RUNX3 Hypermethylation Research Articles

Association between the methylations of RUNX3 in peripheral blood and lung cancer: a case-control study

Background RUNX3 is hypermethylated in multiple cancers. TIMP2 also functions as a regulator of tumors. However, there are only very few reports on the association of methylation of RUNX3 and TIMP2 with lung cancer (LC) in peripheral blood. Methods 426 LC patients and 428 age- and sex-matched healthy controls were recruited. DNA methylation in blood was semi-quantitively assessed by mass spectrometry. For the association analysis, binary logistic regression analysis adjusted covariant was applied, and ORs were presented as per +10% methylation. Results Hypermethylation of CpG_1, CpG_5 and CpG_8 in RUNX3 was significantly associated with LC (ORs = 1.45, 1.35 and 1.35, respectively, adjusted p < 0.05), and even stage I LC. The association between the three RUNX3 CpG sites and LC was enhanced by increased age (> 55 years, ORs ranged from 1.43 to 1.75, adjusted p < 0.05), male gender (ORs ranged from 1.47 to 1.59, adjusted p < 0.05) and tumor stage (stage II&III&IV, ORs ranged from 1.86 to 3.03, adjusted p < 0.05). Conclusions This study suggests a significant association between blood-based RUNX3 hypermethylation and LC, especially in elder people, in males and in LC patients with advanced stage.

METHYLATION PATTERN OF THE RUNX3 GENE AND ITS IMPACT ON RESPONSE TO IMATINIB THERAPY IN CHRONIC MYELOID LEUKEMIA

BackgroundChronic Myelogenous Leukemia (CML) is a clonal stem cell disease with deregulated tyrosine kinase activity of BCR-ABL. DNA methylation in gene promoters influences disease development, therapeutic response, and clinical outcome in various diseases.&#x0D; ObjectivesThis study aimed to investigate the methylation pattern in promoter regions of the runt-related transcription factor 3 (RUNX3) gene and its effect on the response to imatinib therapy, among CML patients.&#x0D; Patients and MethodsBlood samples were collected from 100 participants from November 2020 to February 2022, in two groups 75 samples of CML patients and 25 samples of healthy controls, genomic DNA was extracted from the samples by using the salting-out method, then Isolated DNA was treated with sodium bisulfite. By Methylation-Sensitive High-Resolution Melting (MS-HRM), the samples were analyzed.&#x0D; ResultsThe promoter sequence methylation level is significantly higher (P&lt;0.05) in DNA samples from CML patients than in the control group, the methylation level in most of the healthy control samples 96% was detected between 0-24% while in CML patients was 16%, in 25-49%, RUNX3 methylation levels in Health individuals were 4%, moreover in CML patients were 24% also, in 50-100% of methylation level, health control was 0%, in CML patient showed 60%. According to methylation detection of RUNX3 among Imatinib resistance and good response, the results of IM resistance were detected between 0-40% was 15.21%, Furthermore, in good response was 79.31%. In other hand at 41-100% RUNX3 methylation levels in IM resistance was 84.78%, while a good response was recorded at 20.68%.&#x0D; ConclusionThe study concluded that RUNX3 gene hypermethylation often occurs in CML patients. Additionally, there is a strong correlation between RUNX3 hypermethylation and poor imatinib respondents. We found that both IM resistance and CML patients have higher levels of RUNX3 gene hypermethylation. Moreover, research on a larger sample size is required to validate these findings, which may serve as possible indicators of disease progression and imatinib resistance.

Analysis of Intrinsic Breast Cancer Subtypes: The Clinical Utility of Epigenetic Biomarkers and TP53 Mutation Status in Triple-Negative Cases

This study aimed at analyzing the DNA methylation pattern and TP53 mutation status of intrinsic breast cancer (BC) subtypes for improved characterization and survival prediction. DNA methylation of 17 genes was tested by methylation-specific PCR in 116 non-familial BRCA mutation-negative BC and 29 control noncancerous cases. At least one gene methylation was detected in all BC specimens and a 10-gene panel statistically significantly separated tumors from noncancerous breast tissues. Methylation of FILIP1L and MT1E was predominant in triple-negative (TN) BC, while other BC subtypes were characterized by RASSF1, PRKCB, MT1G, APC, and RUNX3 hypermethylation. TP53 mutation (TP53-mut) was found in 38% of sequenced samples and mainly affected TN BC cases (87%). Cox analysis revealed that TN status, age at diagnosis, and RUNX3 methylation are independent prognostic factors for overall survival (OS) in BC. The combinations of methylated biomarkers, RUNX3 with MT1E or FILIP1L, were also predictive for shorter OS, whereas methylated FILIP1L was predictive of a poor outcome in the TP53-mut subgroup. Therefore, DNA methylation patterns of specific genes significantly separate BC from noncancerous breast tissues and distinguishes TN cases from non-TN BC, whereas the combination of two-to-three epigenetic biomarkers can be an informative tool for BC outcome predictions.

Aneuploidy in targeted endoscopic biopsies outperforms other tissue biomarkers in the prediction of histologic progression of Barrett's oesophagus: A multi-centre prospective cohort study.

BackgroundThe cancer risk in Barrett's oesophagus (BO) is difficult to estimate. Histologic dysplasia has strong predictive power, but can be missed by random biopsies. Other clinical parameters have limited utility for risk stratification. We aimed to assess whether a molecular biomarker panel on targeted biopsies can predict neoplastic progression of BO.Methods203 patients with BO were tested at index endoscopy for 9 biomarkers (p53 and cyclin A expression; aneuploidy and tetraploidy; CDKN2A (p16), RUNX3 and HPP1 hypermethylation; 9p and 17p loss of heterozygosity) on autofluorescence-targeted biopsies and followed-up prospectively. Data comparing progressors to non-progressors were evaluated by univariate and multivariate analyses using survival curves, Cox-proportional hazards and logistic regression models.Findings127 patients without high-grade dysplasia (HGD) or oesophageal adenocarcinoma (OAC) at index endoscopy were included, of which 42 had evidence of any histologic progression over time. Aneuploidy was the only predictor of progression from non-dysplastic BO (NDBO) to any grade of neoplasia (p = 0.013) and HGD/OAC (p = 0.002). Aberrant p53 expression correlated with risk of short-term progression within 12 months, with an odds ratio of 6.0 (95% CI: 3.1–11.2). A panel comprising aneuploidy and p53 had an area under the receiving operator characteristics curve of 0.68 (95% CI: 0.59–0.77) for prediction of any progression.InterpretationAneuploidy is the only biomarker that predicts neoplastic progression of NDBO. Aberrant p53 expression suggests prevalent dysplasia, which might have been missed by random biopsies, and warrants early follow up.

Aneuploidy in Targeted Endoscopic Biopsies Outperforms Other Tissue Biomarkers in the Prediction of Histologic Progression of Barrett's Oesophagus: A Multi-Centre Prospective Cohort Study

Introduction: The cancer risk in Barrett’s oesophagus (BO) is difficult to estimate. Confirmed histologic dysplasia has strong predictive power, but can be missed by random biopsies, while other clinical parameters have limited utility for risk stratification. We aimed to assess the utility of a large panel of molecular biomarkers on targeted biopsies to predict neoplastic progression of BO. Methods: In a prospective study in three tertiary centres, 203 patients with BO were tested for 9 biomarkers (p53 and cyclin A expression; aneuploidy and tetraploidy; CDKN2A (encoding for p16), RUNX3 and HPP1 hypermethylation; 9p and 17p loss of heterozygosity) on autofluorescence-targeted biopsies taken at index endoscopy and followed-up as per clinical standard. Data comparing progressors to non-progressors were evaluated by univariate and multivariate analyses using survival curves, Cox-proportional hazards and logistic regression models. Findings: 127 patients with no high-grade dysplasia (HGD) or early oesophageal adenocarcinoma (OAC) were included, of which 42 had evidence of any histologic progression over time. Aneuploidy was the only predictor of progression from non-dysplastic BO (NDBO) to any grade of neoplasia (p=0.013) and HGD/OAC (p=0.002). Aberrant p53 expression correlated with the risk of short-term progression within 12 months, with an odds ratio for histologically missed dysplasia of 6.0 (95% CI: 3.1-11.2). A biomarker panel comprising aneuploidy and p53 had an area under the ROC curve of 0.68 (95% CI: 0.59-0.77) for prediction of any histologic progression. Interpretation: In our study, aneuploidy is the only biomarker that predicts neoplastic progression of NDBO. Aberrant p53 expression suggests prevalent dysplasia, which might have been missed by random biopsies, and warrants early follow up. Funding Statement: This study was funded by a Medical Research Council Program Grant to RCF and by a Lister Institute for Preventive Medicine prize to RCF, with additional clinical research infrastructure support from the Experimental Cancer Medicine Centre and the Cambridge Biomedical Research Centre. Declaration of Interests: KR reports grants, personal fees and non-financial support from Olympus, outside the submitted work. JJGHMB reports grants from Olympus Endoscopy, outside the submitted work. Other authors declare no conflicts of interest. Ethics Approval Statement: This was a prospective study approved by the Cambridgeshire 2 Research Ethics Committee (09/H0308/118) and the Amsterdam University Medical Centre (AUMC) Medical Ethics Committee (MEC 09/073). This was a National Institute of Health research (NIHR) portfolio study (UKCRN ID 7561).

Abstract GMM-028: VALIDATION OF RUNX3 AND CAMKIINα HYPERMETHYLATION AS PROGNOSTIC MARKER FOR OVARIAN CARCINOMA

Abstract INTRODUCTION: Ovarian cancer is still the most lethal gynecological malignancy with a low five-years-overall survival rate. Except for BRCA1/2 mutations there is no predictive nor prognostic marker available indicating whether a patient is in need and eligible for personalized therapy. In a previous genome-wide array study we identified different methylation patterns in type II epithelial ovarian cancer patients with either good or poor outcome (PFS &amp;lt; vs. &amp;gt; 3 years). Using methylation-specific PCR (MSP) five marker candidates showed high prognostic value whereby the marker combination RUNX3/CaMKIINα was the most promising one [Häfner et al., 2015]. Moreover, in vitro experiments provided evidence that a transcript variant of RUNX3 can mediate Cisplatin sensitivity, further underlining the clinical relevance of this gene [Heinze et al., 2018]. METHODS: In this study we aim to validate the previous described prognostic value of the five candidates, especially of RUNX3 and CaMKIINα via MSP. Therefore, 100 fresh-frozen primary type II EOC samples from two different surgical centers were tested. Furthermore, previously analyzed samples were retested to gain insight on the marker distributions throughout the tumor and possible heterogeneity. The DNA was isolated via phenol/chloroform or QiaAmp Kit, converted to bisulfite DNA and tested via optimized MSP. All samples had similar clinical parameter (histology, FIGO grade, chemotherapy). RESULTS AND DISCUSSION: By re-testing a subset of EOC samples previous results could been confirmed. Additionally, the methylation pattern was similar after renewed sectioning for DNA extraction pointing towards little tumor heterogeneity in the analyzed samples. Interestingly the methylation rate is not as high as expected from the initial analyses. Statistical analysis of the data is currently ongoing. REFERENCES Häfner N, Steinbach D, Jansen L, Diebolder H, Dürst M, Runnebaum IB. RUNX3 and CAMK2N1 hypermethylation as prognostic marker for epithelial ovarian cancer, Int J Cancer. 2016 Heinze K, Kritsch D, Mosig AS, Dürst M, Häfner N, Runnebaum IB. Functional Analyses of RUNX3 and CaMKIINα in Ovarian Cancer Cell Lines Reveal Tumor-Suppressive Functions for CaMKIINα and Dichotomous Roles for RUNX3 Transcript Variants, Int J Mol Sci. 2018 Citation Format: Karolin Heinze, Lars Jansen, Leticia Oliveira-Ferrer, Barbara Schmalfeldt, Matthias Dürst, Ingo B Runnebaum, Norman Häfner. VALIDATION OF RUNX3 AND CAMKIINα HYPERMETHYLATION AS PROGNOSTIC MARKER FOR OVARIAN CARCINOMA [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-028.

Epigenetic inactivation of RUNX3 in colorectal cancer.

PurposeEmerging evidence indicates that runt-related transcription factor 3 (RUNX3) is an important tumor suppressor gene in several cancer types, including colorectal cancer (CRC). However, the clinical significance of RUNX3 inactivation in CRC remains unclear. The aim of this study was to examine the correlation between clinicopathologic factors and RUNX3 hypermethylation/expression in CRC.MethodsSixty-two CRC patients who were treated at the Soonchunhyang University College of Medicine were recruited in this study. The hypermethylation of CpG islands in the RUNX3 promoter and the expression of RUNX3 mRNA were identified by methylation-specific polymerase chain reaction (PCR) and reverse transcriptase-PCR, respectively. The expression of RUNX3 was determined by immunohistochemical staining.ResultsOf the 62 CRC tissue samples, 20 (32.3%) presented hypermethylated RUNX3 promoters. Aberrant RUNX3 hypermethylation was found to be associated with vascular (P = 0.006) and lymphatic (P = 0.002) invasion. Hypermethylation of RUNX3 was associated with poor survival outcomes (P = 0.038). However, expression of RUNX3 was not a prognostic factor (P = 0.363).ConclusionHypermethylation of RUNX3 may be a predictor of a poor prognosis in CRC.

An early biomarker and potential therapeutic target of RUNX 3 hypermethylation in breast cancer, a system review and meta-analysis.

Runt-related transcription factor 3 (RUNX3) methylation plays an important role in the carcinogenesis of breast cancer (BC). However, the association between RUNX3 hypermethylation and significance of BC remains under investigation. The purpose of this study is to perform a meta-analysis and literature review to evaluate the clinicopathological significance of RUNX3 hypermethylation in BC. A comprehensive literature search was performed in Medline, Web of Science, EMBASE, Cochrane Library Database, CNKI and Google scholar. A total of 10 studies and 747 patients were included for the meta-analysis. Pooled odds ratios (ORs) with corresponding confidence intervals (CIs) were evaluated and summarized respectively. RUNX3 hypermethylation was significantly correlated with the risk of ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC), OR was 50.37, p < 0.00001 and 22.66, p < 0.00001 respectively. Interestingly, the frequency of RUNX3 hypermethylation increased in estrogen receptor (ER) positive BC, OR was 12.12, p = 0.005. High RUNX3 mRNA expression was strongly associated with better relapse-free survival (RFS) in BC patients. In summary, RUNX3 methylation could be a promising early biomarker for the diagnosis of BC. High RUNX3 mRNA expression is correlated to better RFS in BC patients. RUNX3 could be a potential therapeutic target for the development of personalized therapy.

The clinicopathological significance of RUNX3 hypermethylation and mRNA expression in human breast cancer, a meta-analysis.

Aberrant promoter methylation of RUNX3 has been reported in several tumors including human breast cancer (BC). However, the association between RUNX3 hypermethylation and incidence of BC remains elusive. In this study, a detailed literature search was performed in Medline and Google Scholar for related research publications. Analysis of pooled data were executed. Odds ratios with corresponding confidence intervals were determined and summarized, respectively. Finally, 13 studies were identified for the meta-analysis. Analysis of the pooled data showed that RUNX3 hypermethylation was significantly higher in both ductal carcinoma in situ and invasive ductal carcinoma (IDC) than in normal breast tissues. In addition, RUNX3 methylation was significantly higher in IDC than in benign tumor. However, RUNX3 methylation was not significantly higher in IDC than in ductal carcinoma in situ. We also determined that RUNX3 hypermethylation was significantly higher in ER positive BC than in ER negative BC. In addition, high RUNX3 mRNA expression was found to be correlated with better overall survival and relapse-free survival for all BC patients. Our results strongly support that RUNX3 hypermethylation may play an important role in BC incidence. RUNX3 methylation is a valuable early biomarker for the diagnosis of BC. Further large-scale studies will provide more insight into the role of RUNX3 hypermethylation in the carcinogenesis and clinical diagnosis of BC patients.

Helicobacter pylori Eradication Modulates Aberrant CpG Island Hypermethylation in Gastric Carcinogenesis.

Helicobacter pylori infection induces aberrant DNA methylation in gastric mucosa. We evaluated the long-term effect of H. pylori eradication on promotor CpG island hypermethylation in gastric carcinogenesis. H. pylori-positive patients with gastric adenoma or early gastric cancer who underwent endoscopic resection were enrolled. According to H. pylori eradication after endoscopic resection, the participants were randomly assigned to H. pylori eradication or non-eradication group. H. pylori-negative gastric mucosa from normal participants provided the normal control. CpG island hypermethylation of tumor-related genes (p16, CDH1, and RUNX-3) was evaluated by quantitative MethyLight assay in non-tumorous gastric mucosa. The gene methylation rate and median values of hypermethylation were compared after one year by H. pylori status. In H. pylori-positive patients, hypermethylation of p16 was found in 80.6%, of CDH1 in 80.6%, and of RUNX-3 in 48.4%. This is significantly higher than normal control (p16, 10%; CDH1, 44%; RUNX-3, 16%) (p<0.05). In the H. pylori eradication group, methylation rates of p16 and CDH1 decreased in 58.1% and 61.3% of the patients, and the median values of hypermethylation were significantly lower at one year compared with the non-eradication group. However, RUNX-3 hypermethylation did not differ significantly at one year after H. pylori eradication. The non-eradication group hypermethylation did not change after one year. H. pylori infection was associated with promotor hypermethylation of genes in gastric carcinogenesis, and H. pylori eradication might reverse p16 and CDH1 hypermethylation.

Abstract 3825: Whole genome bisulfite sequencing from plasma of patients with metastatic breast cancer identifies putative biomarkers

Abstract Although several improvements in the management of breast cancer(BC) have been made, an estimated 90% of BC related deaths are due to the development of distant metastasis to organs such as lung, bone, liver, and brain. Numerous studies suggest that cell-free (cf)DNA methylation could serve as a useful biomarker for improving clinical management. The objective of our study was to identify novel blood-based biomarkers that can be used to predict BC patients at high risk of distant metastasis. For the first time we performed paired-end whole genome bisulfite sequencing (WGBS) using 15 ng of cf plasma DNA from three pools of samples which included metastatic BC to various organs (M, n = 40), breast cancer free survivors (BCF n = 40) and healthy individuals (H, n = 40). Sequences were aligned using the bismark tool and data analysis was conducted using the R package methylKit to identify base-pair resolution DNA methylation differences between groups. A minimum of 5 reads in each group, delta beta values ≥0.2 and p values&amp;lt;0.001 were considered differentially methylated loci (DML). Overall, the data revealed that H and BCF had very similar plasma methylomes with approximately 1792 DML, compared with 0.8 million and 1.1 million DML between HvsM and BFSvsM, respectively. The M pool had greater overall hypomethylation across the genome, particularly in gene bodies compared with H and BFS. However, M had greater CpG island and promoter hypermethylation compared with H and BFS. The average coverage of CpG loci across the genome was 18, 11 and 9 for M, BFS, and H, respectively indicating that plasma of M samples has greater genomic representation. Among the genes differentially methylated in plasma of M was RUNX3, which was hypomethylated overall in M compared to H and BFS except for one CpG island hotspot, where methylation and number of reads significantly exceeded that of H and BFS. Other genes with similar hotspots were also identified. We validated these data using bisulfite amplicon sequencing (Ion Torrent) in each pool and individual plasma samples. Using the HumanMethylation27K bead array, we analyzed 32 breast brain metastasis (BBM) tumor tissues compared to a series of 50 unmatched early stage BC samples and identified RUNX3 hypermethylation in the same hotspot region as WGBS. Lastly, comparing 25 early stage BC samples with known outcomes of BBM had RUNX3 hotspot hypermethylation compared with samples from patients who were BM-free for greater than 5 years. This suggested that prediction of metastasis may occur at the time of early stage of disease. Together these data identified DNA-methylation hotspots in circulation and tissue that are unique to distant MBC and which could be translated into predictive biomarkers of metastasis. Biomarkers indicating a high-risk population can shift current paradigms by allowing increased surveillance and/or prophylactic therapies aimed at preventing metastasis and improving outcomes. Citation Format: Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Bodour Salhia. Whole genome bisulfite sequencing from plasma of patients with metastatic breast cancer identifies putative biomarkers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3825. doi:10.1158/1538-7445.AM2015-3825

RUNX3 and CAMK2N1 hypermethylation as prognostic marker for epithelial ovarian cancer.

Treatment of epithelial ovarian cancer consists of surgery plus platinum-taxane based chemotherapy. Neither prognostic nor predictive serum or tissue markers except BRCA1/2 mutations are available thus precluding individualized treatment. Aim of this study is the identification and validation of DNA-methylation markers with prognostic value. Genome-wide array analyses were used to determine methylation patterns in groups of serous EOC with different outcome (PFS < vs. > 3 years, each n = 6) but comparable clinical parameters. Two hundred and twenty differentially methylated regions in tumor tissue of patients with short vs. long PFS (106 hypo- and 114 hypermethylated regions) were identified. Thirty-five of 37 selected CpG islands were validated by MSP using the same samples as for microarray analyses. Six of these regions were analyzed by targeted next-generation bisulfite-sequencing confirming array and MSP results. Validation experiments with an enlarged patient group of Type II EOC samples (PFS <3 years n = 30; >3 years n = 18) revealed the CpG island of RUNX3 as significantly more often methylated in patients with short PFS (10/30 vs. 0/18; p < 0.01). Marker combinations with significantly different methylation frequencies in patient groups reached an increased sensitivity with equal specificity (RUNX3+CAMK2N1; sens 40%; spec 100%; p < 0.01). RUNX3/CAMK2N1 methylation-positive patients of the array-independent subset (n = 36) showed a significantly lower PFS (p < 0.01) but no other difference in clinical parameters compared to methylation-negative patients. Genome-wide methylation analyses reliably identified markers of potentially prognostic value. Hypermethylation of RUNX3/CAMK2N1 is associated with poor clinical outcome in Type II EOC, also after macroscopic complete resection.

Clinicopathological significance and potential drug target of RUNX3 in non-small cell lung cancer: a meta-analysis.

BackgroundEmerging evidence indicates that RUNX3 is a candidate tumor suppressor in several types of human tumors, including non-small cell lung cancer (NSCLC). However, the correlation between RUNX3 hypermethylation and clinicopathological characteristics of NSCLC remains unclear. Here, we conducted a systematic review and meta-analysis to quantitatively evaluate the effects of RUNX3 hypermethylation on the incidence of NSCLC and clinicopathological characteristics.MethodsA detailed literature search was made using Medline, Embase and Web of Science for related research publications written in English. The methodological quality of the studies was evaluated. The data were extracted and assessed independently by two reviewers. Analysis of pooled data was performed. The odds ratio (OR) and hazard ratio were calculated and summarized.ResultsFinal analysis of 911 NSCLC patients from 13 eligible studies was performed. We observed that RUNX3 hypermethylation was significantly higher in NSCLC than in normal lung tissue; the pooled OR from seven studies including 361 NSCLC and 345 normal lung tissue (OR 7.08, confidence interval 4.12–12.17, P<0.00001). RUNX3 hypermethylation may also be associated with pathological types. The pooled OR was obtained from eleven studies including 271 squamous cell carcinoma and 389 adenocarcinoma (OR 0.41, confidence interval 0.19–0.89, P=0.02), which indicated that RUNX3 hypermethylation is significantly higher in adenocarcinoma that in squamous cell carcinoma. We did not find that RUNX3 hypermethylation was correlated with clinical stage or differentiated status. However, NSCLC patients with RUNX3 hypermethylation had a lower survival rate than those without RUNX3 hypermethylation.ConclusionThe results of this meta-analysis suggest that RUNX3 hypermethylation is associated with an increased risk and worse survival in NSCLC. RUNX3 hypermethylation, which induces inactivation of the RUNX3 gene, plays an important role in lung carcinogenesis and clinical outcome.

Abstract P4-02-09: RUNX3 hypermethylation in circulating tumor DNA is a biomarker of breast cancer distant metastasis

Abstract Breast cancer detection has not resulted in the expected decrease in mortality suggesting that current screening strategies are not finding metastasis-prone lesions before metastasis occurs and instead are detecting many lesions that will not progress to metastatic disease. Although several improvements in the management of breast cancer have been made, an estimated 90% of breast cancer related deaths are due to the development of distant metastasis to organs such as lung, bone, liver, and brain. Metastatic breast cancer affects 10-15% of breast cancer patients, is often refractory to therapy and associated with poor outcomes. However, a blood test indicating a high-risk population at the time of breast cancer diagnosis might shift the current strategy and improve outcomes. Efforts for identifying predictive markers of breast cancer metastasis have been impeded by a lack of data defining the genetic and epigenetic determinants of the disease. Numerous studies suggest that DNA methylation could be a useful biomarker for improving the clinical management. Recently circulating tumor (ct)DNA has attracted attention for clinical use in the context of risk prediction, prognostication and prediction in human cancer. Various types of DNA alterations have been reported in ctDNA but methylated DNAs are chemically stable and are among the most sensitive and specific ctDNA cancer markers. The objective of our study was to identify and validate a blood-based DNA methylation biomarker for breast cancer patients at high risk of distant metastasis. Using the HumanMethylation27K bead array, we recently identified RUNX3 hypermethylation involving 3 CpG probes in 32 breast brain metastasis tumor tissue compared to a series of 50 unmatched early stage breast cancer samples. We calculated the area under the curve (AUC) to exceed 0.8, with a higher AUC achieved in Her2-positive samples. In an independent, first of its kind analysis, we performed whole genome bisulfite sequencing (WGBS) of ctDNA from plasma samples representing three pools of 40 women with distant metastatic breast cancer to various organs, 40 women with metastasis-free breast cancer, and 40 non-breast cancer controls. In this unbiased analysis, these data demonstrated RUNX3 hypermethylation in the plasma of patients with metastatic breast cancer in the same region corresponding to the CpG probes of the methylation array. We are now performing bisulfite pyrosequencing of each individual plasma sample, and in an additional cohort of 50 archival primary/brain metastasis tumor pairs with matching serum and clinical outcomes data. To determine regional specific differences we have also selected two additional regions of RUNX3 not differentially methylated for validation by bisulfite pyrosequencing. Determining the extent to which RUNX3 hypermethylation occur in the context of brain metastasis versus other distant sites are ongoing studies. Together these studies point towards RUNX3-regional specific methylation as a potential blood-based biomarker of breast cancer metastasis. Such a biomarker will help establish surveillance methods and eventually preventative regimens that will increase the likelihood of long-term progression-free survival for breast cancer patients at risk of distant relapse. Citation Format: Bodour Salhia, Gerald C Gooden, Kyle N Johnson, Waibhav Tembe, Garrick Wallstrom, Winnie Liang, Manmeet Ahluwalia, Steven N Kalkanis, Tom Mikkelsen, Steven A Toms. RUNX3 hypermethylation in circulating tumor DNA is a biomarker of breast cancer distant metastasis [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-09.

RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype

Correlative and functional studies support the involvement of the RUNX gene family in haematological malignancies. To elucidate the role of epigenetics in RUNX inactivation, we evaluated promoter DNA methylation of RUNX1, 2, and 3 in 23 leukaemia cell lines and samples from acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL) and myelodysplatic syndromes (MDS) patients. RUNX1 and RUNX2 gene promoters were mostly unmethylated in cell lines and clinical samples. Hypermethylation of RUNX3 was frequent among cell lines (74%) and highly variable among patient samples, with clear association to cytogenetic status. High frequency of RUNX3 hypermethylation (85% of the 20 studied cases) was found in AML patients with inv(16)(p13.1q22) compared to other AML subtypes (31% of the other 49 cases). RUNX3 hypermethylation was also frequent in ALL (100% of the six cases) but low in MDS (21%). In support of a functional role, hypermethylation of RUNX3 was correlated with low levels of protein, and treatment of cell lines with the DNA demethylating agent, decitabine, resulted in mRNA re-expression. Furthermore, relapse-free survival of non-inv(16)(p13.1q22) AML patients without RUNX3 methylation was significantly better (P=0·016) than that of methylated cases. These results suggest that RUNX3 silencing is an important event in inv(16)(p13.1q22) leukaemias.

Association Between RUNX3 Hypermethylation and Acute Myeloid Leukemia Inv(16) Subtype

The RUNX family of transcription factors forms the DNA binding α-chain partners of the heterodimeric core binding factor (CBF) complex. Each of the RUNX proteins, RUNX1, RUNX2, and RUNX3, can form heterodimers with CBFβ. In the M4Eo subtype of human acute leukemia, the chromosomal translocation resulting in inversion 16 encodes a chimeric protein in which CBFβ is fused to smooth muscle myosin heavy chain (SMMHC). Although the exact mechanism of leukemogenesis by this chimera is unknown, it is thought that CBFβ-SMMHC sequesters RUNX1 in the cytoplasm and antagonizes its normal function. Although the role of RUNX1 in hematopoiesis has been previously well-established, recent data have indicated that the RUNX3 gene may also play a key role in the development of human acute leukemias.To clarify the role of RUNX3 in acute myeloid leukemia (AML), we investigated its expression and promoter DNA methylation in leukemia cell lines and patient samples. Eleven human leukemia cell lines of myeloid origin and twelve of lymphoid origin were used in this study. Cell suspensions from bone marrow aspirate specimens from patients with AML (69 cases), MDS (19 cases) and ALL (6 cases) were obtained prior to therapy from established tissue blocks. Peripheral blood samples were obtained from four healthy volunteers, and CD34+ cells were obtained from another four individuals. Methylation status of the gene promoters of RUNX1, RUNX2 and RUNX3 were evaluated using the Pyrosequencing Methylation Assay (PMA) method, and expression of RUNX3 was analyzed by quantitative real-time PCR and immunohistochemical staining.Hypermethylation of RUNX1 and RUNX2 was rare in cell lines; RUNX1 was not hypermethylated in any of the studied samples, and RUNX2 was hypermethylated in only two cell lines. In contrast, we found that the RUNX3 promoter was hypermethylated in 17 of the cell lines (74%). Interestingly, we observed a trend toward higher frequency of hypermethylation of RUNX3 in cell lines of myeloid (90%) compared to lymphoid (57%) origin. In patient samples, RUNX3 promoter methylation was below 15% in normal samples, and hypermethylation was found in 32/69 AML samples (46%), 4/19 MDS samples (21%), and 6/6 ALL samples (100%). Of the 69 AML samples, 19 were classified as AML M4Eo, and 50 were other types of AML. 84% of the human AML M4Eo samples were hypermethylated at the RUNX3 promoter region, whereas only 34% of the other AML subtypes were hypermethylated. We also evaluated DNA methylation of RUNX1 and RUNX2 in a subgroup of these samples (66 samples for RUNX1 and 72 for RUNX2) and found that, as in cell lines, these genes are almost universally unmethylated; with the exception of a single AML case, all studied samples presented no promoter methylation. As support of functional outcome, hypermethylation of RUNX3 was correlated with both lower levels of mRNA and protein, as confirmed by qRT-PCR and immunohistochemistry analysis in cell lines and patient samples, and treatment with the DNA demethylating agent Decitabine resulted in mRNA re-expression of RUNX3 concomitantly with decreased promoter methylation.Finally, we compared clinicopathological features of patients with and without RUNX3 methylation. In this analysis, only non-M4Eo AML cases were compared because of the small number of non-methylated patients in the M4Eo group. Differences were found neither for blood counts nor for overall survival probability. However, relapse-free survival was significantly better for the unmethylated group (p=0.016).In summary, we showed that promoter methylation of the RUNX3 gene and down regulation of RUNX3 expression occurs almost universally in M4Eo/inversion 16 AMLs, and that in cell lines, RUNX3 repression can be reversed by treatment with the hypomethylating agent decitabine. These results suggest that silencing of RUNX3 is likely an important target in CBF leukemia and that future studies should be dedicated to further characterize the role of RUNX3 in inversion 16 AML and its predictive value of relapse-free survival in AML. DisclosuresNo relevant conflicts of interest to declare.

Clinicopathological significance and potential drug target of RUNX3 in breast cancer.

BackgroundPrevious reports indicate that RUNX3 is a tumor suppressor in several types of human tumors, including breast cancer (BC). However, the correlation between RUNX3 hypermethylation and the incidence of BC remains unclear. In this study, we conducted a systematic review and meta-analysis aiming to comprehensively assess the potential role of RUNX3 hypermethylation in the pathogenesis of BC.MethodsA detailed literature search was made to identify studies for related research publications. Methodological quality of the studies was evaluated. Analysis of pooled data was performed. Odds ratio (OR) was calculated and summarized respectively.ResultsFinal analysis of 565 BC patients from eleven eligible studies was performed. The results showed that RUNX3 hypermethylation was significantly higher in BC than in normal breast tissue, the pooled OR from nine studies including 339 BC and 248 normal breast tissue (OR =24.12, 95% confidence interval [CI] =13.50–43.11, Z=10.75, P<0.00001). Further analysis also showed significantly increased OR of RUNX3 hypermethylation in estrogen receptor (ER)-positive than in ER-negative BC patients (OR =5.67, 95% CI =2.69–11.95, Z=4.57, P<0.00001). In addition, RUNX3 messenger RNA (mRNA) high expression was found to be correlated to better overall survival in 3,455 cases of BC patients that were followed up for 20 years (hazard ratio [HR] 0.79, P=8.8×10−5). Interestingly, RUNX3 mRNA overexpression was found to be correlated to better overall survival in only 668 cases of ER-negative patients (HR 0.72, P=0.01), but not in 1,767 cases of ER-positive patients (HR 0.87, P=0.13).ConclusionThe results of this meta-analysis suggest that RUNX3 hypermethylation may be implicated in the pathogenesis of BC. Detection of RUNX3 mRNA may be a helpful and valuable biomarker for diagnosis of BC, especially in ER-negative BC. We also discussed the significance of RUNX3 as a potential drug target.

Clinicopathological significance of RUNX3 gene hypermethylation in hepatocellular carcinoma.

Emerging evidence indicates that RUNX3 is a candidate tumor suppressor in several types of human tumors including hepatocellular carcinoma (HCC). However, the correlation between RUNX3 hypermethylation and incidence of HCC remains unclear. Here, we conducted a systematic review and meta-analysis aiming to comprehensively assess the potential role of RUNX3 hypermethylation in the pathogenesis of HCC. A detailed literature search was made from PubMed, EMBASE, and ISI web of knowledge to identify studies for related research publications. Methodological quality of the studies was also evaluated. The data were extracted and assessed by two reviewers independently. Analysis of pooled data was performed. Odds ratio (OR) was calculated and summarized, respectively. Final analysis of 821 HCC patients from 14 eligible studies was performed. We observed that RUNX3 hypermethylation was significantly higher in HCC than in normal liver tissue, the pooled OR from eight studies including 382 HCC and 161 normal liver tissue (OR = 39.32, 95 % confidence interval (CI) = 13.72-112.7, p < 0.00001). The pooled analysis showed significantly increased OR of RUNX3 hypermethylation (OR = 5.4, 95 % CI = 2.06-14.17, p < 0.00001) in HCC tissues and non-tumor liver tissues. In addition, statistically significant OR of RUNX3 hypermethylation was obtained from non-tumorous liver tissue of HCC patients and normal liver tissue (OR = 12.57, 95 % CI = 3.56-44.35, p < 0.0001). The results of this meta-analysis suggest that RUNX3 hypermethylation may be implicated in the pathogenesis of HCC. Thus, detection of RUNX3 hypermethylation may be a helpful and valuable biomarker for diagnosis of HCC.

Clinical significance and association of RUNX3 hypermethylation frequency with colorectal cancer: a meta-analysis.

BackgroundThe RUNX family, which is composed of RUNX1, RUNX2, and RUNX3, is a sequence-specific transcription factor family and is closely involved in a variety of cellular processes including development, differentiation, participation in the regulation of p53-dependent DNA damage response and/or tumorigenesis. Emerging evidence indicates that RUNX3 is a candidate tumor suppressor in several types of human tumors including colorectal cancer (CRC). However, the correlation of RUNX3 inactivation with CRC remains unclear. In the study reported here, we conducted a systematic review and meta-analysis to quantitatively evaluate the effects of RUNX3 hypermethylation/expression on the incidence of CRC.MethodsA detailed search of the literature was made using Medline® and Web of Science for related research publications written in English. The methodological quality of the studies was also evaluated. The data were extracted and assessed by two reviewers independently. Analyses of the pooled data were performed. Odds ratios (ORs) and hazard ratios were calculated and summarized, respectively.ResultsA final analysis of 1,427 CRC patients from eleven eligible studies was performed. We observed that RUNX3 hypermethylation was significantly higher in CRC than in normal colorectal mucosa. The pooled OR from six studies comprising 289 CRC and 188 normal colorectal mucosa was OR =0.07 (confidence interval [CI] =0.03–0.18, P<0.00001). Aberrant RUNX3 hypermethylation/expression was significantly higher in advanced CRC than in early staged CRC (OR =0.54, CI =0.41–0.71, P<0.0001). Aberrant RUNX3 hypermethylation/expression was also significantly higher in microsatellite instability (MSI)-positive CRC than in MSI-negative CRC (OR =0.44, CI =0.3–0.66, P<0.0001). In addition, CRC patients with RUNX3 hypermethylation or lacking RUNX3 protein expression had a lower survival rate than those without RUNX3 hypermethylation or those who did not express RUNX3 protein.ConclusionThe results of this meta-analysis suggest that RUNX3 hypermethylation is associated with an increased risk of CRC, increased risk of progression of CRC, and a poorer CRC survival rate. RUNX3 hypermethylation, which induces the inactivation of RUNX3 gene, plays an important role in colorectal carcinogenesis, high levels of MSI, as well as CRC progression and development.

Circulating HPV DNA as a Marker of Treatment Response of Head-and-Neck Cancer Patients Treated With Radiation Therapy or Chemoradiation Therapy: Molecular Biology and Therapeutics

HRZ3.51, 95% CI: 1.56-7.90, pZ0.001). Interrogation of The Cancer Genome Atlas database for HNSCC samples with both methylation and outcome data available (nZ305), revealed a similarly absent or low frequency of methylation events for the loci investigated. However, the presence of RUNX3 hypermethylation did not correlate with worse outcome for patients (HR Z 1.27; 95% CI: 0.56 2.88; pZ0.57 and HR Z 1.08; 95% CI: 0.65 1.82; p Z0.76, OTSCC and HNSCC, respectively). Conclusion: In OTSCC, we found little evidence of promoter hypermethylation of genes previously reported to be frequently methylated in HNSCC. Whilst OTSCC may have subsite-specific methylation for the loci examined, it is likely that previously reports have overestimated methylation events with the use of non-quantitative methodology. Author Disclosure: A.M. Lim: None. I.L.M. Candiloro: None. N. Wong: None. M. Collins: None. H. Do: None. C. Angel: None. J. Corry: None. D. Rischin: None. B. Solomon: None. A. Dobrovic: None.