Gene Promoter CpG Island Research Articles

Abstract PO2-08-11: The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours

Abstract Background: Identification of germline mutations in hereditary breast cancer (HBC) genes can have profound benefits in the treatment of breast cancer (BC) and manging risk for patient and the family. In addition, sequencing of the tumours can reveal clinically relevant somatic features, such as homologous recombination deficiency (HRD) and mutational signatures, that can guide treatment which are not discernible by germline sequencing alone. We hypothesised that current standard of care where women diagnosed with BC are not routinely offered tumour sequencing is suboptimal as fails to exploit all therapeutic vulnerabilities which can be exploited in the treatment of BC. The MAGIC study is the first prospective trial in Australia of unselected invasive BCs in general oncology practice combining both germline and tumour sequencing. Methods: The MAGIC study included a total of 651 consecutive consented patients presenting with non-metastatic BC between June 2020 to March 2023. It included invasive BC, high-grade DCIS and pleomorphic LCIS. The sequencing was conducted in two phases; for phase one, 157 cases underwent whole genome sequencing (WGS) on both germline and matched BC DNA while for phase two, 494 cases underwent only germline whole exome sequencing. Germline variants were interrogated for pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, BARD1, BRIP1, RAD51B, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2, CDH1, PTEN, STK11, TP53 and NTHL1. Tumour homologous recombination (HR) repair deficiency was calculated using HRDetect (Nat Med 2017;23:517). For BCs showing a high HRDetect score ( >0.75) all HBC gene promoter CpG islands were assessed for hypermethylation using the Twist NGS Methylation system. Mutational signatures were calculated from somatic mutations identified from whole genome sequenced BCs using the DeconstructSig package in R (Genome Biol. 2016;17:31) and referenced against the COSMIC v2 signature catalogue. Results: Actionable germline variants in any HBC gene were identified in 7.7% of cases (7.8% of invasive and 6.1% of in situ BC) with 5.2% having an actionable mutation in an HR pathway gene (BRCA1, BRCA2, PALB2 and RAD51C). Most cases with pathogenic variants showed bi-allelic inactivation in the tumour. All BRCA1, BRCA2 and PALB2 tumours showed high HRDetect and/or HRD scores consistent with loss of HR repair function, indicating them to be the underlying hereditary driver of the BC. One BC with a pathogenic PMS2 variant showed retention of the wild-type allele with no evidence of a mismatch repair mutational signature suggesting PMS2 was not the driver of this BC. Of the 157 BC in phase one that underwent WGS and did not have a germline pathogenic HBC gene variant, 16% (18/117 invasive and 3/13 DCIS) had an HRDetect score of >0.7 indicative of a homologous recombination repair defect and therefore biologically a “BRCA-like” tumour. Of these 21 BRCA-like cases, only 3 invasive BCs had clear somatic bi-allelic inactivation of an HBC gene that could explain the high HRDetect score (2 BRCA1 and 1 BRCA2). One of the 21 BRCA-like cases had a germline variant of unknown significance (VUS) in an HBC gene (a BRCA2 missense variant in an ER+ tumour. The tumour showed loss of the wild-type allele). Of the BRCA-like cases, 71% were ER positive which included 3 invasive lobular cancers. Conclusion: Tumour sequencing identified three times as many cases that might be eligible for HR repair defect targeted therapy than germline testing alone (16% versus 5.2%). Unlike a previous study (Ann Oncol., 2019 30:1071-1079), the majority of the BRCA-like BCs were ER+ with no evidence of a VUS in a known HBC gene suggesting these are driven by novel germline or somatic mutations in genes involved in DNA HR repair. Citation Format: Ian Campbell, Lisa Devereux, Kirsten Hogg, Luxi Lal, Michelle Sinclair, Lesley Stafford, Magnus Zethoven, Anita Skandarajah, Paul James, Geoffrey Lindeman, Bruce Mann, Dilanka De Silva. The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-08-11.

CXXC5 drove inflammation and ovarian cancer proliferation via transcriptional activation of ZNF143 and EGR1

CXXC5, a zinc-finger protein, is known for its role in epigenetic regulation via binding to unmethylated CpG islands in gene promoters. As a transcription factor and epigenetic regulator, CXXC5 modulates various signaling processes and acts as a key coordinator. Altered expression or activity of CXXC5 has been linked to various pathological conditions, including tumorigenesis. Despite its known role in cancer, CXXC5's function and mechanism in ovarian cancer are unclear. We analyzed multiple public databases and found that CXXC5 is highly expressed in ovarian cancer, with high expression correlating with poor patient prognosis. We show that CXXC5 expression is regulated by oxygen concentration and is a direct target of HIF1A. CXXC5 is critical for maintaining the proliferative potential of ovarian cancer cells, with knockdown decreasing and overexpression increasing cell proliferation. Loss of CXXC5 led to inactivation of multiple inflammatory signaling pathways, while overexpression activated these pathways. Through in vitro and in vivo experiments, we confirmed ZNF143 and EGR1 as downstream transcription factors of CXXC5, mediating its proliferative potential in ovarian cancer. Our findings suggest that the CXXC5-ZNF143/EGR1 axis forms a network driving ovarian cell proliferation and tumorigenesis, and highlight CXXC5 as a potential therapeutic target for ovarian cancer treatment.

Severe induction of aberrant DNA methylation by nodular gastritis in adults.

Nodular gastritis (NG) is characterized by marked antral lymphoid follicle formation, and is a strong risk factor for diffuse-type gastric cancer in adults. However, it is unknown whether aberrant DNA methylation, which is induced by atrophic gastritis (AG) and is a risk for gastric cancer, is induced by NG. Here, we analyzed methylation induction by NG. Gastric mucosal samples were obtained from non-cancerous antral tissues of 16 NG and 20 AG patients with gastric cancer and 5 NG and 6 AG patients without, all age- and gender-matched. Genome-wide methylation analysis and expression analysis were conducted by a BeadChip array and RNA-sequencing, respectively. Clustering analysis of non-cancerous antral tissues of NG and AG patients with gastric cancer was conducted using methylation levels of 585 promoter CpG islands (CGIs) of methylation-resistant genes, and a large fraction of NG samples formed a cluster with strong methylation induction. Promoter CGIs of CDH1 and DAPK1 tumor-suppressor genes were more methylated in NG than in AG. Notably, methylation levels of these genes were also higher in the antrum of NG patients without cancer. Genes related to lymphoid follicle formation, such as CXCL13/CXCR5 and CXCL12/CXCR4, had higher expression in NG, and genes involved in DNA demethylation TET2 and IDH1, had only half the expression in NG. Severe aberrant methylation, involving multiple tumor-suppressor genes, was induced in the gastric antrum and body of patients with NG, in accordance with their high gastric cancer risk.

Retraction: Zinc sulfate contributes to promote telomere length extension via increasing telomerase gene expression, telomerase activity and change in the TERT gene promoter CpG island methylation status of human adipose-derived mesenchymal stem cells.

Retraction: Zinc sulfate contributes to promote telomere length extension via increasing telomerase gene expression, telomerase activity and change in the TERT gene promoter CpG island methylation status of human adipose-derived mesenchymal stem cells.

Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome.

Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (tet2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene. The tet2m/m-mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia, but normal circulating blood counts by 11 months of age and accompanying anemia, signifying the onset of MDS, by 24 months of age. In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and conducted enhanced reduced representation of bisulfite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of hematopoietic stem and progenitor cells (HSPCs). A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared with the wild type. Furthermore, hypermethylated genes were significantly enriched for targets of SUZ12 and the metal-response-element-binding transcription factor 2 (MTF2)-involved in the polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analyses identified upregulation of genes associated with mTORC1 signaling and interferon gamma and alpha responses in tet2m/m HSPCs at 4 months of age when compared with the wild type. Downregulated genes in HSPCs of tet2-mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and interleukin 2 (IL2)/signal transducer and activator of transcription 5 (STAT5) signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.

Abstract 4288: Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction

Abstract In cervical cancer, the promoter CpG islands of several tumor suppressor genes have been found with abnormal DNA methylation (DNAm) levels, which results in transcriptional silencing. Genetic databases from tumor samples are available without the corresponding DNAm profile. To fulfill this gap and contribute to deciphering the link between genetic variants and DNAm, we performed this study to find a good statistical model for predicting DNAm using genetic data. To address this, we downloaded from the TCGA dataset the genes with significant somatic mutations, as reported by the BROAD Institute, and the DNAm beta values, in known CpG sites, from 307 Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) samples. Clinical data were also downloaded from patients, including race, age, gender, and cancer stage. We tested five mixed models containing both fixed and random effects to include the unmeasured source of variations in DNAm, for which we used the clustering of samples based on DNAm patterns. Models tested were: Classified mixed model prediction (CMMP), Linear regression model (LM), High dimensional shrinkage estimator based on the elastic net (ENET), a combination of CMMP - ENET, and Random Forest prediction (RF). Besides the significantly mutated genes, the clinical variables were also included as covariates to predict DNAm. We used shared random effects to borrow strength across racial groups, which improves predictive accuracy. Models were enhanced by combining other types of cancers to increase data heterogeneity and the number of samples. Lung Adenocarcinoma (LUAD) and Liver Hepatocellular Carcinoma (LIHC) were selected using Gini and Gap statistics for optimal clustering. Model fitting was evaluated using the average mean squared prediction error (MSPE). Results revealed that the CMMP model with CESC LIHC and LUAD data combined showed the best prediction results (lowest MSPE). The plot of the averaged estimated ENET coefficients indicated that the most important-significantly mutated genes to predict DNAm were CTNNB1, DMD, XIRP2, and PIK3CA. SNPs in these genes linked to cervical cancer include rs121913396, rs121913403 (CTNNB1), rs867262025, and rs121913279 (PIK3CA).In summary, we developed a mixed-effects model for accurately predicting DNAm levels in cervical cancer, using genes with significant somatic mutations (SNVs and INDELs). These results also align with growing evidence suggesting that genetic variation plays a role in DNAm. Citation Format: Jairo D. Ramos, J. Sunil Rao. Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4288.

25P Relationship between aberrant methylation of CpG islands of microRNA gene promoters and changes in their expression in epithelial ovarian cancer

25P Relationship between aberrant methylation of CpG islands of microRNA gene promoters and changes in their expression in epithelial ovarian cancer

Adipose Tissue-Mesenchymal Stem Cells Caused to Change the Methylation Status of hTERT Gene Promoter CpG Islands of Molt-4 Leukemia Cells as Cell-based Therapy.

DNA methylation was considered as prognostic information in some hematological malignancies. Previous studies have reported the in vitro and in vivo biology role of mesenchymal stem cells (MSCs) on leukemic cells. The aim of this study was to investigate the effect of MSCs on the promoter methylation status of hTERT as a catalytic subunit of telomerase enzyme. In the experimental study, the Molt-4 leukemic cells were co-cultured with MSCs for 7 days. At the end of the co-culture period, the Molt-4 cells were collected, DNA and protein were extracted. Then methylation specific-PCR and western blotting were done for evaluating the hTERT gene promoter methylation status and cyclin D1 and hTERT protein expression, respectively. In the following, the flow cytometry was done for cell cycle distribution assay. It was found that MSCs resulted in a significant decrease in the cyclin D1 and hTERT protein expression levels. Also, MSCs caused changes in the methylation status of the CpG islands in the hTERT gene promoter region. The following results showed that MSCs caused a significant increase in the number of cells at G0/G1 phase and arrest the G0/G1 phase as well as decrease in the cell proliferation of Molt-4 cells. It is concluded that co-culture of MSCs with Molt-4 cells could be involved in changing the methylation status of hTERT gene promoter, cell cycle and hTERT protein expression; it could be potentially beneficial for further investigations regarding the cell transplantation and cell-based therapy.

13P Hypermethylation of microRNA gene: Potential in the diagnosis of lung cancer

Non-small cell lung cancer (NSCLC) is one of the most common human cancers. In this regard, the search for new biomarkers for detecting NSCLC at early stages is relevant, and one of these markers may be the methylation of CpG-islands of miRNA genes. The aim of this work was to study the level of methylation of promoter CpG-islands of miRNA genes as promising NSCLC markers.

A study on methylation of two CpG islands of MAOA gene promoter among opium-addicted males undergoing methadone treatment

The association between methylation of MAOA gene promoter and alcohol and nicotine dependence has been demonstrated in women but not in men yet. Antisocial personality disorder (ASPD) and substance use disorders (SUD) are two types of disorders that could highly be influenced by methylation-induced changes in MAOA function. The aim of the current study is to investigate the effect of opioid addiction on methylation of MAOA gene promoter in males. DNA was extracted from the whole blood of all samples (29 opium-addicted individuals undergoing methadone treatment and 28 healthy people) according to the extraction protocol, followed by treating these samples with bisulfite kits. The investigated region including two CpG islands in the promoter region of MAOA gene contained 35 CpG dinucleotides investigated through Sanger sequencing method. The frequency of methylation at two CpG islands of MAOA gene promoter regions was equal to zero among addicted individuals undergoing methadone treatment and healthy peoples. Then, comparing methylation levels among the study group is not applicable. In conclusion, there was no association between opium addiction and methylation of the MAOA promoter regions in opium-addicted male undergoing methadone treatment.

Targeting DNA Methylation as an Epigenetic Leukocyte Counting Tool.

The methylation of CpG islands in gene promoters is a well-stablished epigenetic mechanism essential to mammalian development. During development, a dynamic process involving both de novo DNA methylation and demethylation in the genome affects the pattern of DNA methylation. This process results in differentiated cells with distinctive and stable DNA methylation signatures that regulate tissue-specific transcriptional programming of genes (1). Specific patterns of DNA methylation can therefore be explored as valuable biomarkers to stratify cell lineage and cell subsets in complex samples such as whole blood. DNA methylation markers that can be used to distinguish and quantify T cells, B cells, monocytes, eosinophils, basophils, neutrophils, and natural killer cells may have a broad clinical application. Leukocyte counts are usually determined based on morphological analysis, flow cytometric measurements, and immunophenotypic classification of lymphocyte subsets. New techniques based on DNA methylation signature may complement and help to overcome several limitations from conventional methods.

Epimutation in inherited metabolic disorders: the influence of aberrant transcription in adjacent genes.

Epigenetic diseases can be produced by a stable alteration, called an epimutation, in DNA methylation, in which epigenome alterations are directly involved in the underlying molecular mechanisms of the disease. This review focuses on the epigenetics of two inherited metabolic diseases, epi-cblC, an inherited metabolic disorder of cobalamin (vitamin B12) metabolism, and alpha-thalassemia type α-ZF, an inherited disorder of α2-globin synthesis, with a particular interest in the role of aberrant antisense transcription of flanking genes in the generation of epimutations in CpG islands of gene promoters. In both disorders, the epimutation is triggered by an aberrant antisense transcription through the promoter, which produces an H3K36me3 histone mark involved in the recruitment of DNA methyltransferases. It results from diverse genetic alterations. In alpha-thalassemia type α-ZF, a deletion removes HBA1 and HBQ1 genes and juxtaposes the antisense LUC7L gene to the HBA2 gene. In epi-cblC, the epimutation in the MMACHC promoter is produced by mutations in the antisense flanking gene PRDX1, which induces a prolonged antisense transcription through the MMACHC promoter. The presence of the epimutation in sperm, its transgenerational inheritance via the mutated PRDX1, and the high expression of PRDX1 in spermatogonia but its nearly undetectable transcription in spermatids and spermatocytes, suggest that the epimutation could be maintained during germline reprogramming and despite removal of aberrant transcription. The epivariation seen in the MMACHC promoter (0.95 × 10-3) is highly frequent compared to epivariations affecting other genes of the Online Catalog of Human Genes and Genetic Disorders in an epigenome-wide dataset of 23,116 individuals. This and the comparison of epigrams of two monozygotic twins suggest that the aberrant transcription could also be influenced by post-zygotic environmental exposures.

Autoimmune gastritis induces aberrant DNA methylation reflecting its carcinogenic potential.

Autoimmune gastritis (AIG) is a chronic inflammatory condition in gastric mucosa and is associated with increased cancer risk, though not as high as that by Helicobacter pylori (H. pylori)-associated gastritis (HPG). Although aberrant DNA methylation is induced by HPG and the level correlates with the risk of gastric cancer, DNA methylation induction by AIG is unknown. Gastric mucosa samples from the corpus were collected from 12 people with AIG without H. pylori infection, 10 people with HPG, and eight healthy volunteers. Genome-wide DNA methylation analysis was conducted using Infinium Methylation EPIC array. Gene expression was analyzed by quantitative RT-PCR. The AIG samples had extensive aberrant DNA methylation but presented unique methylation profiles against the HPG samples after correction of leucocyte fractions. Comparison between the AIG and HPG samples showed that AIG induced methylation, but less than HPG, in overall CpG sites and also in promoter CpG islands. Promoter CpG islands of tumor-suppressor genes in the pathway of cell cycle, cell adhesion, p53, and WNT were highly methylated in the AIG samples, but more so in the HPG samples. The expression levels of IL1B and IL8, secreted by macrophage, were significantly lower in the AIG samples than in the HPG samples, suggesting that a difference in inflammatory response affected the degree and patterns of aberrant DNA methylation. AIG induced aberrant DNA methylation in gastric mucosa. However, the degree of DNA methylation was less than that by HPG, which reflected carcinogenic risk.

Study of vitamin D receptor gene methylation and the risk of gestational diabetes mellitus in Iranian pregnant women

Vitamin D acting through vitamin D receptor (VDR) plays a crucial role in regulating multiple pathways, including immunomodulatory properties, insulin secretion, and calcium homeostasis. Gestational diabetes mellitus (GDM) is a metabolic disorder with glucose intolerance that occurs in pregnancy. It has been lately suggested that epigenetic mechanisms as well as genetic factors have a significant role in GDM pathogenesis. Our study's intention was to investigate the methylation pattern of CpG islands of the VDR gene promoter in GDM and non-GDM population and predisposition to GDM in Iranian pregnant women. A total of 240 of pregnant Iranian women including, 120 women with GDM and 120 non-GDM were recruited in this study. Diagnosis of GDM was confirmed via a 75 g oral glucose tolerance test (OGTT) at 24–28 weeks of pregnancy. Peripheral blood DNA was isolated and underwent chemical modification using sodium bisulfite. The status of VDR promoter methylation of was determined by methylation-specific PCR (MSP). Analysis of MSP data uncovered the unmethylated promoter of VDR gene both in GDM and non-GDM pregnant women. Indeed, we found no differences in the DNA methylation patterns of the VDR promoter between GDM and non-GDM groups. Our study was the first report of VDR promoter methylation in GDM. In conclusion, we found no significant association between methylation status of VDR promoter and susceptibility to GDM in our studied population.

Contribution of Dopamine Transporter Gene Methylation Status to Cannabis Dependency.

The susceptibility to cannabis dependency results from the influence of numerous factors such as social, genetic, as well as epigenetic factors. Many studies have attempted to discover a molecular basis for this disease. However, our study aimed at evaluating the connection between altered methylation of the dopamine transporter gene (DAT1) promoter CpG sites and cannabis dependency. In the cases of some DNA sequences, including the DAT1 gene region, their methylation status in blood cells may reflect a systemic modulation in the whole organism. Consequently, we isolated the DNA from the peripheral blood cells from a group of 201 cannabis-dependent patients and 285 controls who were healthy volunteers and who were matched for age and sex. The DNA was subjected to bisulfite conversion and sequencing. Our analysis revealed no statistical differences in the general methylation status of the DAT1 gene promoter CpG island between the patients and controls. Yet, the analysis of individual CpG sites where methylation occurred indicated significant differences. These sites are known to be bound by transcription factors (e.g., SP1, p53, PAX5, or GR), which, apart from other functions, were shown to play a role in the development of the nervous system. Therefore, DAT1 gene promoter methylation studies may provide important insight into the mechanism of cannabis dependency.

Hepatic DNA Methylation in Response to Early Stimulation of Microbiota with Lactobacillus Synbiotics in Broiler Chickens

DNA methylation inhibits DNA transcription by the addition of methyl residues to cysteine within the CpG islands of gene promoters. The process of DNA methylation can be modulated by environmental factors such as intestinal microbiota. In poultry, the composition of the intestinal microbiota can be stimulated by in ovo delivery of synbiotics. The present study aims to determine the effect of Lactobacillus synbiotics delivered in ovo on the level of hepatic DNA methylation in broiler chickens. In ovo stimulation was performed on day 12 of egg incubation. Bioactive compounds delivered in ovo included (S1)—Lactobacillus salivarius with GOS and (S2)—Lactobacillus plantarum with RFO. Samples were collected from six individuals from each group on day 42 post-hatching. DNA methylation of five genes selected on the basis of the transcriptome data were analyzed using the qMSP method. Significant changes were observed in DNA methylation of genes in liver including ANGPTL4 and NR4A3, after S2 delivery. The obtained results confirm that the downregulation of metabolic gene expression in the liver mediated by in ovo stimulation had epigenetic characteristics.

Site-Specific DNA Demethylation as a Potential Target for Cancer Epigenetic Therapy.

Aberrant promoter DNA hypermethylation is a typical characteristic of cancer and it is often seen in malignancies. Recent studies showed that regulatory cis-elements found up-stream of many tumor suppressor gene promoter CpG island (CGI) attract DNA methyltransferases (DNMT) that hypermethylates and silence the genes. As epigenetic alterations are potentially reversible, they make attractive targets for therapeutic intervention. The currently used decitabine (DAC) and azacitidine (AZA) are DNMT inhibitors that follow the passive demethylation pathway. However, they lead to genome-wide demethylation of CpGs in cells, which makes difficult to use it for causal effect analysis and treatment of specific epimutations. Demethylation through specific demethylase enzymes is thus critical for epigenetic resetting of silenced genes and modified chromatins. Yet DNA-binding factors likely play a major role to guide the candidate demethylase enzymes upon its fusion. Before the advent of clustered regulatory interspaced short palindromic repeats (CRISPR), both zinc finger proteins (ZNFs) and transcription activator-like effector protein (TALEs) were used as binding platforms for ten-eleven translocation (TET) enzymes and both systems were able to induce transcription at targeted loci in an in vitro as well as in vivo model. Consequently, the development of site-specific and active demethylation molecular trackers becomes more than hypothetical to makes a big difference in the treatment of cancer in the future. This review is thus to recap the novel albeit distinct studies on the potential use of site-specific demethylation for the development of epigenetic based cancer therapy.

Aberrant Methylation of Suppressor of Cytokine Signaling 1 (SOCS1) Gene as a Biomarker for Early Prediction and Diagnosis of Bladder Cancer.

SOCS1 protein, the negative regulatory protein of the Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling pathway, may inhibit signaling of JAK-STAT pathway by several cytokines and has tumor suppressor activity. Methylation of CpG island in the promoter region of SOCS1 gene has often been shown to inactivate the SOCS1 gene in certain human cancers. However, the precise role of SOCS1 in bladder cancer is unclear. Two hundred forty-seven patients with BCa and 243 healthy controls were enrolled from Tumour Hospital Affiliated to Harbin Medical University, Hongqi Hospital Affiliated to Mudanjiang Medical University, and Mudanjiang Tumour Hospital from September 2013 to March 2019. The methylation rate in the promoter region of the SOCS1 among all participants were detected using the MassARRAY EpiTYPER system. A ROC curve was set out to analyze SOCS1 gene promoter CpG island methylation for BCa diagnosis. There was a significantly higher methylation rate in BCa compared to controls. Then we assessed the methylation rate of different CpG islands in SOCS1 gene among BCa cases and normal controls. Methylation rate was shown to vary among different CpG islands. The methylation rates of CpG islands were shown to vary among different grades. We observed that the methylation rate of different CpG islands vary according to pathological grades. Our study demonstrates that aberrant methylation of CpG island in the promoter region of SOCS1 gene may be involved in occurrence, progression, and prognosis of BCa and, thus, may serve as an independent diagnosis and prognostic biomarker.

Dose Dependence of Hypermethylation of Gene Promoters in Blood Leukocytes in Humans Occupationally Exposed to External γ-Radiation

Abstract—A study of promoter hypermethylation of cell cycle (RASSF1A, p16/INK4A, p14/ARF, p53, АТМ), xenobiotic detoxification (GSTP1), antioxidant defense (SOD3), and estrogen receptor (ESR1) genes in blood leukocytes of 88 nuclear industry workers from the Mayak facility (53–86 years old at sampling) exposed to prolonged external γ-radiation was carried out. Accumulated doses to red bone marrow (RBM) ranged from 0.2 to 2.95 Gy. The time between the end of work with radiation and blood sampling was on average 15.95 ± 1.22 years. Fifty unirradiated residents of Ozyorsk matched by age to the exposed group were enrolled as a control group. Promoter hypermethylation was analyzed using methylation-sensitive polymerase chain reaction (PCR) assay. The trend towards dependence of promoter hypermethylation of p14/ARF and RASSFA genes on age rather than radiation exposure (logistic regression: p = 0.072) confirms previous results. The frequency of individuals with promoter methylation of at least one of the following six genes: p16/INK4A, GSTP1, р53, АТМ,SOD3,ESR1, in irradiated group was significantly higher than in the control group (62.5 versus 34%, respectively, p = 0.001, OR = 3.24, 95% CI 1.56–6.69). A significantly elevated frequency of individuals with hypermethylated СpG islands in GSTP1 and SOD3 promoters was revealed among exposed subjects compared to the control group (p = 0.014 and p = 0.021, respectively). A statistically significant association between the cumulative dose and the number of methylated promoters was revealed (r = 0.304, р = 3.2 × 10–4). Therefore, the dose-dependent hypermethylation of CpG islands in gene promoters that is revealed in blood leukocytes long term after external exposure to γ-radiation was found.

Abstract GMM-055: BMI1 AND RING1A ARE INVOLVED IN H2A UBIQUITINATION AT SITES OF PLATINUM-INDUCED DAMAGE

Abstract Ovarian cancer is the 5th leading cause of death among women with the five year survival rate for ovarian cancer patients being only 46%. The standard of care for treatment of ovarian cancer patients is debulking surgery followed by platinum-taxane based chemotherapy. However, the major obstacle in the treatment of these patients with platinum based agents is development of chemoresistance. The platinum agents, cisplatin and carboplatin damage DNA by forming adducts with adjacent guanines, a high density of which are found in the promoter CpG islands of genes. Aberrant promoter DNA hypermethylation of genes and their subsequent transcriptional repression has been associated with development of cisplatin resistance. However, the mechanism of initiation of this aberrant DNA methylation and subsequent transcriptional repression is not known. Our overall hypothesis is that platinum induced DNA damage or repair of the damage leads to recruitment of repressive proteins to sites of damage. These repressive proteins transiently repress transcription in vicinity of damage to promote repair. However, similar to our findings with enzyme induced double strand breaks, repressive proteins may be retained at some key loci causing persistent transcriptional repression and gene silencing contributing to the development of platinum resistance. Our preliminary data demonstrates that BMI1, a member of polycomb repressive complex 1, localizes to sites of damage after cisplatin treatment. We also observe mono-ubiquitination of H2AX after cisplatin treatment and we hypothesize that this ubiquitination is occurring on K119. Mono-ubiquitination of H2A/H2AX at K119 has been associated with transcriptional repression and gene silencing during development and differentiation and also during repair of ionizing radiation and enzyme induced double strand breaks. Our data suggests that knockdown of RING1A reduces the cisplatin induced H2AX ubiquitination. We are currently determining which repair pathways and/or proteins result in recruitment of BMI1, RING1A to sites of damage. Importantly, after acute cisplatin treatment we also observe a reduction in expression of candidate genes which are known to be methylated in cisplatin resistant cells. We plan to determine if RING1A mediated ubiquitination is responsible for reduction in expression of target genes after acute cisplatin treatment and their methylation in cisplatin resistant cells. Understanding the mechanism of platinum induced gene silencing will enable us to design therapies to avert the development of drug resistant ovarian cancers. Citation Format: Shruthi Sriramkumar, Heather M. O'Hagan. BMI1 AND RING1A ARE INVOLVED IN H2A UBIQUITINATION AT SITES OF PLATINUM-INDUCED DAMAGE [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-055.