Abstract A011: Epigenetic vulnerabilities in patient-derived colorectal cancer organoids

Colorectal cancer (CRC) is a major cause of cancer-related deaths worldwide. Here, we established human patient-derived colorectal cancer organoid cultures (PDOs) to decipher the patient-specific DNA methylation profile and drug sensitivity towards 5-aza-2’-deoxycytidine, a DNA methyltransferase inhibitor. Organoid lines (n=15) were generated from adjacent normal mucosa and tumor tissue located in different anatomical sites of the colon and rectum. The derived PDOs were characterized on a histopathological level and reproduced the grade and differentiation capacity of their parental tumors. Additional genotypic profiling of PDOs showed a high degree of similarity to the original patient tumors. However, the stability of the DNA methylation landscape of human cancer organoids remains largely unknown. In genome-wide methylation analysis of long-term organoid cultures (up to 6 months in culture), we observed surprisingly stable methylation signatures that recapitulates the patient’s profile whilst demonstrating the vast intertumoral heterogeneity among patients. Strikingly, we identified a tumor-specific methylation signature that consisted of 39 CpG sites, which were unmethylated in normal epithelial cells but highly (91-96%) methylated in all tumor cells analyzed. This signature allows for the estimation of the percentage of tumor content in resected tissues and might represent potent biomarkers for early CRC diagnostics. Notably, it has been demonstrated that PDOs have the potential to predict clinical outcome and response to chemo- and radiation therapy in patients. Herein, drug screening with 5-aza-2’-deoxycytidine revealed heterogeneous responses and a clustering into drug sensitive, median and resistant organoid lines. ATAC- and RNA-seq analyses identified pathways rendering drug sensitivity and resistance. Our findings highlight the utility of PDOs as an advanced model system to study the role of the epigenome, especially DNA methylation, and its impact on tumor burden and vulnerability towards epigenetic modifiers.

Citation Format: Loan Tran, Raheleh Sheibani Tezerji, Carlos Uziel Perez Malla, Anna Malzer, Ajna Logo, Katarina Misura, Theresia Mair, Thomas Dillinger, Madeleine Kuroll, Velina Atanasova, Julijan Kabiljo, Helga Schachner, Katharina Wöran, Judith Stift, Helmut Dolznig, Walter Pulverer, Michael Bergmann, Gerda Egger. Epigenetic vulnerabilities in patient-derived colorectal cancer organoids. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A011.

Multiplexed DNA Methylation Analysis in Colorectal Cancer Using Liquid Biopsy and Its Diagnostic and Predictive Value

Early diagnosis of colorectal cancer (CRC) is of high importance as prognosis depends on tumour stage at the time of diagnosis. Detection of tumour-specific DNA methylation marks in cfDNA has several advantages over other approaches and has great potential for solving diagnostic needs. We report here the identification of DNA methylation biomarkers for CRC and give insights in our methylation-sensitive restriction enzyme coupled qPCR (MSRE-qPCR) system. Targeted microarrays were used to investigate the DNA methylation status of 360 cancer-associated genes. Validation was done by qPCR-based approaches. A focus was on investigating marker performance in cfDNA from 88 patients (44 CRC, 44 controls). Finally, the workflow was scaled-up to perform 180plex analysis on 110 cfDNA samples, to identify a DNA methylation signature for advanced colonic adenomas (AA). A DNA methylation signature (n = 44) was deduced from microarray experiments and confirmed by quantitative methylation-specific PCR (qMSP) and by MSRE-qPCR, providing for six genes’ single areas under the curve (AUC) values of >0.85 (WT1, PENK, SPARC, GDNF, TMEFF2, DCC). A subset of the signatures can be used for patient stratification and therapy monitoring for progressed CRC with liver metastasis using cfDNA. Furthermore, we identified a 35-plex classifier for the identification of AAs with an AUC of 0.80.

Salivary biomarkers in cardiovascular disease: An insight into the current evidence

Cardiovascular diseases (CVDs) are the most common cause of mortality worldwide. In acute cardiovascular conditions, time is a crucial player in the outcomes of disease management. Given the ease and noninvasiveness of obtaining saliva, salivary biomarkers may provide a rapid and efficient diagnosis of CVD. Here, we reviewed the published data on the value of salivary molecules for diagnosis of CVD, especially in acute care settings. In this review, we show that some biomarkers such as salivary creatinine kinase myocardial band, C-reactive protein, troponin-1, and myoglobin exhibited promising diagnostic values that were comparable to their serum counterparts. Other molecules were also investigated and showed controversial results, including myeloperoxidase, brain natriuretic peptide, and some oxidative stress markers. Based on our review, we concluded that the clinical use of salivary biomarkers to diagnose CVD is promising; however, it is still in the early stage of development. Further studies are needed to validate these findings, determine cutoff values for diagnosis, and compare them to other established biomarkers currently in clinical use.

Discovery of Molecular DNA Methylation-Based Biomarkers through Genome-Wide Analysis of Response Patterns to BCG for Bladder Cancer

Background: Bacillus Calmette-Guérin (BCG) immunotherapy, the standard adjuvant intravesical therapy for some intermediate and most high-risk non-muscle invasive bladder cancers (NMIBCs), suffers from a heterogenous response rate. Molecular markers to help guide responses are scarce and currently not used in the clinical setting. Methods: To identify novel biomarkers and pathways involved in response to BCG immunotherapy, we performed a genome-wide DNA methylation analysis of NMIBCs before BCG therapy. Genome-wide DNA methylation profiles of DNA isolated from tumors of 26 BCG responders and 27 failures were obtained using the Infinium MethylationEPIC BeadChip. Results: Distinct DNA methylation patterns were found by genome-wide analysis in the two groups. Differentially methylated CpG sites were predominantly located in gene promoters and gene bodies associated with bacterial invasion of epithelial cells, chemokine signaling, endocytosis, and focal adhesion. In total, 40 genomic regions with a significant difference in methylation between responders and failures were detected. The differential methylation state of six of these regions, localized in the promoters of the genes GPR158, KLF8, C12orf42, WDR44, FLT1, and CHST11, were internally validated by bisulfite-sequencing. GPR158 promoter hypermethylation was the best predictor of BCG failure with an AUC of 0.809 (p-value < 0.001). Conclusions: Tumors from BCG responders and BCG failures harbor distinct DNA methylation profiles. Differentially methylated DNA regions were detected in genes related to pathways involved in bacterial invasion of cells or focal adhesion. We identified candidate DNA methylation biomarkers that may help to predict patient prognosis after external validation in larger, well-designed cohorts.

Abstract A05: Development and clinical performance of an accurate cell-free DNA (cfDNA) methylation assay for early detection of colorectal cancer

Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, and its incidence is increasing in younger persons. Established CRC screening methods include fecal immunochemical testing, which requires handling of stool, and colonoscopy, which is invasive. Many persons who remain unscreened might accept a blood-based screening test, which could have profound public health impact. DNA methylation is a stable, early, and tissue-specific event in cancer development and progression. Measuring the methylation status of tumor-derived cell-free DNA in plasma could enable identification of early-stage CRC. We first developed a plasma-based methylated DNA panel for all stages of CRC (Study 1). We then validated this panel in a subsequent study with independent samples (Study 2).

Methods: Differentially methylated regions (DMRs) were initially selected by analyzing tissue data from The Cancer Genome Atlas (TCGA) database. In Study 1, candidate regions were evaluated in plasma samples of 215 patients (93 CRC, 122 controls including 31 with non-advanced adenoma) using methylation-sensitive restriction enzyme qPCR (MSRE-qPCR). This training set was used for marker evaluation and construction of a prediction model. The most promising methylation markers were selected by a support vector machine (SVM)-based machine learning classifier using a random forest algorithm. In Study 2, the selected markers were validated in an independent validation set of 724 samples collected in Spain, Ukraine, the UK, and the US (152 CRC, 622 controls including 148 with non-advanced adenoma and 52 with non-CRC cancer).

Results: Tissue data analysis yielded 180 potential DMRs. In Study 1, a panel consisting of the top 12 methylation markers was selected. In Study 2, the prediction model based on this panel correctly classified 117/152 CRC (77%) patients. Sensitivity improved with CRC stage, ranging from 71% (25/35) for stage I, 76% (37/49) for stage II, 77% (37/48) for stage III, to 100% (14/14) for stage IV. Specificity of the model was 88% (544/622). Among non-CRC cancer cases, specificity was 83% overall (73% [19/26] for lung cancer and 92% [24/26] for breast cancer).

Conclusions: We developed a prediction model based on a novel plasma 12-marker methylation panel that demonstrated highly promising test performance characteristics for early-stage CRC detection in a validation study using independent samples. This method could serve as the basis for a highly accurate and minimally invasive blood-based CRC screening test.

Citation Format: Kristi Kruusmaa, Marko Bitenc, Walter Pulverer, Andreas Weinhaeusel, José Luis Rodrigo Agudo, Andrés Barrientos Delgado, Andrés Sánchez Yagüe, José Manuel Rodríguez Laiz, Marko Chersicola, Primož Knap, Silvia Schönthaler, Uri Ladabaum. Development and clinical performance of an accurate cell-free DNA (cfDNA) methylation assay for early detection of colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A05.

EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies

DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/.

Abstract P3-10-07: A 3-gene DNA methylation signature fails to predict response to bevacizumab in metastatic breast cancer patients treated within the TANIA phase III trial

Background: Biomarkers predicting response to bevacizumab containing therapy in metastatic breast cancer (MBC) are of urgent need. In a retrospective single-institution analysis we have previously shown that a 3-gene methylation signature (MLH1,POLKand TMBIM6) could discriminate between responders and non-responders to a bevacizumab-based therapy in two independent cohorts of patients with MBC with an AUC of 0.94 and 0.86, respectively (Gampenrieder SP et al. Theranostics. 2018. 8(8):2278-2288). Here, we present the validation of these findings within the prospective phase III trial TANIA (Vrdoljak E et al. Ann Oncol. 2016. 27(11):2046-52) randomizing 494 patients with HER2-negative MBC to chemotherapy plus bevacizumab or chemotherapy alone for two consecutive treatment lines (second- and third-line). All patients had already received bevacizumab-containing therapy in the first-line setting.

Patients and methods: DNA isolated from archival FFPE tumor samples was available from 200 patients consenting to optional translational research within the TANIA trial. Out of these, 176 samples were collected prior to first-line bevacizumab therapy and were analyzed retrospectively. Sufficient DNA for methylation analysis was available from 124 patients: 64 treated with chemotherapy plus bevacizumab and 60 treated with chemotherapy alone. All samples were isolated from the primary tumor. Quantitative methylation analysis was performed by pyrosequencing on the PyroMark Q24 Advanced System (Qiagen). PFS and OS analyses were performed in both study arms comparing “predicted responders” (PRED_R) versus “predicted non-responders” (PRED_NR) based either on median dichotomization or according to the cutoffs for individual CpG and the combined 3-CpG methylation logistic regression model.

Results:Out of the 124 evaluable patients, 32 (25.8%) were classified as PRED_R and 92 as RED_NR by the 3-gene methylation signature. PRED_R did not have a significantly different second-line PFS (HR 0.95, 95%CI 0.57-1.57; P = 0.84) or OS (HR 0.91, 95%CI 0.51-1.60; P = 0.73) when treated in the bevacizumab-containing study arm compared to PRED_NR. In addition, PRED_R did not show a longer PFS when treated with bevacizumab compared to PRED_R treated with chemotherapy alone (HR 0.95, 95%CI 0.59-1.54; P = 0.83). Furthermore, there was no difference in third-line PFS and the combination of second- and third-line PFS between PRED_R and PRED-NR in the bevacizumab arm. In the control arm, PRED_NR showed a statistically significant shorter PFS compared to PRED_R (HR 0.50, 95%CI 0.22-0.77; P = 0.006), but not OS (HR 0.95, 95%CI 0.51-1.77; P = 0.86).

Conclusion: Our 3-gene methylation signature was not confirmed as predictive biomarker for bevacizumab efficacy in metastatic breast cancer.

(This research project was partially supported by ROCHE Austria GmbH)

Citation Format: Gampenrieder SP, Angela R, Rinnerthaler G, Hackl H, Steiner M, Pulverer W, Weinhaeusel A, Klinglmayr E, Karl T, Ilic S, Hufnagl C, Hauser-Kronberger C, Egle A, Greil R. A 3-gene DNA methylation signature fails to predict response to bevacizumab in metastatic breast cancer patients treated within the TANIA phase III trial [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-07.

Acute Exercise Increases the Expression of KIR2DS4 by Promoter Demethylation in NK Cells

Positive effects of exercise on cancer prevention and progression have been proposed to be mediated by stimulating natural killer (NK) cells. Because NK cell receptors are regulated by epigenetic modifications, we investigated whether acute aerobic exercise and training change promoter DNA methylation and gene expression of the activating KIR2DS4 and the inhibiting KIR3DL1 gene. Sixteen healthy women (50-60 years) performed a graded exercise test (GXT) and were randomized into either a passive control group or an intervention group performing a four-week endurance exercise intervention. Blood samples (pre-, post-GXT and post-training) were used for isolation of DNA/RNA of NK cells to assess DNA promoter methylation by targeted deep-amplicon sequencing and gene expression by qRT-PCR. Potential changes in NK cell subsets were determined by flow cytometry. Acute and chronic exercise did not provoke significant alterations of NK cell proportions. Promoter methylation decreased and gene expression increased for KIR2DS4 after acute exercise. A high gene expression correlated with a low methylation of CpGs that were altered by acute exercise. Chronic exercise resulted in a minor decrease of DNA methylation and did not alter gene expression. Acute exercise provokes epigenetic modifications, affecting the balance between the activating KIR2DS4 and the inhibiting KIR3DL1, with potential benefits on NK cell function.

DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer

Background: Biomarkers predicting response to bevacizumab in breast cancer are still missing. Since epigenetic modifications can contribute to an aberrant regulation of angiogenesis and treatment resistance, we investigated the influence of DNA methylation patterns on bevacizumab efficacy. Methods: Genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in archival FFPE specimens of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (learning set). Based on objective response and progression-free survival (PFS) and considering ER expression, patients were divided in responders (R) and non-responders (NR). Significantly differentially methylated gene loci (CpGs) with a strong change in methylation levels (Δβ>0.15 or Δβ<-0.15) between R and NR were identified and further investigated in 80 bevacizumab-treated breast cancer patients (optimization set) and in 15 patients treated with chemotherapy alone (control set) using targeted deep amplicon bisulfite sequencing. Methylated gene loci were considered predictive if there was a significant association with outcome (PFS) in the optimization set but not in the control set using Spearman rank correlation, Cox regression, and logrank test. Results: Differentially methylated loci in 48 genes were identified, allowing a good separation between R and NR (odds ratio (OR) 101, p<0.0001). Methylation of at least one cytosine in 26 gene-regions was significantly associated with progression-free survival (PFS) in the optimization set, but not in the control set. Using information from the optimization set, the panel was reduced to a 9-gene signature, which could divide patients from the learning set into 2 clusters, thereby predicting response with an OR of 40 (p<0.001) and an AUC of 0.91 (LOOCV). A further restricted 3-gene methylation model showed a significant association of predicted responders with longer PFS in the learning and optimization set even in multivariate analysis with an excellent and good separation of R and NR with AUC=0.94 and AUC=0.86, respectively. Conclusion: Both a 9-gene and 3-gene methylation signature can discriminate between R and NR to a bevacizumab-based therapy in MBC and could help identify patients deriving greater benefit from bevacizumab.

Insights into the Pathogenesis of Anaplastic Large-Cell Lymphoma through Genome-wide DNA Methylation Profiling

Aberrant DNA methylation patterns in malignant cells allow insight into tumor evolution and development and can be used for disease classification. Here, we describe the genome-wide DNA methylation signatures of NPM-ALK-positive (ALK+) and NPM-ALK-negative (ALK−) anaplastic large-cell lymphoma (ALCL). We find that ALK+ and ALK− ALCL share common DNA methylation changes for genes involved in T cell differentiation and immune response, including TCR and CTLA-4, without an ALK-specific impact on tumor DNA methylation in gene promoters. Furthermore, we uncover a close relationship between global ALCL DNA methylation patterns and those in distinct thymic developmental stages and observe tumor-specific DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs such as AP1. Our results indicate similarity between ALCL tumor cells and thymic T cell subsets and a direct relationship between ALCL oncogenic signaling and DNA methylation through transcription factor induction and occupancy.

Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients

BACKGROUND

Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance. If the tissue showing pre-neoplastic lesions is not removed by surgery, it may develop into invasive carcinoma.

METHODS

We investigated the prevalence of gene-specific and global DNA methylation changes in tumor-adjacent and tumor-distant tissues in comparison to tumor tissues from the same breast cancer patients (n = 18) and normal breast tissues from healthy women (n = 4). Methylation-sensitive high resolution melting (MS-HRM) analysis was applied to determine methylation levels in the promoters of APC, BRCA1, CDKN2A (p16), ESR1, HER2/neu and PTEN, in CDKN2A exon 2 and in LINE-1, as indicator for the global DNA methylation extent. The methylation status of the ESR2 promoter was determined by pyrosequencing.

RESULTS

Tumor-adjacent and tumor-distant tissues frequently showed pre-neoplastic gene-specific and global DNA methylation changes. The APC promoter (p = 0.003) and exon 2 of CDKN2A (p < 0.001) were significantly higher methylated in tumors than in normal breast tissues from healthy women. For both regions, significant differences were also found between tumor and tumor-adjacent tissues (p = 0.001 and p < 0.001, respectively) and tumor and tumor-distant tissues (p = 0.001 and p < 0.001, respectively) from breast cancer patients. In addition, tumor-adjacent (p = 0.002) and tumor-distant tissues (p = 0.005) showed significantly higher methylation levels of CDKN2A exon 2 than normal breast tissues serving as control. Significant correlations were found between the proliferative activity and the methylation status of CDKN2A exon 2 in tumor (r = -0.485, p = 0.041) and tumor-distant tissues (r = -0.498, p = 0.036).

CONCLUSIONS

From our results we can conclude that methylation changes in CDKN2A exon 2 are associated with breast carcinogenesis. Further investigations are, however, necessary to confirm that hypermethylation of CDKN2A exon 2 is associated with tumor proliferative activity.

Abstract P6-07-10: DNA methylation signature predicting bevacizumab efficacy in metastatic breast cancer

Background: Biomarkers predicting response to bevacizumab containing therapy in breast cancer are still missing. Since epigenetic modifications can contribute to an aberrant regulation of angiogenesis and to treatment resistance, we investigated the influence of DNA methylation on bevacizumab efficacy.

Patients and methods: A genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in archival FFPE specimen of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (learning set). Based on objective response and progression-free survival (PFS) and considering ER expression, patients were divided in responders (R) and non-responders (NR). Differentially methylated gene loci (methylation variable position = MVP) and differentially methylated regions (DMR) between R and NR were identified. Only significant sites with a strong change in methylation levels (Δβ&gt;0.15 or Δβ&lt;-0.15), an area under the curve of at least 0.85 by logistic regression analysis, and/or sites in proximity to genes functionally involved in angiogenesis and carcinogenesis were selected and further validated. Validation was performed in 81 bevacizumab treated breast cancer patients (validation set) and in 15 patients treated with chemotherapy only (control set) using targeted bisulfite sequencing. Methylated gene loci were considered predictive if there was a significant association with outcome (PFS) in the validation set but not in the control set using Spearman rank correlation, Cox regression, and logrank test.

Results: In the learning set 435 MVPs (p&lt;0.001) and 144 DMRs (adjusted combined p&lt;0.0001 with at least 3 significant MVPs p&lt;0.05 in the same region) showed significantly different methylation between R and NR. In R 152 sites were hypermethylated with a median change of methylation (Δβ) of 0.13; 283 sites were hypomethylated with a median Δβ of -0.09. A methylation signature of 48 genes was specified allowing a good separation between responders and non-responders (odds ratio=101, p&lt;0.0001; data presented at the 38th SABCS 2015, P3-07-43). At least one methylated cytosine in close proximity to 24 of these genes showed a significant association with PFS in the validation set but was not (or in the other direction) in the control set. Based on these data the methylation signature predicting long lasting response to bevacizumab could be reduced to 24 genes including several genes involved in angiogenesis and carcinogenesis, respectively (FLT1 also known as VEGFR-1, MLH1, GNAS, APC, DKK3, WNT2B and COL4A1).

Conclusion: A 24-gene methylation signature can reproducible discriminate between responders and non-responders to a bevacizumab-based therapy in breast cancer and could help to identify patients deriving greater benefit from anti-VEGF agents.

Citation Format: Gampenrieder SP, Rinnerthaler G, Pulverer W, Weinhäusel A, Hufnagl C, Hackl H, Hauser-Kronberger C, Mlineritsch B, Greil R. DNA methylation signature predicting bevacizumab efficacy in metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-07-10.

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

Background

Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful.

Results

We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format.

Conclusions

MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic strands to increase the success rate. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 66 BSP primer pairs, 63 were successfully validated without any further optimization step and using the same qPCR conditions. The MSP-HTPrimer pipeline is freely available from http://sourceforge.net/p/msp-htprimer.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-016-0269-3) contains supplementary material, which is available to authorized users.

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely available under a GNU General Public License version 3.0 (GPLv3) at https://github.com/tadkeys/tabsat/ and http://demo.platomics.com/.

MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples

AIM

Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples.

MATERIALS & METHODS

Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H.

RESULTS

MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data.

CONCLUSION

MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.

EPMA-World Congress 2015

A1 Predictive and prognostic biomarker panel for targeted application of radioembolisation improving individual outcomes in hepatocellular carcinoma

Jella-Andrea Abraham, Olga Golubnitschaja

A2 Integrated market access approach amplifying value of “Rx-CDx”

Ildar Akhmetov

A3 Disaster response: an opportunity to improve global healthcare

Russell J. Andrews, Leonidas Quintana

A4 USA PPPM: proscriptive, profligate, profiteering medicine-good for 1 % wealthy, not for 99 % unhealthy

Russell J. Andrews

A5 The role of IDO in a murine model of gingivitis: predictive and therapeutic potentials

Babak Baban, Jun Yao Liu, Xu Qin, Tailing Wang, Mahmood S. Mozaffari

A6 Specific diets for personalised treatment of diabetes type 2

Viktoriia V. Bati, Tamara V. Meleshko, Olga B. Levchuk, Nadiya V. Boyko

A7 Towards personalized physiotherapeutic approach

Joanna Bauer, Ewa Boerner, Halina Podbielska

A8 Cells, animal, SHIME and in silico models for detection and verification of specific biomarkers of non-communicable chronic diseases

Alojz Bomba, Viktor O. Petrov, Volodymyr G. Drobnych, Rostyslav V. Bubnov, Oksana M. Bykova, Nadiya V. Boyko

A9 INTERACT-chronic care model: Self-treatment by patients with decision support e-Health solution

Hans-Peter Brunner-La Rocca, Lutz Fleischhacker, Olga Golubnitschaja, Frank Heemskerk, Thomas Helms, Tiny Jaarsma, Judita Kinkorova, Jan Ramaekers, Peter Ruff, Ivana Schnur, Emilio Vanoli, Jose Verdu

A10 PPPM in cardiovascular medicine in 2015

Hans-Peter Brunner-La Rocca

A11 Magnetic resonance imaging of nanoparticles in mice, potential for theranostic and contrast media development – pilot results

Rostyslav V. Bubnov, Sergiy A. Grabovetskyi, Olena M. Mykhalchenko, Natalia O. Tymoshok, Oleksandr B. Shcherbakov, Igor P. Semeniv, Mykola Y. Spivak

A12 Ultrasound diagnosis for diabetic neuropathy - comparative study

Rostyslav V. Bubnov, Tetyana V. Ostapenko

A13 Ultrasound for stratification patients with diabetic foot ulcers for prevention and personalized treatment - pilot results

Rostyslav V. Bubnov, Nazarii M. Kobyliak, Nadiya M. Zholobak, Mykola Ya. Spivak

A14 Project ImaGenX – designing and executing a questionnaire on environment and lifestyle risk of breast cancer

John Paul Cauchi

A15 Genomics – a new structural brand of predictive, preventive and personalized medicine or the new driver as well?

Dmitrii Cherepakhin, Marina Bakay, Artem Borovikov, Sergey Suchkov

A16 Survey of questionnaires for evaluation of the quality of life in various medical fields

Barbara Cieślik, Agnieszka Migasiewicz, Maria-Luiza Podbielska, Markus Pelleter, Agnieszka Giemza, Halina Podbielska

A17 Personalized molecular treatment for muscular dystrophies

Sebahattin Cirak

A18 Secondary mutations in circulating tumour DNA for acquired drug resistance in patients with advanced ALK + NSCLC

Marzia Del Re, Paola Bordi, Valentina Citi, Marta Palombi, Carmine Pinto, Marcello Tiseo, Romano Danesi

A19 Recombinant species-specific FcεRI alpha proteins for diagnosis of IgE-mediated allergies in dogs, cats and horses

Lukas Einhorn, Judit Fazekas, Martina Muhr, Alexandra Schoos, Lucia Panakova, Ina Herrmann, Krisztina Manzano-Szalai, Kumiko Oida, Edda Fiebiger, Josef Singer, Erika Jensen-Jarolim

A20 Global methodology for developmental neurotoxicity testing in humans and animals early and chronically exposed to chemical contaminants

Arpiné A. Elnar, Nadia Ouamara, Nadiya Boyko, Xavier Coumoul, Jean-Philippe Antignac, Bruno Le Bizec, Gauthier Eppe, Jenny Renaut, Torsten Bonn, Cédric Guignard, Margherita Ferrante, Maria Liusa Chiusano, Salvatore Cuzzocrea, Gerard O'Keeffe, John Cryan, Michelle Bisson, Amina Barakat, Ihsane Hmamouchi, Nasser Zawia, Anumantha Kanthasamy, Glen E. Kisby, Rui Alves, Oscar Villacañas Pérez, Kim Burgard, Peter Spencer, Norbert Bomba, Martin Haranta, Nina Zaitseva, Irina May, Stéphanie Grojean, Mathilde Body-Malapel, Florencia Harari, Raul Harari, Kristina Yeghiazaryan, Olga Golubnitschaja, Vittorio Calabrese, Christophe Nemos, Rachid Soulimani

A21 Mental indicators at young people with attributes hypertension and pre-hypertension

Maria E. Evsevyeva, Elena A. Mishenko, Zurida V. Kumukova, Evgeniy V. Chudnovsky, Tatyana A. Smirnova

A22 On the approaches to the early diagnosis of stress-induced hypertension in young employees of State law enforcement agencies

Maria E. Evsevyeva, Ludmila V. Ivanova, Michail V. Eremin, Maria V. Rostovtseva

A23 Сentral aortic pressure and indexes of augmentation in young persons in view of risk factors

Maria E. Evsevyeva, Michail V. Eremin, Vladimir I. Koshel, Oksana V. Sergeeva, Nadesgda M. Konovalova

A24 Breast cancer prediction and prevention: Are reliable biomarkers in horizon?

Shantanu Girotra, Olga Golubnitschaja

A25 Flammer Syndrome and potential formation of pre-metastatic niches: A multi-centred study on phenotyping, patient stratification, prediction and potential prevention of aggressive breast cancer and metastatic disease

Olga Golubnitschaja, Manuel Debald, Walther Kuhn, Kristina Yeghiazaryan, Rostyslav V. Bubnov, Vadym M. Goncharenko, Ulyana Lushchyk, Godfrey Grech, Katarzyna Konieczka

A26 Innovative tools for prenatal diagnostics and monitoring: improving individual pregnancy outcomes and health-economy in EU

Olga Golubnitschaja, Jan Jaap Erwich, Vincenzo Costigliola, Kristina Yeghiazaryan, Ulrich Gembruch

A27 Immunohistochemical assessment of APUD cells in endometriosis

Vadym M. Goncharenko, Vasyl O. Beniuk, Olga V. Kalenska, Rostyslav V. Bubnov

A28 Updating personalized management algorithm of endometrial hyperplasia in pre-menopause women

Vadym M. Goncharenko, Vasyl O. Beniuk, Rostyslav V. Bubnov, Olga Melnychuk

A29 The personified treatment approach of polimorbid patients with periodontal inflammatory diseases

Irina A. Gorbacheva, Lyudmila Y. Orekhova, Vadim V. Tachalov

A30 Ukrainian experience in hybrid war – the challenge to update algorithms for personalized care and early prevention of different military injuries

Olena I. Grechanyk, Rizvan Ya. Abdullaiev, Rostyslav V. Bubnov

A31 Tear fluid biomarkers: a comparison of tear fluid sampling and storage protocols

Suzanne Hagan, Eilidh Martin, Ian Pearce, Katherine Oliver

A32 The correlation of dietary habits with gingival problems during menstruation

Cenk Haytac, Fariz Salimov, Servin Yoksul, Anatoly A. Kunin, Natalia S. Moiseeva

A33 Genomic medicine in a contemporary Spanish population of prostate cancer: our experience

Bernardo Herrera-Imbroda, Sergio del Río-González, Maria Fernanda Lara, Antonia Angulo, Francisco Javier Machuca Santa-Cruz

A34 Challenges, opportunities and collaborations for personalized medicine applicability in uro-oncological disease

Bernardo Herrera-Imbroda, Sergio del Río-González, Maria Fernanda Lara

A35 Metabolic hallmarks of cancer as targets for a personalized therapy

John Ionescu

A36 Influence of genetic polymorphism as a predictor of the development of periodontal disease in patients with gastric ulcer and 12 duodenal ulcer

Alfiya Z. Isamulaeva, Anatoly A. Kunin, Shamil Sh. Magomedov, Aida I. Isamulaeva

A37 Challenges in diabetic macular edema

Tatjana Josifova

A38 Overview of the EPMA strategies in laboratory medicine relevant for PPPM

Marko Kapalla, Juraj Kubáň, Olga Golubnitschaja, Vincenzo Costigliola

A39 EPMA initiative for effective organization of medical travel: European concepts and criteria

Vincenzo Costigliola, Marko Kapalla, Juraj Kubáň, Olga Golubnitschaja

A40 Design and innovation in e-textiles: implications for PPPM

Anthony Kent, Tom Fisher, Tilak Dias

A41 Biobank in Pilsen as a member of national node BBMRI_CZ

Judita Kinkorová, Ondřej Topolčan

A42 Big data in personalized medicine: hype and hope

Matthias Kohl

A43 The 3P approach as the platform of the European Dentistry Department (DPPPD)

Anatoly A. Kunin, Natalia S. Moiseeva

A44 The endometrium cytokine patterns for predictive diagnosis of proliferation severity and cancer prevention

Andrii I. Kurchenko, Vasyl A. Beniuk, Vadym M. Goncharenko, Rostyslav V. Bubnov, Nadiya V. Boyko, Andriy M. Strokan

A45 A monocyte-based in-vitro system for testing individual responses to the implanted material: future for personalized implant construction

Julia Kzhyshkowska, Alexandru Gudima, Ksenia S. Stankevich, Victor D. Filimonov⁴, Harald Klüter, Evgeniya M. Mamontova, Sergei I. Tverdokhlebov

A46 Prediction and prevention of adverse health effects by meteorological factors: Biomarker patterns and creation of a device for self-monitoring and integrated care

Ulyana B. Lushchyk, Viktor V. Novytskyy, Igor P. Babii, Nadiya G. Lushchyk, Lyudmyla S. Riabets, Ivanna I. Legka

A47 Targeting "disease signatures" towards personalized healthcare

Mira Marcus-Kalish, Alexis Mitelpunkt, Tal Galili, Neta Shachar, Yoav Benjamini

A48 Influence of the skin imperfection on the personal quality of life and possible tools for objective diagnosis

Agnieszka Migasiewicz, Markus Pelleter, Joanna Bauer, Ewelina Dereń, Halina Podbielska

A49 The new direction in caries prevention based on the ultrastructure of dental hard tissues and filling materials

Natalia S. Moiseeva, Anatoly A. Kunin, Dmitry A. Kunin

A50 The use of LED radiation in prevention of dental diseases

Natalia S. Moiseeva, Yury A. Ippolitov, Dmitry A. Kunin, Alexei N. Morozov, Natalia V. Chirkova, Nakhid T. Aliev

A51 Status of endothelial progenitor cells in diabetic nephropathy: predictive and preventive potentials

Mahmood S. Mozaffari, Jun Yao Liu, Babak Baban

A52 The status of glucocorticoid-induced leucine zipper protein in salivary gland in Sjögren’s syndrome: predictive and personalized treatment potentials

Mahmood S. Mozaffari, Jun Yao Liu, Rafik Abdelsayed, Xing-Ming Shi, Babak Baban

A53 Maximal aerobic capacity - important quality marker of health

Jaroslav Novák, Milan Štork, Václav Zeman

A54 The EMPOWER project: laboratory medicine and Horizon 2020

Wytze P. Oosterhuis, Elvar Theodorsson

A55 Personality profile manifestations in patient’s attitude to oral care and adherence to doctor’s prescriptions

Lyudmila Y. Orekhova, Tatyana V. Kudryavtseva, Elena R. Isaeva, Vadim V. Tachalov, Ekaterina S. Loboda

A56 Results of an European survey on personalized medicine addressed to directions of laboratory medicine

Mario Pazzagli, Francesca Malentacchi, Irene Mancini, Ivan Brandslund, Pieter Vermeersch, Matthias Schwab, Janja Marc, Ron H.N. van Schaik, Gerard Siest, Elvar Theodorsson, Chiara Di Resta

A57 MCI or early dementia predictive speech based diagnosis techniques

Matus Pleva, Jozef Juhar

A58 Personalized speech based mobile application for eHealth

Matus Pleva, Jozef Juhar

A59 Circulating tumor cell-free DNA as the biomarker in the management of cancer patients

Jiří Polívka jr., Filip Janků, Martin Pešta, Jan Doležal, Milena Králíčková, Jiří Polívka

A60 Complex stroke care – educational programme in Stroke Centre University Hospital Plzen

Jiří Polívka, Alena Lukešová, Nina Müllerová, Petr Ševčík, Vladimír Rohan

A61 Sleep apnea and sleep fragmentation contribute to brain aging

Kneginja Richter, Lence Miloseva, Günter Niklewski

A62 Personalised approach for sleep disturbances in shift workers

Kneginja Richter, Jens Acker, Guenter Niklewski

A63 Medical travel and innovative PPPM clusters: new concept of integration

Olga Safonicheva, Vincenzo Costigliola

A64 Medical travel and women health

Olga Safonicheva

A65 Continuity of generations in the training of specialists in the field of reconstructive microsurgery

Maxim Sautin, Janna Sinelnikova, Sergey Suchkov

A66 Telemonitoring of stroke patients – empirical evidence of individual risk management results from an observational study in Germany

Songül Secer, Stephan von Bandemer

A67 Women’s increasing breast cancer risk with n-6 fatty acid intake explained by estrogen-fatty acid interactive effect on DNA damage: implications for gender-specific nutrition within personalized medicine

Niva Shapira

A68 Cytobacterioscopy of the gingival crevicular fluid as a method for preventive diagnosis of periodontal diseases

Aleksandr Shcherbakov, Anatoly A. Kunin, Natalia S. Moiseeva

A69 Use of specially treated composites in dentistry to avoid violations of aesthetics

Bogdan R. Shumilovich, Zhanna Lipkind, Yulia Vorobieva, Dmitry A. Kunin, Anastasiia V. Sudareva

A70 National eHealth system – platform for preventive, predictive and personalized diabetes care

Ivica Smokovski, Tatjana Milenkovic

A72 The common energy levels of Prof. Szent-Györgyi, the intrinsic chemistry of melanin, and the muscle physiopathology. Implications in the context of Preventive, Predictive, and Personalized Medicine

Arturo Solís-Herrera, María del Carmen Arias-Esparza, Sergey Suchkov

A73 Plurality and individuality of hepatocellular carcinoma: PPPM perspectives

Krishna Chander Sridhar, Olga Golubnitschaja

A74 Strategic aspects of higher medical education reforms to secure newer educational platforms for getting biopharma professionals matures

Maria Studneva, Sihong Song, James Creeden, Мark Мandrik, Sergey Suchkov

A75 Overview of the strategies and activities of the European Federation of Clinical Chemistry and Laboratory Medicine, (EFLM)

Elvar Theodorsson, EFLM

A76 New spectroscopic techniques for point of care label free diagnostics

Syed A. M. Tofail

A77 Tumor markers for personalized medicine and oncology - the role of Laboratory Medicine

Ondřej Topolčan, Judita Kinkorová, Ondřej Fiala, Marie Karlíková, Šárka Svobodová, Radek Kučera, Radka Fuchsová, Vladislav Třeška, Václav Šimánek, Ladislav Pecen, Jan Šoupal, Štěpán Svačina²

A78 Modern medical terminology (MMT) as a driver of the global educational reforms

Evgeniya Tretyak, Maria Studneva, Sergey Suchkov

A79 Juvenile hypertension; the relevance of novel predictive, preventive and personalized assessment of its determinants

Francesca M. Trovato, G. Fabio Martines, Daniela Brischetto, Daniela Catalano, Giuseppe Musumeci, Guglielmo M. Trovato

A80 Proteomarkers Biotech

George Th. Tsangaris, Athanasios K. Anagnostopoulos

A81 Proteomics and mass spectrometry based non-invasive prenatal testing of fetal health and pregnancy complications

George Th. Tsangaris, Athanasios K. Anagnostopoulos

A82 Integrated Ecosystem for an Integrated Care model for Heart Failure (HF) patients including related comorbidities (ZENITH)

José Verdú, German Gutiérrez, Jordi Rovira, Marta Martinez, Lutz Fleischhacker, Donna Green, Arthur Garson, Elena Tamburini, Stefano Cuomo, Juan Martinez-Leon, Teresa Abrisqueta, Hans-Peter Brunner-La Rocca, Tiny Jaarsma, Teresa Arredondo, Cecilia Vera, Giuseppe Fico, Olga Golubnitschaja, Fernando Arribas, Martina Onderco, Isabel Vara, on behalf of ZENITH consortium

A83 Predictive, preventive and personalized medicine in diabetes onset and complication (MOSAIC project)

José Verdú, Francesco Sambo, Barbara Di Camillo, Claudio Cobelli, Andrea Facchinetti, Giuseppe Fico, Riccardo Bellazzi, Lucia Sacchi, Arianna Dagliati, Daniele Segnani, Valentina Tibollo, Manuel Ottaviano, Rafael Gabriel, Leif Groop, Jacqueline Postma, Antonio Martinez, Liisa Hakaste, Tiinamaija Tuomi, Konstantia Zarkogianni, on behalf of MOSAIC consortium

A84 Possibilities for personalized therapy of diabetes using in vitro screening of insulin and oral hypoglycemic agents

Igor Volchek, Nina Pototskaya, Andrey Petrov

A85 The innovative technology for personalized therapy of human diseases based on in vitro drug screening

Igor Volchek, Nadezhda Pototskaya, Andrey Petrov

A86 Bone destruction and temporomandibular joint: predictive markers, pathogenetic aspects and quality of life

Ülle Voog-Oras, Oksana Jagur, Edvitar Leibur, Priit Niibo, Triin Jagomägi, Minh Son Nguyen, Chris Pruunsild, Dagmar Piikov, Mare Saag

A87 Sub-optimal health management – global vision for concepts in medical travel

Wei Wang

A88 Sub-optimal health management: synergic PPPM-TCAM approach

Wei Wang

A89 Innovative technologies for minimal invasive diagnostics

Andreas Weinhäusel, Walter Pulverer, Matthias Wielscher, Manuela Hofner, Christa Noehammer, Regina Soldo, Peter Hettegger, Istvan Gyurjan, Ronald Kulovics, Silvia Schönthaler, Gabriel Beikircher, Albert Kriegner, Stephan Pabinger, Klemens Vierlinger

A90 Rare disease diobanks for personalized medicine

Ayşe Yüzbaşıoğlu, Meral Özgüç, Member of EuroBioBank - European Network of DNA, Cell and Tissue Banks for Rare Diseases

MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research

Background

Methylation-sensitive restriction enzymes—polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discovery studies provide many candidate regions for which the MSREqPCR approach can be very effective to confirm the findings. MSREqPCR provides high multiplexing capabilities also when starting with limited amount of DNA-like cfDNA to validate many targets in a time- and cost-effective manner. Multiplex design is challenging and cumbersome to define specific primers in an effective manner, and no suitable software tools are freely available for high-throughput primer design in a time-effective manner and to automatically annotate the resulting primers with known SNPs, CpG, repeats, and RefSeq genes. Therefore a robust, powerful, high-throughput, optimized, and methylation-specific primer design tool with great accuracy will be very useful.

Results

We have developed a novel pipeline, called MSRE-HTPrimer, to design MSRE-PCR and genomic PCR primers pairs in a very efficient manner and with high success rate. First, our pipeline designs all possible PCR primer pairs and oligos, followed by filtering for SNPs loci and repeat regions. Next, each primer pair is annotated with the number of cut sites in primers and amplicons, upstream and downstream genes, and CpG islands loci. Finally, MSRE-HTPrimer selects resulting primer pairs for all target sequences based on a custom quality matrix defined by the user. MSRE-HTPrimer produces a table for all resulting primer pairs as well as a custom track in GTF file format for each target sequence to visualize it in UCSC genome browser.

Conclusions

MSRE-HTPrimer, based on Primer3, is a high-throughput pipeline and has no limitation on the number and size of target sequences for primer design and provides full flexibility to customize it for specific requirements. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 190 primer pairs, 71 % could be successfully validated. The MSRE-HTPrimer software is freely available from http://sourceforge.net/p/msrehtprimer/wiki/Virtual_Machine/ as a virtual machine.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-016-0190-9) contains supplementary material, which is available to authorized users.

Abstract P3-07-43: DNA methylation patterns correlating with outcome in patients treated with first-line bevacizumab for metastatic breast cancer

Background: Biomarkers predicting response to bevacizumab containing therapy in breast cancer are of urgent need for a personalized treatment approach. DNA methylation is involved in regulation of angiogenesis and development of treatment resistance and could therefore provide predictive information for bevacizumab efficacy.

Patients and methods: A genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in FFPE specimen of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (discovery set). Twenty-eight (78%) samples came from primary tumor and 8 (22%) from metastasis (2 lung mets., 1 pleural met., 1 liver met., 2 soft tissue mets., 1 ovarial met, 1 bone marrow infiltration). Based on progression-free survival (PFS) and breast cancer subtype (ER+ vs. triple-negative) patients were divided in responder (R) and non-responder (NR). By biostatistical methods differences in the methylation pattern between R and NR were detected. The 48 most interesting genes (e.g. because of there involvement in angiogenesis or carcinogenesis) showing a differential methylation status between R and NR are currently validated in two further metastatic breast cancer cohorts treated with (main set) and without bevacizumab (validation set), respectively. These validated results will be presented at the meeting.

Citation Format: Gampenrieder SP, Rinnerthaler G, Weinhäusel A, Pulverer W, Hugnagl C, Hackl H, Romeder F, Monzo Fuentes C, Hauser-Kronberger C, Mlineritsch B, Greil R. DNA methylation patterns correlating with outcome in patients treated with first-line bevacizumab for metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-43.

Strategies for validation and testing of DNA methylation biomarkers

DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.

Cytosine 5-Hydroxymethylation of the LZTS1 Gene Is Reduced in Breast Cancer

Change of DNA cytosine methylation (5mC) is an early event in the development of cancer, and the recent discovery of a 5-hydroxymethylated form (5hmC) of cytosine suggests a regulatory epigenetic role that might be different from 5-methylcytosine. Here, we aimed at elucidating the role of 5hmC in breast cancer. To interrogate the 5hmC levels of the leucine zipper, putative tumor suppressor 1 (LZTS1) gene in detail, we analyzed 75 primary breast cancer tissue samples from initial diagnosis and 12 normal breast tissue samples derived from healthy persons. Samples were subjected to 5hmC glucosyltransferase treatment followed by restriction digestion and segment-specific amplification of 11 polymerase chain reaction products. Nine of the 11 5'LZTS1 fragments showed significantly lower (fold change of 1.61-6.01, P < .05) 5hmC content in primary breast cancer tissue compared to normal breast tissue samples. No significant differences were observed for 5mC DNA methylation. Furthermore, both LZTS1 and TET1 mRNA expressions were significantly reduced in tumor samples (n = 75, P < .001, Student's t test), which correlated significantly with 5hmC levels in samples. 5hmC levels in breast cancer tissues were associated with unfavorable histopathologic parameters such as lymph node involvement (P < .05, Student's t test). A decrease of 5hmC levels of LZTS1, a classic tumor suppressor gene known to influence metastasis in breast cancer progression, is correlated to down-regulation of LZTS1 mRNA expression in breast cancer and might epigenetically enhance carcinogenesis. The study provides support for the novel hypothesis that suggests a strong influence of 5hmC on mRNA expression. Finally, one may also consider 5hmC as a new biomarker.

Validation and comparison of a sandwich ELISA, two competitive ELISAs and a real-time PCR method for the detection of lupine in food

Methods applied in food allergen analysis should be specific, sensitive and applicable to both raw and highly processed foods. The performance of the most commonly used methods, ELISA and real-time PCR, may, however, be influenced by food processing steps, e.g., heat treatment. The present study compares the applicability of four in-house developed methods, one sandwich ELISA, two competitive ELISAs and a real-time PCR method, for the detection of lupine in four different food matrices, comprising bread, biscuits, rice patties and noodles. In order to investigate the influence of food processing on the detectability, not only the heat treated model foods but also the corresponding doughs were analysed. The sandwich ELISA proved to be the most sensitive method. The LOD was found to be 10 ppm lupine, independent from the food matrix and independent if the dough or the heat treated food was analysed. In addition, the methods were applied to the analysis of commercial foodstuffs differing in their labelling.

The stem cell signature of CHH/CHG methylation is not present in 271 cancer associated 5'UTR gene regions

Non-CpG methylation is frequently present in stem cell DNA. We investigated the value of this epigenetic modification in cancerous DNA in order to establish the implications of CHH/CHG methylation for biomarker development. Therefore we used the restriction enzymes BstNI and PspGI within a combined multiplex PCR and targeted microarray approach for the elucidation of non-CpG (CCWGG) methylation. Targeting 544 CCWGG sites in 271 5' gene regions, the CHH/CHG methylation status of the MCF7 breast cancer cell line and blood from healthy volunteers and childhood ALL was analyzed. Statistical analysis of microarray data and subsequent SYBR green based qPCR on DNA digests was applied to confirm the results from the microarray screen.

RESULT/CONCLUSION

The microarray experiments identified for the MCF7 cell line the genes MSH2 (p < 0.001), EREG (p < 0.001) and HSPA2 (p = 0.029) with CHH/CHG methylation, and in childhood ALL the genes HIST1H2AG (p = 0.003), PGF (p = 0.02), CPEB4 (p = 0.039) and TJP2 (p = 0.04). Validation using qPCR upon restriction digestion did not confirm the presence of CHH/CHG methylation in MCF7 DNA. In ALL samples only TJP2 was found harboring CHH/CHG methylation (p = 0.02). However, applying Bonferroni-correction for multiple testing that qPCR-result was not rated as statistically significant anymore. We concluded that non-CpG methylation in 544 CCWGG sites analyzed did not change in tumor cells. Thus any change of the CHH/CHG methylation pattern is a minor event in tumorigenesis, even if the stem cell markers OCT4, NANOG, STELLAR and GDF3 are expressed like in the MCF7 breast cancer cell line.

DNA methylation testing and marker validation using PCR: diagnostic applications

DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.

Methyl-binding domain protein-based DNA isolation from human blood serum combines DNA analyses and serum-autoantibody testing

Background

Circulating cell free DNA in serum as well as serum-autoantibodies and the serum proteome have great potential to contribute to early cancer diagnostics via non invasive blood tests. However, most DNA preparation protocols destroy the protein fraction and therefore do not allow subsequent protein analyses. In this study a novel approach based on methyl binding domain protein (MBD) is described to overcome the technical difficulties of combining DNA and protein analysis out of one single serum sample.

Methods

Serum or plasma samples from 98 control individuals and 54 breast cancer patients were evaluated upon silica membrane- or MBD affinity-based DNA isolation via qPCR targeting potential DNA methylation markers as well as by protein-microarrays for tumor-autoantibody testing.

Results

In control individuals, an average DNA level of 22.8 ± 25.7 ng/ml was detected applying the silica membrane based protocol and 8.5 ± 7.5 ng/ml using the MBD-approach, both values strongly dependent on the serum sample preparation methods used. In contrast to malignant and benign tumor serum samples, cell free DNA concentrations were significantly elevated in sera of metastasizing breast cancer patients. Technical evaluation revealed that serum upon MBD-based DNA isolation is suitable for protein-array analyses when data are consistent to untreated serum samples.

Conclusion

MBD affinity purification allows DNA isolations under native conditions retaining the protein function, thus for example enabling combined analyses of DNA methylation and autoantigene-profiles from the same serum sample and thereby improving minimal invasive diagnostics.