Marker Discovery

With the MeD-seq sequencing data from (cell population enriched) laser capture microdissected (LCM) formalin-fixed and paraffin-embedded tissue samples we construct genome-wide DNA methylation profiles for normal and diseased tissue types (Figure 1). 

Comparison of cancer and control methylation profiles by an in house developed bioinformatics pipeline Mimir
facilitates the identification of specific or general Differentially Methylated Regions (DMR) in a genome wide fashion (Figure 2).

Mimir is capable of detecting the following types of DMR’s

  • General, for example regions methylated in all cancer types of the female genital zone
  • Regional, for example methylated in 2 or more cancer types (Cervix and Vulva carcinoma)
  • Specific, for example methylated in one specific cancer type (Cx-AdC or Vul-SCC-) 

Figure 1. female urogenital zone, methylations profiles are generated for both control and cancer tissue samples. 

Figure 2. illustrative representation of IGV captions of the 5 DMR types: Two general markers where all cancers have methylation reads and all controls do not have methylation reads. One regional marker with high methylation for cervix and vulva cancers, low methylation for cervical and vulva controls, all other controls and all other cancers. Two specific regions; one region with only methylation for cervical adenocarcinoma samples and one  region with only methylation for vulva squamous cell carcinoma HPV negative samples.

Assay design and primer and probe selection:

From the DMR regions Methylomics develops specific, regional and general markers. However, not all DMR’s are suitable to create powerful cancer detection markers. To determine whether a DMR is discriminating enough and suitable to create a powerful marker, quality scores, predictive scores and visualizations are applied to select candidate markers for assay development.

Visualization of these selected DMR’s in grouped DNA methylation profiles through an Integrative Genomics Viewer (IGV) facilitates the identification of promising target sequences for the development of quantitative Methylation-Specific PCR (qMSP) assays (Figure 2).

Methylomics develops multiplex assays detecting the methylation status of multiple regions at once. To assess the potential of the newly discovered markers the developed assays are tested on bisulfite-converted DNA of relevant samples.

Publications about our techniques

Can we use a simple blood test to reduce unnecessary adverse effects from radiotherapy by timely identification of radiotherapy-resistant rectal cancers? MeD-Seq rectal study protocol BMC Cancer. 2023 Dec 23, 1187

Hypermethylation of DNA Methylation Markers in Non-Cirrhotic Hepatocellular Carcinoma Cancers (Basel). 2023 Sep 28;15(19):4784

Liquid Biopsies for Colorectal Cancer and Advanced Adenoma Screening and Surveillance: What to Measure? Cancers (Basel). 2023 Sep 17;15(18):4607

Genome-wide analysis toward the epigenetic aetiology of myelodysplastic syndrome disease progression and pharmacoepigenomic basis of hypomethylating agents drug treatment response Hum Genomics. 2023 Apr 25;17(1):37

Methylated Cell-Free DNA Sequencing (MeD-seq) of LpnPI Digested Fragments to Identify Early Progression in Metastatic Renal Cell Carcinoma Patients on Watchful Waiting Cancers (Basel). 2023 Feb 21;15(5):1374

Retrospective analysis of enhancer activity and transcriptome history Nat Biotechnol. 2023 Feb 23

Kidney Organoids Are Capable of Forming Tumors, but Not Teratomas Stem Cells. 2022 Jun 22;40(6):577-591

Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells Stem Cell Reports. 2022 Mar 8;17(3):693-706

Genome-wide aberrant methylation in primary metastatic UM and their matched metastases Sci Rep. 2022 Jan 7;12(1):42

High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments Clin Epigenetics. 2021 Oct 20;13(1):196

CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells Nat Cell Biol. 2021 Aug 23(8):881-893

Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus Clin Epigenetics. 2021 Jul 29;13(1):148

Differentially Methylated Regions in Desmoid-Type Fibromatosis: A Comparison Between CTNNB1 S45F and T41A Tumors Front Oncol. 2020 Oct 29;10:565031

Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation PLoS Pathog. 2020 Jun 24;16(6):e1008555

Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients Stem Cells Transl Med. 2020 Apr 9(4):478-490

MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma PLoS One. 2020 Jan 23;15(1):e0228014

Gestational jet lag predisposes to later-life skeletal and cardiac disease Chronobiol Int. 2019 May 36(5):657-671

Perturbed maintenance of transcriptional repression on the inactive X-chromosome in the mouse brain after Xist deletion Epigenetics Chromatin. 2018 Aug 31;11(1):50

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI Genome Res. 2018 Jan 28(1):88-99

Cancer risk stratification of anal intraepithelial neoplasia in HIV-positive men by validated methylation markers associated with progression to cancer. Clin Infect Dis. 2021 Jun 15;72(12):2154-2163

Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study Int J Cancer. 2021 Jan 15;148(2):396-405

FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study Int J Cancer. 2020 Aug 15;147(4):1215-1221

Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions Cancer Med. 2020 Apr 9(7):2454-2461

Intra- and inter-laboratory agreement of the FAM19A4/mir124-2 methylation test: Results from an international study Clin Lab Anal. 2019 May 33(4):e22854

Host Cell Deoxyribonucleic Acid Methylation Markers for the Detection of High-grade Anal Intraepithelial Neoplasia and Anal Cancer Clin Infect Dis. 2019 Mar 19;68(7):1110-1117

Reliable identification of women with CIN3+ using hrHPV genotyping and methylation markers in a cytology-screened referral population Int J Cancer. 2019 Jan 1;144(1):160-168

CADM1 and MAL methylation status in cervical scrapes is representative of the most severe underlying lesion in women with multiple cervical biopsies Int J Cancer. 2016 Jan 15;138(2):463-71

Defining hrHPV genotypes in cervical intraepithelial neoplasia by laser capture microdissection supports reflex triage of self-samples using HPV16/18 and FAM19A4/miR124-2 methylation Gynecol Oncol. 2018 Nov 151(2):311-318

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