Unmethylated Alleles Research Articles

Pyrimidine-Dependent UV-Mediated Cross-Linking Magnifies Minor Genetic or Epigenetic Changes in Clinical Samples.

Detection of minor DNA allele alterations is becoming increasingly important for early detection and monitoring of cancer. We describe a new method that uses ultraviolet light to eliminate wild-type DNA alleles and enables improved detection of minor genetic or epigenetic changes. Pyrimidine-dependent UV-based minor-allele enrichment (PD-UVME) employed oligonucleotide probes that incorporated a UVA-sensitive 3-cyanovinylcarbazole (CNVK), placed directly opposite interrogated pyrimidines, such as thymine (T) or cytosine (C) in wild-type (WT) DNA. Upon UVA-illumination, CNVK cross-linked with T/C, preventing subsequent amplification. Mutations that removed the T/C escaped cross-linking and were amplified and detected. Similarly, CNVK discriminated between methylated and unmethylated cytosine in CpG dinucleotides, enabling direct enrichment of unmethylated DNA targets. PD-UVME was combined with digital droplet PCR (ddPCR) to detect serine/threonine-protein kinase B-Raf (BRAF) V600E mutations in model systems, thyroid patient cancer tissue samples, and circulating DNA of tumor origin (ctDNA) from melanoma patients. One thyroid cancer sample out of 9, and 6 circulating-DNA samples out of 7 were found to be BRAF V600E-positive via PD-UVME while classified as negative by conventional ddPCR. Positive samples via conventional ddPCR were also found positive via PD-UVME. All 10 circulating cell-free DNA (cfDNA) samples obtained from normal volunteers were negative via both approaches. Furthermore, preferential enrichment of unmethylated alleles in MAGEA1 promoters using PD-UVME was demonstrated. PD-UVME mutation/methylation enrichment performed prior to ddPCR magnifies low-level mutations or epigenetic changes and increases sensitivity and confidence in the results. It can assist with clinical decisions that hinge on the presence of trace alterations like BRAF V600E.

Aberrant methylation scanning by quantitative DNA melting analysis with hybridization probes as exemplified by liquid biopsy of SEPT9 and HIST1H4F in colorectal cancer

ObjectiveThe generally accepted method of quantifying hypermethylated DNA by qPCR using methylation-specific primers has the risk of underestimating DNA methylation and requires data normalization. This makes the analysis complicated and less reliable. MethodsThe end-point PCR method, called qDMA-HP (for quantitative DNA Melting Analysis with hybridization probes), which excludes the normalization procedure, is multiplexed and quantitative, has been proposed. qDMA-HP is characterized by the following features: (i) asymmetric PCR with methylation-independent primers; (ii) fluorescent dual-labeled, self-quenched probes (commonly known as TaqMan probes) covering several interrogated CpGs; (iii) post-PCR melting analysis of amplicon/probe hybrids; (iv) quantitation of unmethylated and methylated DNA alleles by measuring the areas under the corresponding melt peaks. ResultsqDMA-HP was tested in liquid biopsy of colorectal cancer by evaluating SEPT9 and HIST1H4F methylations simultaneously in the single-tube reaction. Differences in the methylation levels in healthy donors versus cancer patients were statistically significant (p < 0.0001), AUCROC values were 0.795–0.921 for various marker combinations. ConclusionsThis proof-of-concept study shows that qDMA-HP is a simple, normalization-independent, quantitative, multiplex and “closed tube” method easily adapted to clinical settings. It is demonstrated, for the first time, that HIST1H4F is a perspective marker for liquid biopsy of colorectal cancer.

Institutional Validation Study Inferring 2% MGMT Methylation Positive Impact on Survival in Newly Diagnosed Glioblastoma (GBM) Patients

O6-methylguanine DNA methyltransferase (MGMT) MATERIALS/METHODS: is a well-established prognostic factor in patients with newly diagnosed glioblastoma (GBM). However, there is no consensus on a standardized method of threshold for MGMT testing. Previous studies have reported levels of as little as 1-3% to confer better prognosis. This study reports a single institutional experience of determining methylation status via methylation-sensitive high-resolution melting (MS-HRM). Previous literature suggests 10% cutoff for MGMT methylation using MS-HRM. We hereby report clinical outcomes using a lower threshold of 2%. GBM patients treated at our institution retrospectively reviewed between the years 2013 and 2022 were included in the study. Patients who received hypofractionated radiation (<60 Gy) were excluded. All patients had MS-HRM test for MGMT methylation status. A real-time PCR assay was used to amplify a 62 base-pair region of MGMT for both methylated and unmethylated alleles. PCR products underwent HRM analysis and the fraction of methylated DNA was determined by comparison with a standard curve. Clinical data were collected retrospectively. Kaplan-Meier and log-rank tests were performed to compare survival. A total of 181 patients with newly diagnosed GBM were initially included in this study. 42 patients treated with hypofractionated radiation were excluded. All patients received concurrent and maintenance temozolomide. Median age was 61.5 years. A total of 84 patients had MGMT methylation levels <2%, and 55 patients had MGMT methylation level ≥ 2% with a median methylation level of 28.5% (Range 0.8%-100%). Patients with MGMT methylation level ≥ 2% had an improved median overall survival (25.1 vs 16.0 months; p = 0.006) and improved median progression free survival (11.3 vs 7.9 months; p = 0.017). In a multivariable mode that included age, use of tumor-treating fields, KPS, sex, and BMI, only age, KPS, and MGMT remained significant. Our institutional review confirmed low level of MGMT hypermethylation (≥ 2%) predicts improved outcome in patients with newly diagnosed GBM. Further investigation on optimal cut off level for MGMT methylation is still warranted.

Constitutional MLH1 Methylation Is a Major Contributor to Mismatch Repair-Deficient, MLH1-Methylated Colorectal Cancer in Patients Aged 55 Years and Younger.

Most mismatch repair-deficient (MMRd) colorectal cancer (CRC) cases arise sporadically, associated with somatic MLH1 methylation, whereas approximately 20% have germline mismatch repair pathogenic variants causing Lynch syndrome (LS). Universal screening of incident CRC uses presence of MLH1 methylation in MMRd tumors to exclude sporadic cases from germline testing for LS. However, this overlooks rare cases with constitutional MLH1 methylation (epimutation), a poorly recognized mechanism for LS. We aimed to assess the frequency and age distribution of constitutional MLH1 methylation among incident CRC cases with MMRd, MLH1-methylated tumors. In retrospective population-based studies, we selected all CRC cases with MMRd, MLH1-methylated tumors, regardless of age, prior cancer, family history, or BRAF V600E status, from the Columbus-area HNPCC study (Columbus) and Ohio Colorectal Cancer Prevention Initiative (OCCPI) cohorts. Blood DNA was tested for constitutional MLH1 methylation by pyrosequencing and real-time methylation-specific PCR, then confirmed with bisulfite-sequencing. Results were achieved for 95 of 98 Columbus cases and all 281 OCCPI cases. Constitutional MLH1 methylation was identified in 4 of 95 (4%) Columbus cases, ages 34, 38, 52, and 74 years, and 4 of 281 (1.4%) OCCPI cases, ages 20, 34, 50, and 55 years, with 3 showing low-level mosaic methylation. Mosaicism in blood and normal colon, plus tumor loss of heterozygosity of the unmethylated allele, demonstrated causality in 1 case with sample availability. Age stratification showed high rates of constitutional MLH1 methylation among younger patients. In the Columbus and OCCPI cohorts, respectively, these rates were 67% (2 of 3) and 25% (2 of 8) of patients aged <50 years but with half of the cases missed, and 75% (3 of 4) and 23.5% (4 of 17) of patients aged ≤55 years with most cases detected. Although rare overall, a significant proportion of younger patients with MLH1-methylated CRC had underlying constitutional MLH1 methylation. Routine testing for this high-risk mechanism is warranted in patients aged ≤55 years for a timely and accurate molecular diagnosis that will significantly alter their clinical management while minimizing additional testing.

High-risk constitutional MLH1 methylation as a cause of early-onset colorectal and endometrial cancers displaying mismatch repair deficiency and MLH1 methylation.

10518 Background: Mismatch repair deficiency (MMRd) occurs in ~15% of colorectal (CRC) and ~30% of endometrial (EC) cancers, of which ~20% are caused by Lynch syndrome (LS). Universal screening of all incident CRC and EC for MMRd uses MLH1 methylation (in tumors with MLH1-loss by immunohistochemistry) to omit common sporadic cases from follow-up germline testing for LS. However, this overlooks unusual cases with constitutional MLH1 methylation (epimutation), a poorly-recognized high-risk mechanism for LS-type cancers that are MLH1 methylated. We aimed to determine the role and prevalence of constitutional MLH1 methylation among CRC and EC cases with tumor MLH1 methylation from clinical and population-based series and if age limits could be used to triage cases warranting additional germline methylation testing. Methods: We screened blood DNA for constitutional MLH1 methylation by pyrosequencing and methylation-specific qPCR in patients with MLH1-loss, MLH1 methylated CRC and EC ascertained from: i) cancer clinics, referred by oncologists and genetic counsellors; ii) Ohio population-based “Columbus” and “OCCPI” cohorts. Bisulfite sequencing confirmed constitutional MLH1 methylation. Results: In clinical cases, constitutional MLH1 methylation was identified in 3/7 EC and 3/8 CRC cases &lt; 60 years. In population-based cohorts, constitutional MLH1 methylation was identified in 4/95 (4.2%) and 4/281 (1.4%) CRC cases of all ages from Columbus and OCCPI, respectively. Highest rates of detection with the majority of cases detected were at age ≤55 years, with 3/4 (75%) in Columbus and 4/17 (23.5%) in OCCPI ≤55 years. For EC, constitutional MLH1 methylation was identified in 0/68 Columbus cases of all ages and 1/24 OCCPI cases &lt; 60 years (age-limited testing). She was one of six (~17%) cases &lt; 50 years in the combined cohorts. EC was the first/dual-first presenting “sentinel” cancer in three female patients with constitutional MLH1 methylation. Of the 14 cases with constitutional MLH1 methylation, nine had hemiallelic methylation (~50% alleles methylated, affecting a single parental allele) and five had mosaicism across various normal tissues. Somatic “second-hits” affecting the unmethylated allele were found in the tumors of mosaic cases, demonstrating causation. Conclusions: A correct diagnosis of constitutional MLH1 methylation at first cancer presentation is important as it will significantly alter clinical management of these high-risk patients. Although rare overall, high rates of detection were found ≤55 years for CRC and ≤50 years for EC cases with a MMRd, MLH1 methylated tumor, entailing minimal extra screening. Testing for constitutional MLH1 methylation is warranted in patients with young-onset CRC or EC, or syn/metachronous cancers at any age, with MMRd and MLH1 methylated tumor(s).

MLH1-methylated endometrial cancer under 60 years of age as the “sentinel” cancer in female carriers of high-risk constitutional MLH1 epimutation

ObjectiveUniversal screening of endometrial carcinoma (EC) for mismatch repair deficiency (MMRd) and Lynch syndrome uses presence of MLH1 methylation to omit common sporadic cases from follow-up germline testing. However, this overlooks rare cases with high-risk constitutional MLH1 methylation (epimutation), a poorly-recognized mechanism that predisposes to Lynch-type cancers with MLH1 methylation. We aimed to determine the role and frequency of constitutional MLH1 methylation among EC cases with MMRd, MLH1-methylated tumors. MethodsWe screened blood for constitutional MLH1 methylation using pyrosequencing and real-time methylation-specific PCR in patients with MMRd, MLH1-methylated EC ascertained from (i) cancer clinics (n = 4, <60 years), and (ii) two population-based cohorts; “Columbus-area” (n = 68, all ages) and “Ohio Colorectal Cancer Prevention Initiative (OCCPI)” (n = 24, <60 years). ResultsConstitutional MLH1 methylation was identified in three out of four patients diagnosed between 36 and 59 years from cancer clinics. Two had mono−/hemiallelic epimutation (∼50% alleles methylated). One with multiple primaries had low-level mosaicism in normal tissues and somatic “second-hits” affecting the unmethylated allele in all tumors, demonstrating causation. In the population-based cohorts, all 68 cases from the Columbus-area cohort were negative and low-level mosaic constitutional MLH1 methylation was identified in one patient aged 36 years out of 24 from the OCCPI cohort, representing one of six (∼17%) patients <50 years and one of 45 patients (∼2%) <60 years in the combined cohorts. EC was the first/dual-first cancer in three patients with underlying constitutional MLH1 methylation. ConclusionsA correct diagnosis at first presentation of cancer is important as it will significantly alter clinical management. Screening for constitutional MLH1 methylation is warranted in patients with early-onset EC or synchronous/metachronous tumors (any age) displaying MLH1 methylation.

Abstract PD5-01: PD5-01 Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in triple negative breast cancer and ovarian carcinoma

Abstract Background. Homologous recombination deficiency (HRD), induced by germline and somatic BRCA1 or BRCA2 gene mutations (BRCAmut) and by BRCA1 promoter methylation (BRCA1meth), has been associated with better response to platinum agents in both triple negative breast cancer (TNBC) and ovarian carcinoma (OvCa). A major conundrum arising from recent studies is why patients with BRCA1meth cancers do more poorly compared to those with BRCAmut cancers given the biologically equivalent HRD in both states. Here, we address this question by performing detailed genomic analyses of primary TNBC and OvCa cohorts and through patient-derived xenografts (PDXs) and their derivative cell lines. Methods. Both new and publicly available cohorts of primary TNBC and OvCa encompassing 499 individuals treated with a combination of platinum and taxane chemotherapy were analyzed by whole genome and transcriptome sequencing as well as limited epigenetic analyses. A cohort of 43 PDX models of TNBC was genomically characterized and responses to both single agent platinum and docetaxel were evaluated in vivo. PDX longitudinal studies were performed to assess the dynamics of BRCA1 methylation following treatment. Results. Genomic analyses revealed that BRCA1mut and BRCA1meth cancers share the same pattern of BRCA1-linked genomic rearrangements. Nonetheless, in all four primary cancer cohorts examined we found that patients with BRCAmut cancers, but not those with BRCA1meth cancers, had significantly better response outcomes compared to those with BRCA proficient cancers. A separate analysis of PDX TNBCs with BRCA1 promoter methylation showed that PDXs derived from treatment naïve cancers had complete methylation of the BRCA1 promoter, whereas those derived from post-treatment cancers invariably had only partial methylation. Compared to PDXs with complete methylation, those with partial methylation had a lower response rate to in vivo platinum-based therapy, but not to docetaxel. Using single cell clonal expansions from BRCA1meth PDX models, we confirmed that partial methylation was the result of demethylation of one of the BRCA1 promoter alleles and not of the outgrowth of a non-methylated clone. Exposure of TNBC PDXs with complete methylation to a single course of platinum therapy resulted in the emergence of an unmethylated BRCA1 promoter allele, which associated with an increase in BRCA1 expression. We confirmed that platinum treatment results in progressive loss of BRCA1 methylation and restoration of BRCA1 expression in the clinical setting, by studying the BRCA1 status of a longitudinal series of four TNBC PDX models established from the same patient at different stages of her clinical history. Differential gene expression analysis revealed an increased immune transcriptional signal, especially an elevated M1 macrophage signature, associated with enhanced response to platinum therapy only in patients with BRCA proficient cancers, in both TNBC and OvCa. Integrating both the strength of this cancer immune signature and the presence of BRCA mutations resulted in more accurate predictions of response when compared to either HRD or BRCA status alone. Conclusions. These results suggest that unlike BRCAmut cancers, where BRCA deficiency is more genetically stable, BRCA1meth cancers are highly adaptive to genotoxin exposure resulting in demethylation of one allele, recovery of BRCA1 expression and acquired insensitivity to platinum. On the other end, a high immune transcriptional signature identifies patients with BRCA proficient cancers that are more likely to benefit from platinum therapy. Taken together, our study underscores the importance of characterizing molecular heterogeneity to optimize predictive precision in assigning response probabilities in TNBC and OvCa. Citation Format: Francesca Menghi, Kalyan Banda, Pooja Kumar, Robert Straub, Lacey E. Dobrolecki, Isabel Rodriguez, Susan E. Yost, Harshpreet Chandok, Marc Radke, George Somlo, Yuan Yuan, Michael T. Lewis, Elizabeth Swisher, Edison Liu. PD5-01 Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in triple negative breast cancer and ovarian carcinoma [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-01.

DNA methylation profile of single in vitro matured bovine oocytes.

Somatic cell nuclear transfer (SCNT) is commercially used despite incomplete nuclear reprogramming of the somatic cell nucleus by the enucleated oocyte compromising its efficiency. Oocyte selection is a key factor in increasing this efficiency as its cytoplasm reprograms the differentiated cell. In this study, we adapted a methodology to characterize epialleles in potential epigenetic markers in single in vitro matured oocytes. Characterization of the regions that control the expression of imprinted genes, X-chromosome inactivation, and satellite I DNA (IGF2, ICR-H19, XIST, RepA, and SAT1) showed methylated and unmethylated alleles in the imprinted genes IGF2 and ICR-H19 while XIST-DMR1 and RepA showed hypermethylated alleles. There was great variation in methylation patterns for candidate regions which may be related to oocyte quality. Moreover, the identification of different epialleles in the same oocyte suggests that, at least for those loci, the epigenome of the metaphase plate and polar body is different. The single-cell bisulfite polymerase chain reaction technique can be used to improve the precision of selecting the best oocytes for SCNT procedures, thereby increasing its efficiency.

Diagnosis of Prader-Willi syndrome and Angelman syndrome by targeted nanopore long-read sequencing

The CpG island flanking the promoter region of SNRPN on chromosome 15q11.2 contains CpG sites that are completely methylated in the maternally derived allele and unmethylated in the paternally derived allele. Both unmethylated and methylated alleles are observed in normal individuals. Only the methylated allele is observed in patients with Prader-Willi syndrome, whereas only the unmethylated allele is observed in those with Angelman syndrome. Hence, detection of aberrant methylation at the differentially methylated region is fundamental to the molecular diagnosis of Prader-Willi syndrome and Angelman syndromes. Traditionally, bisulfite treatment and methylation-sensitive restriction enzyme treatment or methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) have been used. We here developed a long-read sequencing assay that can distinguish methylated and unmethylated CpG sites at 15q11.2 by the difference in current intensity generated from nanopore reads. We successfully diagnosed 4 Prader-Willi syndrome patients and 3 Angelman syndrome patients by targeting differentially methylated regions. Concurrent copy number analysis, homozygosity analysis, and structural variant analysis also allowed us to precisely delineate the underlying pathogenic mechanisms, including gross deletion, uniparental heterodisomy, uniparental isodisomy, or imprinting defect. Furthermore, we showed allele-specific methylation in imprinting-related differentially methylated regions on chromosomes 6, 7, 11, 14, and 20 in a normal individual together with 4 Prader-Willi patients and 3 Angelman syndrome patients. Hence, presently reported method is likely to be applicable to the diagnosis of imprinting disorders other than Prader-Willi syndrome and Angelman syndrome as well.

Prader-Willi syndrome patient with atypical phenotypes caused by mosaic deletion in the paternal 15q11-q13 region: a case report

BackgroundPrader-Willi syndrome (PWS) is a multisystemic complex genetic disorder caused by the loss of paternally expressed genes in the human chromosome region 15q11.2-q13. It is characterized by severe hypotonia and feeding difficulties in early infancy, followed in later infancy or early childhood by excessive eating and gradual development of morbid obesity. Motor milestones and language development are delayed and most patients have intellectual disability.Case presentationHere we describe a rare PWS case caused by mosaic imprinting defect in the region 15q11.2-q13 of paternal origin. The proband was a male child with a clinical presentation of global developmental delay and hypotonia with specific facial features. Karyotype of the child was noted as mosaic: 45XY,der(15)?t(15;21),-21[26]/46,XY[24]. Whole-exome sequencing (WES) identified a deletion of 22.7 Mb in size at chr15q11.2q21.1 region and a deletion of 2.1 Mb in size at chr21q22.3 region. The Methylation-specific multiplex ligation-dependent probe amplification(MS-MLPA) of the 15q11.2-q13 region showed that the loading ratio of methylated alleles was 70% and that of unmethylated alleles was 30%(50% normal), which confirmed that the loss of mosaic imprinted defects in the paternal allele led to the diagnosis of PWS.ConclusionsWe propose that complete clinical criteria for PWS should not be considered sensitive in diagnosing partial atypical PWS due to mosaic imprinting defects. In contrast, clinical suspicion based on less restrictive criteria followed by multiple techniques is a more powerful approach.

Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader\u2013Willi/Angelman syndromes?

BackgroundCopy-neutral absence of heterozygosity (CN-AOH) observed on a single chromosome or part of a chromosome may be indicative of uniparental disomy (UPD) and may require additional testing when such chromosomes or chromosome regions are known to harbor imprinted genes.Case presentationHere we report 2 cases of neonates that presented to clinic with hypotonia, poor oral skills including inability to feed by mouth, weak cry, no response to noxious stimulation and vertical plantar creases (case 1) and hypotonia and respiratory distress (case 2). A preliminary chromosome analysis showed normal karyotypes in both cases while the high-resolution single nucleotide polymorphism (SNP) microarray showed copy neutral absence of heterozygosity involving chromosome 15 distal long arm. In case 1, the CN-AOH involved a 28.7 Mb block from genomic coordinates 73703619_102429049. In case 2, the CN-AOH involved a 15.3 Mb block from genomic coordinates 54729197_70057534. In both cases, methylation-specific PCR did not detect an unmethylated allele for the SNRPN gene suggesting either a deletion of paternal allele or maternal UPD for chromosome 15. Since microarray analysis did not show any copy number alterations on chromosome 15, a microdeletion was ruled out.ConclusionsBased on our cases, we suggest that CN-AOH on chromosome 15, even if it does not involve the critical region of 15q12q13, should warrant additional studies for diagnosis of Prader–Willi/Angelman syndromes.

BiasCorrector: Fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies.

Quantification of DNA methylation in neoplastic cells is crucial both from mechanistic and diagnostic perspectives. However, such measurements are prone to different experimental biases. Polymerase chain reaction (PCR) bias results in an unequal recovery of methylated and unmethylated alleles at the sample preparation step. Post-PCR biases get introduced additionally by the readout processes. Correcting the biases is more practicable than optimising experimental conditions, as demonstrated previously. However, utilisation of our earlier developed algorithm strongly necessitates automation. Here, we present two R packages: rBiasCorrection, the core algorithms to correct biases; and BiasCorrector, its web-based graphical user interface frontend. The software detects and analyses experimental biases in calibration DNA samples at a single base resolution by using cubic polynomial and hyperbolic regression. The correction coefficients from the best regression type are employed to compensate for the bias. Three common technologies-bisulphite pyrosequencing, next-generation sequencing and oligonucleotide microarrays-were used to comprehensively test BiasCorrector. We demonstrate the accuracy of BiasCorrector's performance and reveal technology-specific PCR- and post-PCR biases. BiasCorrector effectively eliminates biases regardless of their nature, locus, the number of interrogated methylation sites and the detection method, thus representing a user-friendly tool for producing accurate epigenetic results.

Gene body methylation is under selection in Arabidopsis thaliana.

In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.

Baculoviral inhibitor of apoptosis family of proteins repeat-containing 5 gene methylation status in peripheral blood mononuclear cells and plasma survivin levels in patients with Behçet's disease.

Objectives This study aims to evaluate the baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) gene methylation in the peripheral blood mononuclear cells (PBMCs) in patients with Behçet’s disease (BD) compared to healthy controls and the association of survivin with BD activity.Patients and methods A cross-sectional study was conducted on 43 BD patients (22 males, 21 females; mean age 36.6±10.1 years; range, 18 to 66 years) and 44 age- and sex-matched healthy controls (23 males, 21 females; mean age 35.4±7.5 years; range, 18 to 61 years) between August 2019 and December 2019. Sample size was calculated guided by taking into account the difference of 1.5 units between the mean expression of BIRC5 gene in the BD and control groups, as well as considering α=0.5 and power=80%. We assessed the methylation status of the BIRC5 gene in PBMCs of BD and control groups by methylation-specific polymerase chain reaction (MS-PCR). Plasma levels of survivin were measured by enzyme- linked immunosorbent assay.Results Oral aphthous ulcer, genital ulcer, and skin lesions were the most common clinical manifestations in BD group. MS-PCR showed that the deoxyribonucleic acid samples of BD and control groups were not different in methylated and unmethylated areas and alleles were heterozygote. No significant difference was observed in the plasma levels of survivin in BD (98.86±25.5 pg/mL) and control (118.16±37.4 pg/mL) groups. There was no significant correlation between survivin plasma levels and BD activity.ConclusionOur study did not show any evidence of association between the alteration in the BIRC5 gene methylation, survivin production, and apoptosis dysregulation in BD.

Abstract 157: Pervasive promoter hypermethylation of silenced TERT alleles in human cancers

Abstract In cancers, the epigenetic regulation of telomerase expression is not fully characterized, with multiple conflicting reports. In particular, the role of DNA methylation of cytosine residues in the control of TERT expression remains unclear. Here, we have carried out the most comprehensive characterization of TERT promoter methylation using ultra-deep bisulfite sequencing spanning more than 310 CpGs within and surrounding the core TERT promoter in 96 different cell lines, including primary, immortalized, and cancer cell types, as well as in control and reference samples. In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent G228A and G250A TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. Notably, in cancers, the hypermethylated alleles were associated with repressed expression while remaining unmethylated alleles were enriched with the open chromatin marks, H3K4me3 and H3K27ac. Furthermore, the hypomethylated alleles of the TERT promoter were responsible for the observed TERT expression in cancer. This association of hypomethylated alleles with active expression and hypermethylated alleles with repressed expression is particularly evident in cancers harboring TERT promoter mutations, and cancers displaying allele-specific expression. Reporter assays confirmed that DNA methylation of the TERT promoter greatly suppressed reporter expression in heterologous TERT promoter-reporter constructs. Overall, our findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to the attenuation of TERT activation in cancer cells. Citation Format: Mindy K. Graham, David Esopi, Jacqueline A. Brosnan-Cashman, Anuj Gupta, Angelo De Marzo, William G. Nelson, Christopher M. Heaphy, Alan K. Meeker, Sarah J. Wheelan, Srinivasan Yegnasubramanian. Pervasive promoter hypermethylation of silenced TERT alleles in human cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 157.

Pervasive promoter hypermethylation of silenced TERT alleles in human cancers

BackgroundIn cancers, maintenance of telomeres often occurs through activation of the catalytic subunit of telomerase, encoded by TERT. Yet, most cancers show only modest levels of TERT gene expression, even in the context of activating hotspot promoter mutations (C228T and C250T). The role of epigenetic mechanisms, including DNA methylation, in regulating TERT gene expression in cancer cells is as yet not fully understood.MethodsHere, we have carried out the most comprehensive characterization to date of TERT promoter methylation using ultra-deep bisulfite sequencing spanning the CpG island surrounding the core TERT promoter in 96 different human cell lines, including primary, immortalized and cancer cell types, as well as in control and reference samples.ResultsIn general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent C228T and C250T TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. However, at the allele-level, we generally found that hypermethylation of promoter sequences in cancer cells is associated with repressed expression, and the remaining unmethylated alleles marked with open chromatin are largely responsible for the observed TERT expression in cancer cells.ConclusionsOur findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to attenuation of TERT activation in cancer cells. This type of fine tuning of TERT expression may account for the modest activation of TERT expression in most cancers.

Investigation of promoter methylation of FSCN1 gene and FSCN1 protein expression in differentiated thyroid carcinomas.

FSCN1 gene encodes an actin-bundling protein, FSCN1, which is involved in formation of actin-based structures that contribute to cell migration. High levels of FSCN1 expression is observed in cells with extended membranes and protrusions. Moreover, up-regulation of FSCN1 has been reported in several epithelial carcinomas. Therefore, FSCN1 is thought to play a role in cell movement and invasion. However, the mechanism behind FSCN1 up-regulation is not known. We investigated the expression of FSCN1 using immunohistochemistry. Methylation-specific PCR was adopted to analyze the methylation status of FSCN1 promoter as a potential regulatory mechanism in FSCN1 expression. The samples included papillary thyroid carcinoma, follicular thyroid carcinoma and goiter samples (controls). Methylation of FSCN1 promoter was observed in 50% of follicular, 48.6% of papillary and 60% of controls. The promoter was unmethylated in 16.7% of follicular samples, 5.7% of papillary samples and 26.7% of controls. In the remaining 33.3% of follicular and 45.7% of papillary samples as well as 13.3% of controls, both methylated and unmethylated alleles were amplified, a condition referred to as semi-methylation. The results showed that FSCN1 promoter was significantly hypomethylated in papillary cases while the methylation status was not significantly altered in follicular cases. On the other hand, FSCN1 was expressed in only nine papillary samples. Regarding protein expression and methylation status, we suggest that hypomethylation of FSCN1 promoter in papillary thyroid carcinoma does not lead to overexpression of FSCN1 and that there might be other regulatory mechanisms involved in FSCN1 up-regulation.

Low Levels of Quantified MGMT Methylation Status Impart Positive Impact on Survival

MGMT methylation status is a significant prognostic factor for glioblastoma (GBM), particularly in the era of temozolomide (TMZ). However, there is no standardization of MGMT methylation methodology or optimal cutoff criteria. We developed and implemented a quantitative assay for MGMT methylation (mMGMT) and investigated association with clinical outcomes. We retrospectively reviewed GBM patients at our institution treated with standard chemoradiation, from 2008 to 2018. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue. A real-time PCR assay was performed to amplify a 62 base-pair region of MGMT including the first 12 CpG islands after ATG initiation codon for both methylated and unmethylated alleles. PCR products underwent high-resolution melt (HRM) analysis and the fraction of methylated DNA was determined by comparison with a standard curve generated from specimens with known percentages of methylation. Patient demographics, treatment records, and clinical outcomes were collected. Kaplan-Meier and log-rank tests were performed to compare survival. Cox proportional hazard model was used for predicting prognostic factors. Optimal cutoff point was evaluated with maximally selected log-rank statistics. Statistical analysis was conducted on R (v3.5). A total of 108 patients (68 men, 40 women) with newly diagnosed GBM were included in the study. Median age was 61 years old (31-85), and KPS was 80 (50-100). A total of 32 pts (29.6%) had gross total resection (GTR), 61 pts (56.4%) had subtotal resection, and 15 pts (13.9%) had biopsy only. With a median follow-up of 9 months (1-73 months), the median PFS and OS were 6 months and 14.4 months, respectively. At 1 and 2 years, PFS was 25.2% and 17.8% while OS was 58.1% and 23.8%, respectively. A total of 44 patients (40.7%) had detectable MGMT methylation, with median methylation level of 23.36% (range 0.2%-78.2%; IQR 4.77-31.88%). On both univariate and multivariate analysis, detectable MGMT methylation (HR 0.06, 95% CI [0.008-0.4223]; p=0.004) and GTR (HR 0.18, 95% CI [0.07-0.43]; p>0.001) were associated with improved OS, while GTR alone improved PFS (HR 0.38, 95% CI [0.16-0.89]; p=0.028). Patients with any detectable mMGMT had improved OS (19.3 vs 11.1 months; p=0.003). Optimal cutoff point for quantifying MGMT methylation for maximum survival difference was estimated as ∼ 1.9% (p=0.007). MGMT methylation at even low levels may have a positive impact on survival for GBM patients. Further refinement of a cutoff point for our MGMT assay with a validation set is warranted.

Abstract 823: A case-control study of constitutional BRCA1 methylation in a mammographically screened cohort

Abstract Introduction: Over 90% of breast cancers occur sporadically with no obvious hereditary factors at play, therefore highlighting the need for biomarkers that can identify women who are predisposed to developing breast cancer. DNA methylation of the BRCA1 promoter region is detectable at low levels in the peripheral blood of some women. This phenomenon is referred to as constitutional BRCA1 methylation. Peripheral blood methylation of the BRCA1 gene has been identified as a predisposition factor to the development of BRCA1 methylated tumors. We performed a case-control study to assess peripheral blood BRCA1 methylation from healthy women, and from women with breast cancer. This study aimed to establish the frequency of peripheral blood methylation of the BRCA1 gene in women with and without breast cancer, to further our understanding of the role of constitutional BRCA1 methylation in breast cancer predisposition. Methods: Constitutional BRCA1 methylation was assessed in peripheral blood DNA of breast cancer patients and healthy women. Whole blood DNA was obtained from healthy women (n=327 controls) and women with breast cancer (n=300 cases) as part of the LifePool Project. Blood was collected on the day of mammography with BreastScreen Victoria. We used a probe-based droplet digital PCR (ddPCR) assay designed to quantify methylated and unmethylated alleles at the BRCA1 promoter region. Results: Previous research using less-sensitive methodologies has reported a BRCA1 methylation frequency of 2-4% in peripheral blood of healthy women. In this study, there was no significant difference in the observed BRCA1 methylation frequency between cases and controls (6.6% and 6.4% respectively). The discrepancy between our observed methylation frequencies and previously reported data can be attributed to the higher sensitivity of the ddPCR methodology. Nevertheless, the level of BRCA1 methylation in cases was significantly higher than the level of methylation observed in controls, consistent with previous studies. In addition, the frequency of BRCA1 methylation was higher in women diagnosed with breast cancer under the age of 50 compared to women diagnosed over 50 years old (average methylation frequency = 12.5% and 5.3% respectively). Conclusions: ddPCR methodology enabled accurate quantification of methylated BRCA1 alleles in peripheral blood DNA down to less than 0.1%. In this selected population of women undergoing mammography, there was no difference in the frequency of detectable BRCA1 methylation between cases and controls. Once age was considered, detectable BRCA1 methylation showed an association with age of onset. Tumours for the women with breast cancer will be retrieved and tested for BRCA1 methylation, to further examine the link between the methylation observed in peripheral blood DNA and development of a BRCA1-methylated tumor. Citation Format: Basant Ebaid, Hongdo Do, Jia Min Pang, Lisa Devereux, Alexander Dobrovic. A case-control study of constitutional BRCA1 methylation in a mammographically screened cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 823.

Novel Assay for Quantitative Analysis of DNA Methylation at Single-Base Resolution.

The DNA methylation profile provides valuable biological information with potential clinical utility. Several methods, such as quantitative methylation-specific PCR (qMSP), have been developed to examine methylation of specific CpG sites. Existing qMSP-based techniques fail to examine the genomic methylation at a single-base resolution, particularly for loci in gene bodies or extensive CpG open seas lacking flanking CpGs. Therefore, we established a novel assay for quantitative analysis of single-base methylation. To achieve a robust single-base specificity, we developed a PCR-based method using paired probes following bisulfite treatment. The 6-carboxyfluorescein- and 2'-chloro-7'phenyl-1,4-dichloro-6-carboxy-fluorescein-labeled probes conjugated with minor groove binder were designed to specifically bind to the methylated and unmethylated allele of targeted single CpGs at their 3' half regions, respectively. The methylation percentage was calculated by values of methylation / (methylation + unmethylation). In the detection of single CpGs within promoters or bodies of 4 human genes, the quantitative analysis of the single-base methylation assay showed a detection capability in the 1 to 1:10000 dilution experiments with linearity over 4 orders of magnitude (R 2 = 0.989-0.994; all P < 0.001). In a cohort of 10 colorectal cancer samples, the assay showed a comparable detection performance with bisulfite pyrosequencing (R 2 = 0.875-0.990; all P < 0.001), which was better than conventional qMSP methods normalized by input control reaction (R 2 = 0.841 vs 0.769; P = 0.002 vs 0.009). This assay is highly specific and sensitive for determining single-base methylation and, thus, is potentially useful for methylation-based panels in diagnostic and prognostic applications.