO subtype at the time of decitabine treatment was RA in 18, RARS in 2, RCMD in 28, RCRS in 5, RAEB-1 in 46, RAEB-2 in 39, unclassified in 2, and CMML in 9. IPSS risk category was low/intermediate-1 in 72 and intermediate-2/high in 72. Median number of courses delivered to each patient was 5 (range, 1–31) for azacitidine and 4 (range, 1–24) for decitabine (P=0.033). Hematologic responses (CR/PR/mCR) were induced in 9 patients (12.0%) with azacitidine and in 22 (29.7%) with decitabine (P=0.008). The rates of overall response (CR/PR/mCR/HI) was not significantly different between azacitidine (52.0%) and decitabine (63.5%) (P=0.155). Median number of treatment courses to achieve any response was 2 (range, 1–6) for azacitidine and 1 (range, 1–5) for decitabine (P=0.269). Adverse events were evaluated for the first 6 courses for all patients, for a total of 584 courses. Major adverse events were cytopenia and cytopenia-related infection. Grade 3 or higher neutropenia was more frequent with decitabine (79.6%) than with azacitidine (72.2%) (P=0.040), but incidence of febrile episode requiring intravenous antibiotics was similar (12.4% with decitabine vs. 15.4% with azacitidine, P=0.298). Grade 3 or higher non-hematologic toxicities were infrequent and reversible with both agents. Median follow-up duration of surviving patients was 46.9 months (range, 11.8–55.5) for azacitidine and 22.7 months (range 3.3–33.3) for decitabine. Probabilities of overall survival (OS) at 2 years were 43.5% for azacitidine, and 55.5% for decitabine. The difference of OS in favor of decitabine over azacitidine was significant after adjustment for other variables (HR, 0.539; 95% CI, 0.325–0.895; P=0.017). Subgroup analysis showed that the survival superiority of decitabine over azacitidine was evident principally in patients with IPSS low/intermediate-1 (HR, 0.131; P=0.006), MDS duration of 1 year or less (HR, 0.534; P=0.022), or ECOG performance scale of 0–1 (HR, 0.589; P=0.060). In contrast, a tendency was noted for survival superiority of azacitidine over decitabine in patients with MDS duration over 1 year (HR, 2.107; P=0.235) or ECOG scale of 2–3 (HR, 2.492; P=0.074). Conclusions: Although both azacitidine and decitabine were effective in the treatment of patients with MDS, there were some differences between two agents in regards to response patterns, toxicities, and type of subgroups that showed more beneficial effects with the hypomethylating agent. Disclosures:No relevant conflicts of interest to declare.

317 Is epigenetics the holy grail of cancer research?

Epigenetics describes the study of stable, reversible alterations to the genome that affect gene expression and genome function, the most studied mechanisms are DNA methylation and histone modifications. Over recent years there has been rapid progress to elucidate the nature and role of the mechanisms involved in promoter hypermethylation during carcinogenesis, however, the mechanism behind one of the earliest epigenetic observations in cancer, genome-wide hypomethylation, remains unclear. Current evidence is divided between the hypotheses that hypomethylation is either an important early cancer-causing aberration or that it is a passive inconsequential side effect of carcinogenesis. With recent discoveries of gene–body methylation, fast cyclic methylation of hormone dependent genes and candidate proteins involved in DNA demethylation elucidation of the role of hypomethylation and the mechanism behind it appears ever closer. With the burgeoning use of DNA methyltransferase inhibitors as a cancer therapy there is an increased need to understand the mechanisms and importance of genome-wide hypomethylation in cancer. This review will discuss the timing and potential causes of genomic hypomethylation during carcinogenesis and will propose a way forward to understand the underlying mechanisms.

Biological rationale for the use of DNA methyltransferase inhibitors as new strategy for modulation of tumor response to chemotherapy and radiation

Epigenetic modifications play a key role in the patho-physiology of many tumors and the current use of agents targeting epigenetic changes has become a topic of intense interest in cancer research. DNA methyltransferase (DNMT) inhibitors represent a promising class of epigenetic modulators. Research performed yielded promising anti-tumorigenic activity for these agents in vitro and in vivo against a variety of hematologic and solid tumors. These epigenetic modulators cause cell cycle and growth arrest, differentiation and apoptosis. Rationale for combining these agents with cytotoxic therapy or radiation is straightforward since the use of DNMT inhibitor offers greatly improved access for cytotoxic agents or radiation for targeting DNA-protein complex. The positive results obtained with these combined approaches in preclinical cancer models demonstrate the potential impact DNMT inhibitors may have in treatments of different cancer types. Therefore, as the emerging interest in use of DNMT inhibitors as a potential chemo- or radiation sensitizers is constantly increasing, further clinical investigations are inevitable in order to finalize and confirm the consistency of current observations.The present article will provide a brief review of the biological significance and rationale for the clinical potential of DNMT inhibitors in combination with other chemotherapeutics or ionizing radiation. The molecular basis and mechanisms of action for these combined treatments will be discussed herein.

Decitabine in Myelodysplastic Syndromes

Myelodysplastic syndromes (MDS) are a heterogenous group of hematopoietic stem cell disorders that are multifactorial in their etiology. Aberrant DNA hypermethylation is now thought to be involved in MDS, as numerous tumor-suppressor genes have been identified that are silenced in these patients. Thus, the use of DNA methyltransferase inhibitors, such as 5-aza-2'-deoxycytidine (decitabine, Dacogen, MGI Pharma Inc, Bloomington, MN), for reversal of this process appears to be a rational intervention that may influence the course of the disease. Several phase I/II studies have been conducted using a low-dose schedule of decitabine in MDS patients. Based on these studies, decitabine appears to be effective and generally well tolerated, especially in those patients with worse prognostic indicators. Recent results of a phase III study also confirmed that patients treated with decitabine compared to standard supportive care had higher overall response rates and longer time to AML transformation. Decitabine appears to be a promising new therapy for the treatment of MDS; however, defining the optimal dosing schedule and exploring the possible use in combination with other agents such as the histone deacetylase inhibitors need further evaluation.

Transplant strategies for myelodysplastic syndrome

Myelodysplastic syndrome (MDS) is an acquired bone marrow disorder characterized by ineffective hematopoiesis and cellular dysfunction and has an increased risk of transforming into acute myeloid leukemia. Most patients are of advanced age with attendant comorbidities, making treatment difficult. Current treatment options have included supportive care and, in difficult cases, chemotherapy regimens designed for acute leukemia patients. A major effort has been made to determine the role of stem cell transplantation in adult MDS patients, currently the only curative option available for them. Based on relapse rates, studies indicate that allogeneic and autologous transplants provide better antileukemic activity than intensive chemotherapy schedules. Use of DNA methyltransferase inhibitors may assist in managing MDS patients while awaiting a transplant match, but the procedural mortality for transplant remains high. Reduced conditioning or nonmyeloablative conditioning, particularly in the elderly, has been attempted with some success. Reduced conditioning also increases the graft-versus-leukemia effect, allowing for a higher percentage of disease-free survival. Current use of peripheral blood as a source of stem cells for autotransplant is associated with an extremely low procedural mortality. Improvement in such transplant procedures as myeloablation, preparation of the autograft, and posttransplant prophylaxis are improving recovery rates for these patients. In addition, as the biology of this disease is being revealed, newer options will become available in the near future.

The molecular mechanism of fetal hemoglobin reactivation

Increased levels of fetal hemoglobin (HbF) are clinically beneficial in patients with sickle cell disease. Hydroxurea fails to increase HbF in at least 25% of patients, and therefore, better drugs are needed. Recent clinical studies have shown that the DNA methyltransferase (DNMT) inhibitor decitabine effectively increased HbF in hydroxyurea-refractory patients. The rational use of DNMT inhibitors as therapeutic agents to reactivate HbF expression in patients with sickle cell disease is based on nearly 25 years of experimental evidence, reviewed in this article, that supports a fundamental role of DNA methylation in the silencing of gamma-globin gene expression in adults.

Limited gene activation in tumor and normal epithelial cells treated with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine.

It remains unclear to what extent drugs targeting transcriptional repressor complexes affect global gene expression in cells derived from target and nontarget human tissues. To address this question, we used genome-wide expression analysis using microarrays to analyze the response of three tumor and one normal epithelial cell line to treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-CdR). Notably, we found that 5-aza-CdR treatment induced a limited number of genes (mean, 0.67%; range, 0.17-1.8% of 25,940 genes screened) in each cell line tested. The majority of the gene expression changes that followed 5-aza-CdR treatment were conserved in tumor and normal cells, including genes that function in cell proliferation, differentiation, immune presentation, and cytokine signaling. In contrast, 5-aza-CdR treatment induced the expression of cancer-testis class tumor antigens only in tumor cell lines. To explain this tissue-specific response, we analyzed the mechanism of transcriptional regulation of the prototype member of this tumor antigen gene family, MAGE-1. Taken from our analysis of MAGE-1 gene regulation, we propose that 5-aza-CdR-mediated gene activation has two distinct requirements: 1) the reversal of promoter hypermethylation, and 2) the presence of transcriptional activators competent for the activation of hypomethylated target promoters. This latter requirement for gene activation by 5-aza-CdR is probably mediated by sequence-specific transcription factors and may account for the limited number of human genes induced by 5-aza-CdR treatment. This revised model for gene activation by 5-aza-CdR has important implications for the use of DNA methyltransferase inhibitors in clinical settings.