Concurrent IMRT and weekly cisplatin followed by GDP chemotherapy in newly diagnosed, stage IE to IIE, nasal, extranodal NK/T-Cell lymphoma

On the basis of the benefits of frontline radiation in early-stage, extranodal natural killer (NK)/T-cell lymphoma (ENKTL), we conducted the trial of concurrent chemoradiotherapy (CCRT) followed by three cycles of gemcitabine, dexamethasone and cisplatin (GDP). Thirty-two patients with newly diagnosed, stage IE to IIE, nasal ENKTL received CCRT (that is, all patients received intensity-modulated radiotherapy 56 Gy and cisplatin 30 mg/m² weekly, 3–5 weeks). Three cycles of GDP (gemcitabine 1000 mg/m² intravenously (i.v.) on days 1 and 8, dexamethasone 40 mg orally on days 1–4 and cisplatin 75 mg/m² i.v. on day 1 (GDP), every 21 days as an outpatient were scheduled after CCRT. All patients completed CCRT, which resulted in 100% response that included 24 complete responses (CRs) and eight partial responses. The CR rate after CCRT was 75.0% (that is, 24 of 32 responses). Twenty-eight of the 32 patients completed the planned three cycles of GDP, whereas four patients did not because they withdrew (n=1) or because they had an infection (n=3). The overall response rate and the CR rate were 90.6% (that is, 29 of 32 responses) and 84.4% (that is, 27 of 32 responses), respectively. Only two patient experienced grade 3 toxicity during CCRT (nausea), whereas 13 of the 30 patients experienced grade 4 neutropenia. The estimated 3-year overall survival and progression-free rates were 87.50% and 84.38%, respectively. In conclusion, CCRT followed by GDP chemotherapy can be a feasible and effective treatment strategy for stage IE to IIE nasal ENKTL.

A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence

PURPOSE

The high risk of recurrence after transurethral resection of bladder tumor of nonmuscle invasive disease requires lifelong treatment and surveillance. Changes in DNA methylation are chemically stable, occur early during tumorigenesis, and can be quantified in bladder tumors and in cells shed into the urine. Some urine markers have been used to help detect bladder tumors; however, their use in longitudinal tumor recurrence surveillance has yet to be established.

EXPERIMENTAL DESIGN

We analyzed the DNA methylation levels of six markers in 368 urine sediment samples serially collected from 90 patients with noninvasive urothelial carcinoma (Tis, Ta, T1; grade low-high). The optimum marker combination was identified using logistic regression with 5-fold cross-validation, and validated in separate samples.

RESULTS

A panel of three markers discriminated between patients with and without recurrence with the area under the curve of 0.90 [95% confidence interval (CI), 0.86-0.92] and 0.95 (95% CI, 0.90-1.00), sensitivity and specificity of 86%/89% (95% CI, 74%-99% and 81%-97%) and 80%/97% (95% CI, 60%-96% and 91%-100%) in the testing and validation sets, respectively. The three-marker DNA methylation test reliably predicted tumor recurrence in 80% of patients superior to cytology (35%) and cystoscopy (15%) while accurately forecasting no recurrence in 74% of patients that scored negative in the test.

CONCLUSIONS

Given their superior sensitivity and specificity in urine sediments, a combination of hyper- and hypomethylated markers may help avoid unnecessary invasive exams and reveal the importance of DNA methylation in bladder tumorigenesis.

Gene body methylation can alter gene expression and is a therapeutic target in cancer

DNA methylation in promoters is well known to silence genes and is the presumed therapeutic target of methylation inhibitors. Gene body methylation is positively correlated with expression, yet its function is unknown. We show that 5-aza-2'-deoxycytidine treatment not only reactivates genes but decreases the overexpression of genes, many of which are involved in metabolic processes regulated by c-MYC. Downregulation is caused by DNA demethylation of the gene bodies and restoration of high levels of expression requires remethylation by DNMT3B. Gene body methylation may, therefore, be an unexpected therapeutic target for DNA methylation inhibitors, resulting in the normalization of gene overexpression induced during carcinogenesis. Our results provide direct evidence for a causal relationship between gene body methylation and transcription.

Abstract LB-130: Simultaneous evaluation of chromatin accessibility and DNA methylation in clear cell renal cell carcinoma by a newly developed assay, AcceSssIble

Background: Epigenetic changes, such as nucleosome positioning and DNA methylation, control gene expression and are altered in cancer. Therefore, accurately mapping these changes between normal and tumor tissue will provide novel information for identification of epigenetic driver genes, biomarker discovery, and anti-tumor therapy development for clear cell renal cell carcinoma (ccRCC), the most common subtype of renal carcinoma. Current methods are expensive and require a considerable amount of biological tissue.

Methods: We have developed a novel assay (AcceSssIble) to determine DNA methylation and nucleosome occupancy in a single experiment. It is rapid and cost-effective, requiring the Infinium HumanMethylation450 BeadChip platform and the CpG methyltransferase M.SssI. Preliminary studies using fresh and frozen kidney tumors show that the epigenetic profile is maintained in frozen tissues, making this method suitable to interrogate archived clinical samples.

Results: We have used AcceSssIble to assay the epigenomes of 5 fresh ccRCC tumors and their adjacent normal tissue, and have uncovered 257 genes that are associated with changes in chromatin accessibility in at least 4 ccRCC samples; 155 of these genes also show a change in endogenous DNA methylation levels in at least 4 tumors. These chromatin accessibility and DNA methylation changes occurred in the promoter regions, open reading frames, and the 3’ untranslated regions (UTRs) of the genes. Cross-referencing our results to the expression data of 72 matched ccRCC samples from The Cancer Genome Atlas (TCGA), we discovered that 29% (74/257) of these genes exhibited a significant change in gene expression, over half of which had been previously implicated in various cancers, including ccRCC. Furthermore, we observed chromatin accessibility changes in intergenic regions, including several which contain known transcription factor binding sites and ncRNA promoter regions. These sites might serve as potential enhancers for neighboring genes important to the development of ccRCC.

Conclusions: In these studies, we were able to identify epigenetic changes in ccRCC samples associated with known oncogenes and tumor suppressor genes, as well as uncover novel targets. These targets, associated both within genes as well as in intergenic regions, undergo changes in chromatin structure and may be important in the development of ccRCC. Linking these findings to gene expression data revealed functionally relevant targets for ccRCC treatment. Expansion of these studies into a larger number of clinical samples across tumor grades will allow us to uncover biomarkers that can be used for personalized medicine.

Citation Format: Elinne Becket, Christopher Duymich, Yin-Wei Chang, Kurinji Pandiyan, Peter A. Jones, Gangning Liang. Simultaneous evaluation of chromatin accessibility and DNA methylation in clear cell renal cell carcinoma by a newly developed assay, AcceSssIble. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-130. doi:10.1158/1538-7445.AM2014-LB-130

Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2, and Igf2r are associated with chronic cystitis in a cyclophosphamide-induced mouse model

OBJECTIVE

To determine whether epigenetic changes occur during cyclophosphamide-induced chronic bladder inflammation in mice.

MATERIALS AND METHODS

Epigenetic changes play a role in the regulation of inflammatory genes in noncancer diseases such as asthma and chronic obstructive pulmonary disease. However, epigenetic (deoxyribonucleic acid [DNA] methylation) changes during chronic bladder inflammation have not been previously described. Chronic cystitis was induced in 3 groups of adult CD-1 male mice using multiple weight-based intraperitoneal cyclophosphamide injections during a 3-month period. Histopathologic and MethyLight assays were performed on specimens with chronic bladder inflammation at multiple points to monitor cystitis progression and DNA methylation changes compared with the control specimens.

RESULTS

Histopathologic analysis showed the most extensive edema and urothelial sloughing at the 1-month point. MethyLight analyses revealed statistically significant changes in DNA methylation associated with the Calca, Timp3, Mmp2, and Igf2r genes in the chronic bladder injury model. The changes in DNA methylation associated with chronic cystitis were DNA hypomethylation of the Calca gene in the control tissue and DNA hypermethylation for the Calca, Timp3, Mmp2, and Igf2r genes compared with that in the control tissue.

CONCLUSION

DNA methylation changes were noted in the Calca, Timp3, Mmp2, and Igf2r genes during chronic cystitis in a murine model. Epigenetic changes appear to play a role in the regulation of inflammatory bladder genes during chronic cystitis; however, additional studies are needed to elucidate the pathways associated with these genes.

Abstract B56: DNA demethylation in gene bodies is of therapeutic significance

Reversal of aberrant promoter hypermethylation and associated gene silencing has been the primary focus of epigenetic therapy. Recently, gene body methylation has been implicated as having a functional role in the regulation of gene expression; however it is unclear how gene body methylation changes might contribute to the therapeutic effects of epigenetic therapy. To investigate the role of DNA demethylation in inducing gene expression changes in a comprehensive way, we treated the HCT116 colon cancer cell line with 5-Aza-2′-deoxycytidine (5-Aza-CdR) transiently for 24 hours and monitored changes in gene expression and DNA methylation levels at gene bodies and promoters for up to 42 days after treatment using 450K Infinium DNA methylation arrays and expression arrays. We observed that probes that became demethylated and subsequently regained methylation did at different rates. As we expected, demethylation of methylated promoters is negatively correlated with expression (R2≤ -0.75) and considerable demethylation of promoters (485) and the associated gene reactivation could be maintained for up to 42 days after drug treatment. Most of these genes are de novo methylated and their expression is down-regulated in primary colon cancers in the TCGA database. Strikingly, a group of genes shows a positive correlation between demethylation of gene bodies and down-regulation of gene expression after treatment (R2≥ 0.75). Four hundred ninety eight have fast rebound methylation kinetics and decreased expression and they are enriched for genes involved in metabolic process which are over-expressed in primary colon cancer tissues. Furthermore, 494 genes with sustained down-regulation of gene expression maintained their demethylated status and those are enriched for de novo methylation targets and over-expressed genes in colon cancer.

Our results demonstrate that DNA demethylation at gene bodies induced by 5-Aza-CdR can be of therapeutic significance by resulting in the down-regulation of genes that are overexpressed in cancers. Our findings also confirm that demethylation treatment could potentially cause prolonged reactivation of genes that are silenced by promoter methylation while simultaneously down-regulating genes that are overexpressed and have body methylation. Together, demethylation of gene bodies may confer therapeutic benefit in addition to demethylation of gene promoters.

Citation Format: Han Han Zhang, Xiaojing Yang, Daniel D. De Carvalho, Peter A. Jones, Gangning Liang. DNA demethylation in gene bodies is of therapeutic significance. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B56.

Abstract PR07: SNF5 is an essential executor of epigenetic regulation during differentiation

Nucleosome occupancy controls the accessibility of the transcription machinery to DNA regulatory regions and serves an instructive role for gene expression. Chromatin remodelers, such as the BAF complexes, are responsible for establishing nucleosome occupancy patterns, which are key to epigenetic regulation along with DNA methylation and histone modifications. Some reports have assessed the roles of the BAF complex subunits and stemness in murine embryonic stem cells. However, the details of the relationships between remodelers and transcription factors in altering chromatin configuration, which ultimately affects gene expression during cell differentiation, remain unclear. Here for the first time we demonstrate that SNF5, a core subunit of the BAF complex, negatively regulates OCT4 levels in pluripotent cells and is essential for cell survival during differentiation. SNF5 is responsible for generating nucleosomedepleted regions (NDRs) at the regulatory sites of OCT4 repressed target genes such as PAX6 and NEUROG1, which are crucial for cell fate determination. Concurrently, SNF5 closes the NDRs at the regulatory regions of OCT4 activated target genes such as OCT4 itself and NANOG. Furthermore, using loss and gain of function experiments followed by extensive genome-wide analyses including gene expression microarrays and ChIP-sequencing, we highlight that SNF5 plays dual roles during differentiation by antagonizing the expression of genes that were either activated or repressed by OCT4, respectively. Together, we demonstrate that SNF5 executes the switch between pluripotency and differentiation.

This abstract is also presented as Poster A39.

Citation Format: Jueng Soo You, Daniel D. De Carvalho, Chao Dai, Minmin Liu, Kurinji Pandiyan, Xianghong Zhou, Gangning Liang, Peter A. Jones. SNF5 is an essential executor of epigenetic regulation during differentiation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR07.

Diagnostic markers of urothelial cancer based on DNA methylation analysis

Background

Early detection and risk assessment are crucial for treating urothelial cancer (UC), which is characterized by a high recurrence rate, and necessitates frequent and invasive monitoring. We aimed to establish diagnostic markers for UC based on DNA methylation.

Methods

In this multi-center study, three independent sample sets were prepared. First, DNA methylation levels at CpG loci were measured in the training sets (tumor samples from 91 UC patients, corresponding normal-appearing tissue from these patients, and 12 normal tissues from age-matched bladder cancer-free patients) using the Illumina Golden Gate methylation assay to identify differentially methylated loci. Next, these methylated loci were validated by quantitative DNA methylation by pyrosequencing, using another cohort of tissue samples (Tissue validation set). Lastly, methylation of these markers was analyzed in the independent urine samples (Urine validation set). ROC analysis was performed to evaluate the diagnostic accuracy of these 12 selected markers.

Results

Of the 1303 CpG sites, 158 were hyper ethylated and 356 were hypo ethylated in tumor tissues compared to normal tissues. In the panel analysis, 12 loci showed remarkable alterations between tumor and normal samples, with 94.3% sensitivity and 97.8% specificity. Similarly, corresponding normal tissue could be distinguished from normal tissues with 76.0% sensitivity and 100% specificity. Furthermore, the diagnostic accuracy for UC of these markers determined in urine samples was high, with 100% sensitivity and 100% specificity.

Conclusion

Based on these preliminary findings, diagnostic markers based on differential DNA methylation at specific loci can be useful for non-invasive and reliable detection of UC and epigenetic field defect.

SNF5 is an essential executor of epigenetic regulation during differentiation

Nucleosome occupancy controls the accessibility of the transcription machinery to DNA regulatory regions and serves an instructive role for gene expression. Chromatin remodelers, such as the BAF complexes, are responsible for establishing nucleosome occupancy patterns, which are key to epigenetic regulation along with DNA methylation and histone modifications. Some reports have assessed the roles of the BAF complex subunits and stemness in murine embryonic stem cells. However, the details of the relationships between remodelers and transcription factors in altering chromatin configuration, which ultimately affects gene expression during cell differentiation, remain unclear. Here for the first time we demonstrate that SNF5, a core subunit of the BAF complex, negatively regulates OCT4 levels in pluripotent cells and is essential for cell survival during differentiation. SNF5 is responsible for generating nucleosome-depleted regions (NDRs) at the regulatory sites of OCT4 repressed target genes such as PAX6 and NEUROG1, which are crucial for cell fate determination. Concurrently, SNF5 closes the NDRs at the regulatory regions of OCT4-activated target genes such as OCT4 itself and NANOG. Furthermore, using loss- and gain-of-function experiments followed by extensive genome-wide analyses including gene expression microarrays and ChIP-sequencing, we highlight that SNF5 plays dual roles during differentiation by antagonizing the expression of genes that were either activated or repressed by OCT4, respectively. Together, we demonstrate that SNF5 executes the switch between pluripotency and differentiation.

DNA is packaged with proteins into higher-order chromatin structures, which makes genes inherently resistant to transcription initiation. The importance of chromatin remodelers in inducing structural changes to chromatin and, therefore, in controlling the expression of genes has recently resurfaced with the realization that several of them are mutated in human cancers. SNF5, which serves as the core subunit of the BAF remodeling complex, is one such remodeler. In this study, we identify the role of SNF5 induced chromatin remodeling in cell differentiation, the commitment of embryonic cells to a mature lineage-committed state. Importantly, we find that SNF5 establishes appropriate chromatin remodeling patterns during differentiation by controlling the levels of the OCT4 protein, the master determinant of the undifferentiated state. On receipt of differentiation cues, SNF5 opens the chromatin of repressed genes that are occupied by OCT4. SNF5 also induces the closing of genes that are being actively transcribed and OCT4 bound. Further, we show that SNF5 is necessary for cell survival during differentiation, highlighting its crucial role in the process. Together, our data shed novel insights on the importance of SNF5 in maintaining the balance between the embryonic and differentiated states.

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

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

Abstract 677: Transient exposure to decitabine results in sustained cell growth inhibition and long term DNA demethylation at specific loci

Gene silencing mediated by aberrant promoter DNA hypermethylation is one of the key features of cancer. Although such modification is heritable, its dynamic nature and reversibility through pharmacological interventions make it an attractive therapeutic target. Over the past few decades, various DNA methyltransferase inhibitors have been developed with the goal of reactivating aberrantly silenced genes. Two FDA-approved demthylating agents, decitabine and azacitidine are efficacious for the treatment of myeloid malignancies (MDS). It has been shown that transient exposure of tumor cells to low dose decitabine and azacitidine results in reduced tumorigenecity. However, the mechanism underlying clinical efficacies of these DNA methyltransferase inhibitors remains unclear. Here we investigate the long-term effect (up to 10 weeks) on population doubling time and the returning of DNA methylation (rebound methylation) after transient exposure to decitabine in three cancer cell lines, HCT116, T24 and HL-60. We show that transient exposure results in inhibition of cell growth and reduction of their colony formation capacity (up to 42 days). Furthermore, we also show that the rebound methylation occurs at different rates depending on the region and the type of genes. The discrepancy in population doubling time between the vehicle and decitabine treated cells disappears when rebound methylation fully restores, suggesting the presence of a correlation between cell doubling and rebound methylation. The majority of probes, which exhibit fast rebound methylation, are located in gene bodies. We show a positive correlation between gene body methylation and expression. However, there is a small group of fast rebound probes located at the promoters. Many of them belong to cancer-testis antigens, which get reactivated and quickly re-silenced. On the other hand, the majority of probes, which exhibit slow rebound methylation are located at promoters and show an inverse correlation between methylation and expression. The presence of a nucleosome-depleted region and enrichments of active histone marks, H3K4me3 and H2A.Z are observed at the promoters of those genes up to 42 days after drug treatment. Interesting, this group is enriched for genes down-regulated in colon adenocarcinoma when compared to normal colon (p=3.3e−6). Taken together, the sustained reactivation of those genes may be the driving force in reducing tumorigenecity of cancer cells. Our study elucidates the mechanism of decitabine, thus advancing our understanding of epigenetic therapy.

Citation Format: Gangning Liang, Han Han, Daniel D. De Carvalho, Xiaojing Yang, Peter A. Jones. Transient exposure to decitabine results in sustained cell growth inhibition and long term DNA demethylation at specific loci. [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 677. doi:10.1158/1538-7445.AM2013-677

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

High-performance transparent solvent-free silicone resins with stable storage and low viscosity based on new hyperbranched polysiloxanes

Five new hyperbranched polysiloxanes, for example, methylhydrogen siloxanes (MHSis), with varying concentrations of silicon–methyl (Si-Me) groups were synthesized and characterized, and then a series of MHSi/poly(methylphenylvinylsilicone) (PSi) resins were prepared to investigate the influence of the structures and concentrations of MHSi on the integrated properties of both uncured and cured MHSi/PSi resins. The results show that the compatibility between MHSi and PSi is closely related to the concentration of Si-Me groups in the MHSi as well as the molar ratio of MHSi and PSi. If MHSi has a suitable concentration of Si-Me groups, and the molar ratios of MHSi to PSi are appropriate, transparent MHSi/PSi resins with stable compatibility can be obtained. In addition, these compatible resins show good thermal stability with dynamic mechanical and dielectric properties. They exhibit a great potential for use as high-performance solvent-free silicone resins in either vacuum pressure impregnating process or liquid-molding techniques.

Functional DNA demethylation is accompanied by chromatin accessibility

DNA methylation inhibitors such as 5-aza-2′-deoxycytidine (5-Aza-CdR) are currently used for the treatment of myelodysplastic syndrome. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. We use the colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open configuration. Consolidating our findings, we detect nucleosome retention at sites of global DNA methylation loss in DKO1, an HCT116-derived non-tumorigenic cell-line engineered for DNA methyltransferase disruption. Notably, regions that are open in both HCT116 cells after treatment and in DKO1 cells include promoters belonging to tumor suppressors and genes under-expressed in colorectal cancers. Our results indicate that only a minority of demethylated promoters are associated with nucleosome remodeling, and these could potentially be the epigenetic drivers causing the loss of tumorigenicity. Furthermore, we show that the chromatin opening induced by the histone deacetylase inhibitor suberoylanilide hydroxamic acid has strikingly distinct targets compared with those of 5-Aza-CdR, providing a mechanistic explanation for the importance of combinatorial therapy in eliciting maximal de-repression of the cancer epigenome.

Nucleosome occupancy and gene regulation during tumorigenesis

Nucleosomes are the basic structural units of eukaryotic chromatin. In recent years, it has become evident that nucleosomes and their position, in concert with other epigenetic mechanisms (such as DNA methylation, histone modifications, changes in histone variants, as well as small noncoding regulatory RNAs) play essential roles in the control of gene expression. Here, we discuss the mechanisms and factors that regulate nucleosome position and gene expression in normal and cancer cells.

miR-30d, miR-181a and miR-199a-5p cooperatively suppress the endoplasmic reticulum chaperone and signaling regulator GRP78 in cancer

GRP78, a major endoplasmic reticulum chaperone and signaling regulator, is commonly overexpressed in cancer. Moreover, induction of GRP78 by a variety of anti-cancer drugs, including histone deacetylase inhibitors, confers chemoresistance to cancer, thereby contributing to tumorigenesis. Thus, therapies aimed at decreasing GRP78 levels, which results in the inhibition of tumor cell proliferation and resensitization of tumor cells to chemotherapeutic drugs may hold promise for cancer treatment. Despite advances in our understanding of GRP78 actions, little is known about endogenous inhibitors controlling its expression. As endogenous regulators, microRNAs (miRNAs) play important roles in modulating gene expression; therefore, we sought to identify miRNA(s) that target GRP78, under the hypothesis that these miRNAs may serve as therapeutic agents. Here, we report that three miRNAs (miR-30d, miR-181a, miR-199a-5p) predicted to target GRP78 are down-regulated in prostate, colon and bladder tumors, and human cancer cell lines. We show that in C42B prostate cancer cells, these miRNAs down-regulate GRP78 and induce apoptosis by directly targeting its 3' untranslated region. Importantly, we demonstrate that the three miRNAs act cooperatively to decrease GRP78 levels, suggesting that multiple miRNAs may be required to efficiently control the expression of some genes. In addition, delivery of multiple miRNAs by either transient transfection or lentivirus transduction increased the sensitivity of cancer cells to the histone deacetylase inhibitor, trichostatin A, in C42B, HCT116 and HL-60 cells. Together, our results indicate that the delivery of co-transcribed miRNAs can efficiently suppress GRP78 levels and GRP78-mediated chemoresistance, and suggest that this strategy holds therapeutic potential.

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome-depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy.

High dose compressive loads attenuate bone mineral loss in humans with spinal cord injury

People with spinal cord injury (SCI) lose bone and muscle integrity after their injury. Early doses of stress, applied through electrically induced muscle contractions, preserved bone density at high-risk sites. Appropriately prescribed stress early after the injury may be an important consideration to prevent bone loss after SCI.

INTRODUCTION

Skeletal muscle force can deliver high compressive loads to bones of people with spinal cord injury (SCI). The effective osteogenic dose of load for the distal femur, a chief site of fracture, is unknown. The purpose of this study is to compare three doses of bone compressive loads at the distal femur in individuals with complete SCI who receive a novel stand training intervention.

METHODS

Seven participants performed unilateral quadriceps stimulation in supported stance [150% body weight (BW) compressive load-"High Dose" while opposite leg received 40% BW-"Low Dose"]. Five participants stood passively without applying quadriceps electrical stimulation to either leg (40% BW load-"Low Dose"). Fifteen participants performed no standing (0% BW load-"Untrained") and 14 individuals without SCI provided normative data. Participants underwent bone mineral density (BMD) assessment between one and six times over a 3-year training protocol.

RESULTS

BMD for the High Dose group significantly exceeded BMD for both the Low Dose and the Untrained groups (p < 0.05). No significant difference existed between the Low Dose and Untrained groups (p > 0.05), indicating that BMD for participants performing passive stance did not differ from individuals who performed no standing. High-resolution CT imaging of one High Dose participant revealed 86% higher BMD and 67% higher trabecular width in the High Dose limb.

CONCLUSION

Over 3 years of training, 150% BW compressive load in upright stance significantly attenuated BMD decline when compared to passive standing or to no standing. High-resolution CT indicated that trabecular architecture was preserved by the 150% BW dose of load.

CD40L demethylation in CD4(+) T cells from women with rheumatoid arthritis

We have previously demonstrated that DNA demethylation of CD40L on the X chromosome is responsible for female susceptibility to systemic lupus erythematosus (SLE). It is unknown whether aberrant methylation of the CD40L gene also contributes to the higher incidence of rheumatoid arthritis (RA) in females. In this study, we used real-time RT-PCR and flow cytometry to compare CD40L expression levels, and bisulfite sequencing to assess the methylation status of the CD40L promoter region. The results show that CD40L is upregrulated in CD4(+) T cells of female patients with RA. In addition, the CD40L promoter region in CD4(+) T cells from female RA patients was found to be demethylated, which corresponded with increased CD40L mRNA expression. These findings suggest that DNA demethylation contributes to CD40L expression in RA CD4(+) T cells and may in part explain the female preponderance of this disease.

DNA methylation screening identifies driver epigenetic events of cancer cell survival

Cancer cells typically exhibit aberrant DNA methylation patterns that can drive malignant transformation. Whether cancer cells are dependent on these abnormal epigenetic modifications remains elusive. We used experimental and bioinformatic approaches to unveil genomic regions that require DNA methylation for survival of cancer cells. First, we surveyed the residual DNA methylation profiles in cancer cells with highly impaired DNA methyltransferases. Then, we clustered these profiles according to their DNA methylation status in primary normal and tumor tissues. Finally, we used gene expression meta-analysis to identify regions that are dependent on DNA methylation-mediated gene silencing. We further showed experimentally that these genes must be silenced by DNA methylation for cancer cell survival, suggesting these are key epigenetic events associated with tumorigenesis.

Demethylation of the FCER1G promoter leads to FcεRI overexpression on monocytes of patients with atopic dermatitis

BACKGROUND

Overexpression of the high-affinity receptor for immunoglobulin E on atopic monocytes and dendritic cells is known to contribute to the pathogenesis of atopic dermatitis (AD). However, it remains unclear what is the underlying mechanism of FcεRI deregulation. It has been speculated that epigenetic deregulation may play a role.

METHODS

Global DNA methylation levels of monocytes from 10 AD patients and 10 healthy controls were measured using a global DNA methylation kit. Bisulfite sequencing was performed to determine the methylation status of the FCER1G promoter region. FcεRIγ mRNA and FcεRI protein levels were detected by real-time RT-PCR, Western blotting, and flow cytometry, respectively. Patch methylation and the demethylating agent, 5-azacytidine, were used to determine the functional significance of methylation changes on FcεRI expression.

RESULTS

Monocytes from AD patients show a global hypomethylation, as well as a locus-specific hypomethylation at FCER1G promoter, as compared to healthy controls. Furthermore, this hypomethylation of FCER1G is inversely correlated with its expression. Patch methylation in combination with luciferase reporter assay confirmed the direct relationship between methylation and expression. Moreover, treating healthy monocytes with 5-azacytidine caused a reduction in methylation levels and an induction in FcεRIγ transcription and surface expression of FcεRI.

CONCLUSION

Demethylation of specific regulatory elements within the FCER1G locus contributes to FcεRI overexpression on monocytes from patients with AD.