Abstract 779: Integrative analysis reveals therapeutic targets to the DNA methyltransferase inhibitor SGI-110 in hepatocellular carcinoma

Objective There is an urgent need for developing more effective therapies for Hepatocellular carcinoma (HCC) because of its aggressiveness. Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTi. The aim of this study is to identify potential therapeutic targets of SGI-110 for clinical trials.

Design HCC cell lines (SNU398, HepG2 and SNU475) were used to evaluate effects of SGI-110 by an integrative analysis of DNA methylation, nucleosome accessibility and gene expression profiles following the transient SGI-110 treatment and its clinic relevant by comparing HCC clinic data from TCGA.

Results These HCC cell lines represent the three DNA methylation subtypes of primary HCC tumors based on TCGA data. After SGI-110 treatment, all cell lines were sensitive to SGI-110 with prolonged anti-proliferation effects. Up-regulated genes including tumor suppressors were positively correlated with nucleosome accessibility and negatively correlated with gene promoter DNA methylation, while the down-regulated genes, such as oncogenes, were negatively correlated with nucleosome accessibility and positively correlated with gene body DNA methylation. Furthermore, SGI-110 down-regulated PRC2 complex genes by demethylating their gene bodies, resulting in re-activation of PRC2 repressed gene promoters which are independent on DNA methylation. In addition, SGI-110 up-regulated endogenous retroviruses (ERVs) to reactivate immune pathways. Finally, about 45% of frequently altered genes in primary HCC tumors can be re-shaped into a “normal like” expression status through the treatment.

Conclusion Our integrative analysis has successfully linked the anti-tumor effects of SGI-110 to detailed epigenetic alterations in HCC cells and identified potential therapeutic targets. We also provide rationale of combination treatment with immune checkpoint therapies.

Citation Format: Minmin Liu, Toshinori Hinoue, Wanding Zhou, Hitoshi Ohtani, Anthony El-Khoueiry, John Daniels, Casey O'Connell, Tanya B. Dorff, Daniel J. Weisenberger, Gangning Liang. Integrative analysis reveals therapeutic targets to the DNA methyltransferase inhibitor SGI-110 in hepatocellular carcinoma [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 779.

Abstract 2993: A switch in epigenetic silencing mechanisms of endogenous retroviruses during human genome evolution

Approximately 9% of the human genome is derived from Endogenous Retroviruses (ERVs), which are a type of transposable element. ERVs started to become integrated into the ancestral human genome about 100 million years ago. Recent studies have reported that silencing mechanisms of long terminal repeats regions (LTRs), which are the putative promoters of ERVs, depend on DNA methylation, heterochromatin conformation (H3K9me3) and the PRC2 complex (H3K27me3). However, extensive maps of LTR distribution and the associated epigenetic marks have not yet been provided in human cancer cells. Here we report a switch in epigenetic silencing mechanisms of the approximately 450,000 LTR elements present in the non-genic regions of human DNA. Total RNA-seq in human colon cancer HCT116 cells following DNA methylation inhibitor treatment or knockdown of individual H3K9me2/3 histone methyltransferases (G9a, SETDB1, SETDB2, SUV39H1 and SUV39H2), H3K27me3 (EZH2) or a scaffold protein TRIM28 revealed that about 1,000 of evolutionary young LTRs were predominantly silenced by DNA methylation, whereas about 800 of intermediate age LTRs were silenced by histone methylation. They therefore have undergone an “epigenetic switch” in silencing mechanism during host genome evolution. Eventually, evolutionary old LTRs become inactive by accumulation of loss-of-function mutations. Consistent with these results, CpG sites in evolutionary young LTRs were methylated at higher levels than in intermediate age LTRs, whereas H3K9me2 and H3K9me3 marks were enriched on intermediate age LTRs. Interestingly, knockdowns of EZH2 showed limited upregulation of LTRs by itself, but multiple LTRs were upregulated by combination treatment with DNA methylation inhibitor. This is probably due to a process, in which removal of DNA methylation leads to the subsequent recruitment of EZH2 resulting in suppression by the polycomb repressive complex PRC2. Our earlier studies showed that LTR expressions lead to activation of viral defense pathways and apoptosis, however the species of LTRs was not characterized. We found that the activation of viral defense pathway was correlated with the upregulation of evolutionary young, but not intermediate age LTRs. Dual inhibition of DNA methylation and histone modifications by knockdown of G9a, SUV39H1 and EZH2 showed further upregulation of evolutionary young LTRs. Therefore, combination treatment targeting DNA methylation and the histone methyltransferases (G9a, SUV39H1 and EZH2) inhibitor may be useful in epigenetic therapy for cancer patients.

Citation Format: Hitoshi Ohtani, Minmin Liu, Wanding Zhou, Gangning Liang, Peter A. Jones. A switch in epigenetic silencing mechanisms of endogenous retroviruses during human genome evolution [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 2993.

Parent Artery Reconstruction for Large or Giant Cerebral Aneurysms Using the Tubridge Flow Diverter: A Multicenter, Randomized, Controlled Clinical Trial (PARAT)

BACKGROUND AND PURPOSE

Although flow diverters have been reported with favorable clinical and angiographic outcomes in various literatures, randomized trials determining their true effectiveness and safety are still in lack. The Parent Artery Reconstruction for Large or Giant Cerebral Aneurysms Using the Tubridge Flow Diverter (PARAT) trial was designed to evaluate the safety and efficacy of the Tubridge flow diverter in the treatment of large or giant aneurysms in comparison with Enterprise stent-assisted coiling.

MATERIALS AND METHODS

This prospective, multicenter, randomized trial was conducted at 12 hospitals throughout China. Enrolled adults with unruptured large/giant intracranial aneurysms were randomly assigned (1:1) to receive either Enterprise stent-assisted coiling or Tubridge flow diverter implantation. The primary end point was complete occlusion at 6-month follow-up, while secondary end points included technical success, mortality, target vessel-related stroke, aneurysm bleeding, in-stent stenosis, parent artery occlusion, and the frequency of all adverse events.

RESULTS

Among 185 enrolled subjects, 41 withdrew before procedure initiation. Overall, 82 subjects underwent Tubridge implantation, and 62 subjects were primarily treated with stent-assisted coiling. The results of 6-month follow-up imaging included complete occlusion rates of 75.34% versus 24.53% for the Tubridge and stent-assisted coiling groups, respectively, with a calculated common odds ratio of 9.4 (95% confidence interval, 4.14-21.38; P < .001). There was a higher, nonsignificant frequency of complications for Tubridge subjects. Multivariate analysis showed a decreased stroke rate at the primary investigational site, with a marginal P value (P = .051).

CONCLUSIONS

This trial showed an obviously higher rate of large and giant aneurysm obliteration with the Tubridge FD over Enterprise stent-assisted coiling. However, this higher obliteration rate came at the cost of a nonsignificantly higher rate of complications. Investigational site comparisons suggested that a learning curve for flow-diverter implantation should be recognized and factored into trial designs.

S100β in newborns after C-section with general vs. epidural anesthesia: a prospective observational study

BACKGROUND

Preclinical evidence suggests that general anesthetics can dose dependently induce neurodegeneration in the developing brains of animals which can be reliably determined by measurement of blood S100β, but this correlation remains unclear in humans. We hypothesized that S100β would not be increased in cord arterial blood of fetuses exposed briefly to general anesthetics during a C-section, compared with epidural anesthesia.

METHODS

A prospective observational clinical study comparatively measured changes of brain damage biomarker S100β ratio of umbilical artery over vein (changes after fetus circulation) immediately after delivery under C-section with either epidural or general anesthesia. Newborn blood gas measurements, APGAR scores, and maternal well-being were also compared.

RESULTS

Compared with epidural anesthesia, general anesthesia resulted in the lower S100β ratio of umbilical artery over the vein (medium 2.64 [quartiles 1.39, 3.45] vs. medium 1.59 [quartiles 0.88, 2.01], P = 0.031), without changing the S100β level in the vein of the mother. There was no significant difference between general and epidural anesthesia when comparing other maternal and newborn parameters.

CONCLUSION

S100β levels in newborn after C-section is lower with general anesthesia than epidural anesthesia, with unclear mechanisms.

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers

Purpose

The clinical management of small renal masses (SRMs) is challenging since the current methods for distinguishing between benign masses and malignant renal cell carcinomas (RCCs) are frequently inaccurate or inconclusive. In addition, renal cancer subtypes also have different treatments and outcomes. High false negative rates increase the risk of cancer progression and indeterminate diagnoses result in unnecessary and potentially morbid surgical procedures.

Experimental Design

We built a predictive classification model for kidney tumors using 697 DNA methylation profiles from six different subgroups: clear cell, papillary and chromophobe RCC, benign angiomylolipomas, oncocytomas, and normal kidney tissues. Furthermore, the DNA methylation-dependent classifier has been validated in 272 ex vivo needle biopsy samples from 100 renal masses (71% SRMs).

Results

In general, the results were highly reproducible (89%, n=70) in predicting identical malignant subtypes from biopsies. Overall, 98% of adjacent-normals (n=102) were correctly classified as normal, while 92% of tumors (n=71) were correctly classified malignant and 86% of benign (n=29) were correctly classified benign by this classification model.

Conclusions

Overall, this study provides molecular-based support for using routine needle biopsies to determine tumor classification of SRMs and support the clinical decision-making.

Dual inhibition of DNMTs and EZH2 can overcome both intrinsic and acquired resistance of myeloma cells to IMiDs in a cereblon-independent manner

Thalidomide and its derivatives, lenalidomide and pomalidomide (also known as IMiDs), have significantly changed the treatment landscape of multiple myeloma, and the recent discovery of cereblon (CRBN) as their direct biological target has led to a deeper understanding of their complex mechanism of action. In an effort to comprehend the precise mechanisms behind the development of IMiD resistance and examine whether it is potentially reversible, we established lenalidomide‐resistant (‐LR) and pomalidomide‐resistant (‐PR) human myeloma cell lines from two IMiD‐sensitive cell lines, OPM2 and NCI‐H929, by continuous culture in the presence of lenalidomide or pomalidomide for 4–6 months, until acquirement of stable resistance. By assessing genome‐wide DNA methylation and chromatin accessibility in these cell lines, we found that acquired IMiD resistance is associated with an increase in genome‐wide DNA methylation and an even greater reduction in chromatin accessibility. Transcriptome analysis confirmed that resistant cell lines are mainly characterized by a reduction in gene expression, identifying SMAD3 as a commonly downregulated gene in IMiD‐resistant cell lines. Moreover, we show that these changes are potentially reversible, as combination of 5‐azacytidine and EPZ‐6438 not only restored the observed accessibility changes and the expression of SMAD3, but also resensitized the resistant cells to both lenalidomide and pomalidomide. Interestingly, the resensitization process was independent of CRBN. Our data suggest that simultaneous inhibition of DNA methyl transferases and EZH2 leads to an extensive epigenetic reprogramming which allows myeloma cells to (re)gain sensitivity to IMiDs.

DNA methylation aberrancies delineate clinically distinct subsets of colorectal cancer and provide novel targets for epigenetic therapies

Colorectal cancer (CRC) is a worldwide health concern with respect to both incidence and mortality, and as a result, CRC tumorigenesis, progression and metastasis have been heavily studied, especially with respect to identifying genetic, epigenetic, transcriptomic and proteomic profiles of disease. DNA methylation alterations are hallmarks of CRC, and epigenetic driver genes have been identified that are thought to be involved in early stages of tumorigenesis. Moreover, distinct CRC patient subgroups are organized based on DNA methylation profiles. CRC tumors displaying CpG island methylator phenotypes (CIMPs), defined as DNA hypermethylation at specific CpG islands in subsets of tumors, show high concordance with specific genetic alterations, disease risk factors and patient outcome. This review details the DNA methylation alterations in CRC, the significance of CIMP status, the development of treatments based on specific molecular profiles and the application of epigenetic therapies for CRC patient treatment.

Epigenetic landscape change analysis during human EMT sheds light on a key EMT mediator TRIM29

Epithelial to mesenchymal transition (EMT) is a key trans-differentiation process, which plays a critical role in physiology and pathology. Although gene expression changes in EMT have been scrutinized, study of epigenome is in its infancy. To understand epigenetic changes during TWIST-driven EMT, we used the AcceSssIble assay to study DNA methylation and chromatin accessibility in human mammary epithelial cells (HMECs). The DNA methylation changes were found to have functional significance in EMT - i.e. methylated genes were enriched for E-box motifs that can be recognized by TWIST, at the promoters suggesting a potential targeting phenomenon, whereas the demethylated regions were enriched for pro-metastatic genes, supporting the role of EMT in metastasis. TWIST-induced EMT triggers alterations in chromatin accessibility both independent of and dependent on DNA methylation changes, primarily resulting in closed chromatin conformation. By overlapping the genes, whose chromatin structure is changed during early EMT and a known "core EMT signature", we identified 18 driver candidate genes during EMT, 14 upregulated and 4 downregulated genes with corresponding chromatin structure changes. Among 18 genes, we focused on TRIM29 as a novel marker of EMT. Although loss of TRIM29 is insufficient to suppress CDH, it is enough to induce CDH2 and VIM. Gene functional annotation analysis shows the involvement of TRIM29 in epidermal development, cell differentiation and cell migration. Taken together, our results provide a robust snapshot of chromatin state during human EMT and identify TRIM29 as a core mediator of EMT.

Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers

The role of cytosine methylation in the structure and function of enhancers is not well understood. In this study, we investigate the role of DNA methylation at enhancers by comparing the epigenomes of the HCT116 cell line and its highly demethylated derivative, DKO1. Unlike promoters, a portion of regular and super- or stretch enhancers show active H3K27ac marks co-existing with extensive DNA methylation, demonstrating the unexpected presence of bivalent chromatin in both cultured and uncultured cells. Furthermore, our findings also show that bivalent regions have fewer nucleosome-depleted regions and transcription factor-binding sites than monovalent regions. Reduction of DNA methylation genetically or pharmacologically leads to a decrease of the H3K27ac mark. Thus, DNA methylation plays an unexpected dual role at enhancer regions, being anti-correlated focally at transcription factor-binding sites but positively correlated globally with the active H3K27ac mark to ensure structural enhancer integrity.

Hepatitis B virus reactivation in breast cancer patients undergoing chemotherapy: A review and meta-analysis of prophylaxis management

Hepatitis B virus (HBV) reactivation during or after chemotherapy in patients with breast cancer has become a remarkable clinical problem. Prophylactic nucleos(t)ide analogues (NAs) are recommended for patients with breast cancer who are hepatitis B surface antigen (HBsAg) positive before chemotherapy. We performed an up-to-date meta-analysis to compare the efficacy of prophylactic lamivudine use with nonprophylaxis in HBsAg-positive breast cancer patients undergoing chemotherapy. PubMed, the Cochrane Library and China National Knowledge Infrastructure (CNKI) databases were searched for relevant articles until June 2016. Eligible articles comparing the efficacy of prophylactic lamivudine use with nonprophylaxis in HBsAg-positive breast cancer patients undergoing chemotherapy were identified. Eight studies which had enrolled 709 HBsAg-positive breast cancer patients undergoing chemotherapy were analysed. Lamivudine prophylaxis significantly reduced the rates of chemotherapy-associated hepatitis B flares in chronic hepatitis B in breast cancer compared with patients with nonprophylaxis (odds ratio [OR]=0.15, 95% confidence interval [CI]: 0.07-0.35, P<.00001). Chemotherapy disruption rates attributed to HBV reactivation in the prophylaxis groups were significantly lower than the nonprophylaxis groups (OR=0.17, 95% CI: 0.07-0.43, P=.0002). Patients with lamivudine prophylaxis had a higher risk for tyrosine-methionine-aspartate-aspartate (YMDD) motif mutations than patients with nonprophylaxis (OR=6.33, 95% CI: 1.01-39.60, P=.05). Prophylactic antiviral therapy management is necessary for HBsAg-positive breast cancer patients undergoing chemotherapy, in spite of high correlation with lamivudine-resistant HBV variants with YMDD motif mutations.

Down-regulation of ARID1A is sufficient to initiate neoplastic transformation along with epigenetic reprogramming in non-tumorigenic endometriotic cells

The chromatin remodeler AT-Rich Interactive Domain 1A (ARID1A) is frequently mutated in ovarian clear cell carcinoma (OCCC) and endometriosis precursor lesions. Here, we show that knocking down ARID1A in an immortalized endometriosis cell line is sufficient to induce phenotypic changes indicative of neoplastic transformation as evidenced by higher efficiency of anchorage-independent growth, increased propensity to adhere to collagen, and greater capacity to invade basement membrane extract in vitro. ARID1A knockdown is associated with expression dysregulation of 99 target genes, and many of these expression changes are also observed in primary OCCC tissues. Further, pathway analysis indicates these genes fall within networks highly relevant to tumorigenesis including integrin and paxillin pathways. We demonstrate that the down-regulation of ARID1A does not markedly alter global chromatin accessibility or DNA methylation but unexpectedly, we find strong increases in the active H3K27ac mark in promoter regions and decreases of H3K27ac at potential enhancers. Taken together, these data provide evidence that ARID1A mutation can be an early stage event in the oncogenic transformation of endometriosis cells giving rise to OCCC.

DNA methylation aberrancies as a guide for surveillance and treatment of human cancers

DNA methylation aberrancies are hallmarks of human cancers and are characterized by global DNA hypomethylation of repetitive elements and non-CpG rich regions concomitant with locus-specific DNA hypermethylation. DNA methylation changes may result in altered gene expression profiles, most notably the silencing of tumor suppressors, microRNAs, endogenous retorviruses and tumor antigens due to promoter DNA hypermethylation, as well as oncogene upregulation due to gene-body DNA hypermethylation. Here, we review DNA methylation aberrancies in human cancers, their use in cancer surveillance and the interplay between DNA methylation and histone modifications in gene regulation. We also summarize DNA methylation inhibitors and their therapeutic effects in cancer treatment. In this context, we describe the integration of DNA methylation inhibitors with conventional chemotherapies, DNA repair inhibitors and immune-based therapies, to bring the epigenome closer to its normal state and increase sensitivity to other therapeutic agents to improve patient outcome and survival.

[Polymorphism analysis of MTHFR，BMPR1B and TYMS in microtia]

Objective:To explore the relationship between MTHFR，BMPR1B and TYMS polymorphism and congenitial microtia in Chinese Han population.Method:A total of 180 microtia patients and 141 healthy participants were enrolled in this study.The genotyping of MTHFR rs4846049, BMPR1B rs1434536 and TYMS rs2790 of the participants were examined with multiple PCR. Frequencies and allele distribution of MTHFR rs4846049,BMPR1B rs1434536 and TYMS rs2790 between cases and control were analyzed with Chi-square test. Result:The genotype frequency distribution of TYMS rs27901 polymorphism was significantly different between two groups(P<0.05).Furthermore, gender stratified analysis showed that TYMS rs2790 polymorphism mainly increase the risks of congenitial microtia in male(P<0.05).Compared with AA genotype,the mircotia risks of subjects with AG GG AG+GG raised to 1.93, 3.23 and 2.10 times,respectively(95%CI:1.07-3.48、1.12-9.33 and 1.20-3.68).However,there was no relationship between MTHFR rs4846049, BMPR1B rs1434536 and microtia. Conclusion:The TYMS rs2790 polymorphism may be a risk factor of microtia in male.

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data.