MeD-Seq Technology - Methylomics

MeD-seq is a novel method to detect genome wide DNA methylation.

MeD-seq is a novel method to detect genome wide DNA methylation, making use of a methylation dependent restriction enzyme that recognizes methylated CpG sites (CCG, CGG and GCGC). Digestion takes place 16 base pairs downstream of the recognized CpG sites, leading to the production of small DNA fragments (32 bp) when a CpG site is fully methylated. These fragments are isolated and converted into a sequencing library that can be used on common sequencing platforms at a sequencing depth of around 20-30 million reads per sample. The required DNA input is very low (5-10 ng) when compared to other genome wide methods, because the MeD-seq method does not involve a bisulfite conversion step that impairs the DNA quality. This makes MeD-seq compatible with Laser Capture Microdissection and sample types with low DNA concentrations like liquid biopsies. After sequencing, only reads containing CpG sites are used for data analysis, which leads to a very low level of background “noise”. Despite the small fragment size of the reads, mapping efficiency remains very high. Due to its unbiased approach regarding genomic locations that can be analyzed, MeD-seq manages to detect the DNA methylation status of the vast majority of gene promoters, CpG islands and CpG sites in intergenic regions. MeD-seq has been validated by comparison to whole genome bisulfite sequencing (WGBS), MeDIP-seq and the 450K array technology. In the overview below you can see the comparison of Med-Seq to these other methods, showing major advantages with respect to the low DNA input, high coverage and depth, at considerably low costs. Figure 1 displays the MeD-seq technology pipeline.

Figure 1. MeD-seq overview

Publications about our techniques

Fu S, Deger T, Boers RG, Boers JB, Doukas M, Gribnau J, Wilting SM, Debes JD, Boonstra A

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

DOI: 10.3390/cancers15194784

Eikenboom EL, Wilting SM, Deger T, Srebniak MI, Van Veghel-Plandsoen M, Boers RG, Boers JB, van IJcken WFJ, Gribnau JH, Atmodimedjo P, Dubbink HJ, Martens JWM, Spaander MCW, Wagner A

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

DOI: 10.3390/cancers15184607

Siamoglou S, Boers R, Koromina M, Boers J, Tsironi A, Chatzilygeroudi T, Lazaris V, Verigou E, Kourakli A, van IJcken WFJ, Gribnau J, Symeonidis A, Patrinos GP

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

DOI: 10.1186/s40246-023-00483-7

Bos MK, Verhoeff SR, Oosting SF, Menke-van der Houven van Oordt WC, Boers RG, Boers JB, Gribnau J, Martens JWM, Sleijfer S, van Herpen CML, Wilting SM

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

DOI: 10.3390/cancers15051374

Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J

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

DOI: 10.1038/s41587-023-01683-1

Shankar AS, Du Z, Tejeda Mora H, Boers R, Cao W, van den Bosch TPP, Korevaar SS, Boers J, van IJcken WFJ, Bindels EMJ, Eussen B, de Klein A, Pan Q, Oudijk L, Clahsen-van Groningen MC, Hoorn EJ, Baan CC, Gribnau J, Hoogduijn MJ

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

DOI: 10.1093/stmcls/sxac009

Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J

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

DOI: 10.1016/j.stemcr.2022.01.008

Smit KN, Boers R, Vaarwater J, Boers J, Brands T, Mensink H, Verdijk RM, van IJcken WFJ, Gribnau J, de Klein A, Kilic E

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

DOI: 10.1038/s41598-021-03964-8

Deger T, Boers RG, de Weerd V, Angus L, van der Put MMJ, Boers JB, Azmani Z, van IJcken WFJ, Grünhagen DJ, van Dessel LF, Lolkema MPJK, Verhoef C, Sleijfer S, Martens JWM, Gribnau J, Wilting SM

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

DOI: 10.1186/s13148-021-01177-4

Soochit W, Sleutels F, Stik G, Bartkuhn M, Basu S, Hernandez SC, Merzouk S, Vidal E, Boers R, Boers J, van der Reijden M, Geverts B, van Cappellen WA, van den Hout M, Ozgur Z, van IJcken WFJ, Gribnau J, Renkawitz R, Graf T, Houtsmuller A, Grosveld F, Stadhouders R, Galjart N

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

DOI: 10.1038/s41556-021-00722-w

Slot E, Boers R, Boers J, van IJcken WFJ, Tibboel D, Gribnau J, Rottier R, de Klein A

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

DOI: 10.1186/s13148-021-01134-1

Timbergen MJM, Boers R, Vriends ALM, Boers J, van IJcken WFJ, Lavrijsen M, Grünhagen DJ, Verhoef C, Sleijfer S, Smits R, Gribnau J, Wiemer EAC

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

DOI: 10.3389/fonc.2020.565031

Zhao M, Kiernan CH, Stairiker CJ, Hope JL, Leon LG, van Meurs M, Brouwers-Haspels I, Boers R, Boers J, Gribnau J, van IJcken WFJ, Bindels EM, Hoogenboezem RM, Erkeland SJ, Mueller YM, Katsikis PD

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

DOI: 10.1371/journal.ppat.1008555

Kenter AT, Rentmeester E, van Riet J, Boers R, Boers J, Ghazvini M, Xavier VJ, van Leenders GJLH, Verhagen PCMS, van Til ME, Eussen B, Losekoot M, de Klein A, Peters DJM, van IJcken WFJ, van de Werken HJG, Zietse R, Hoorn EJ, Jansen G, Gribnau JH

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

DOI: 10.1002/sctm.18-0283.

Vos M, Boers R, Vriends ALM, Boers J, van Kuijk PF, van Houdt WJ, van Leenders GJLH, Wagrodzki M, van IJcken WFJ, Gribnau J, Grünhagen DJ, Verhoef C, Sleijfer S, Wiemer EAC

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

DOI: 10.1371/journal.pone.0228014

Chaves I, van der Eerden B, Boers R, Boers J, Streng AA, Ridwan Y, Schreuders-Koedam M, Vermeulen M, van der Pluijm I, Essers J, Gribnau J, Reiss IKM, van der Horst GTJ

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

DOI: 10.1080/07420528.2019.1579734

Adrianse RL, Smith K, Gatbonton-Schwager T, Sripathy SP, Lao U, Foss EJ, Boers RG, Boers JB, Gribnau J, Bedalov A

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

DOI: 10.1186/s13072-018-0219-8

Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, van IJcken W, Laven J, Gribnau J

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

DOI: 10.1101/gr.222885.117

van der Zee RP, Richel O, van Noesel CJM, Ciocănea-Teodorescu I, van Splunter AP, Ter Braak TJ, Nathan M, Cuming T, Sheaff M, Kreuter A, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM

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

DOI: 10.1093/cid/ciaa397

Bonde J, Floore A, Ejegod D, Vink FJ, Hesselink A, van de Ven PM, Valenčak AO, Pedersen H, Doorn S, Quint WG, Petry KU, Poljak M, Stanczuk G, Cuschieri K, de Sanjosé S, Bleeker M, Berkhof J, Meijer CJLM, Heideman DAM

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

DOI: 10.1002/ijc.33320

Vink FJ, Meijer CJLM, Clifford GM, Poljak M, Oštrbenk A, Petry KU, Rothe B, Bonde J, Pedersen H, de Sanjosé S, Torres M, Del Pino M, Quint WGV, Cuschieri K, Boada EA, van Trommel NE, Lissenberg-Witte BI, Floore AN, Hesselink AT, Steenbergen RDM, Bleeker MCG, Heideman DAM

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

DOI: 10.1002/ijc.32614

Leeman A, Jenkins D, Del Pino M, Ordi J, Torné A, Doorbar J, Meijer CJLM, van Kemenade FJ, Quint WGV

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

DOI: 10.1002/cam4.2855

Floore A, Hesselink A, Oštrbenk A, Alcaniz E, Rothe B, Pedersen H, Torres Hortal M, Doorn S, Quint W, Petry KU, Poljak M, Cuschieri K, Bonde J, de Sanjosé S, Bleeker M, Heideman D

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

DOI: 10.1002/jcla.22854

van der Zee RP, Richel O, van Noesel CJM, Novianti PW, Ciocanea-Teodorescu I, van Splunter AP, Duin S, van den Berk GEL, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM

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

DOI: 10.1093/cid/ciy601

Leeman A, Del Pino M, Marimon L, Torné A, Ordi J, Ter Harmsel B, Meijer CJLM, Jenkins D, Van Kemenade FJ, Quint WGV

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

DOI: 10.1002/ijc.31787

van Baars R, van der Marel J, Snijders PJ, Rodriquez-Manfredi A, ter Harmsel B, van den Munckhof HA, Ordi J, del Pino M, van de Sandt MM, Wentzensen N, Meijer CJ, Quint WG

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

DOI: 10.1002/ijc.29706

Leeman A, Ebisch RMF, Kasius A, Bosgraaf RP, Jenkins D, van de Sandt MM, de Strooper LMA, Heideman DAM, Snijders PJF, Massuger LFAG, Bekkers RLM, Meijer CJLM, van Kemenade FJ, Quint WGV, Melchers WJG

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

DOI: 10.1016/j.ygyno.2018.09.006