Toward Single Cell MeD-seq

MeD-seq requires a relatively low amount of DNA as input, opening the possibility to work with sample types that give below average DNA yields. The emerging field of liquid biopsy, for example cell free DNA (cfDNA) from blood, shows promising results in oncology for diagnostic purposes or follow-up. In collaboration with academia MeD-seq is already used to detect DNA methylation profiles in cfDNA to setup a tool in the follow-up of surgical treatment of liver metastases in patients with colorectal cancer. Because in healthy individuals the cfDNA mainly originates from blood cell types, both cancer-specific and tissue-specific methylation can be informative in the follow-up of these colon carcinoma patients. These tissue-specific methylations patterns found in cfDNA are also the basis which led to the use of MeD-seq in current studies involved in elaborating on the pathogenesis of various neurodegenerative diseases. Here, cfDNA, DNA from cerebral spinal fluid (CSF) and various sorted populations of cell types from brain tissues are being used for MeD-seq analysis. Our aim for the future is to push MeD-seq towards the single cell level. In close collaboration with multiple academic centers steps are undertaken to optimize the MeD-seq wetlab protocol to look at circulating tumor cells in the blood of cancer patients using single cell MeD-seq.

Publications about our techniques

Boers R, Boers J, de Hoon B, et al. Genome Res. 2018;28(1):88-99. doi:10.1101/gr.222885.117

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

DOI: 10.1101/gr.222885.117

Vos M, Boers R, Vriends ALM, et al. PLoS One. 2020;15(1):e0228014. Published 2020 Jan 23. doi:10.1371/journal.pone.0228014

MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma

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. Int J Cancer. 2020 Sep 30. doi: 10.1002/ijc.33320.

Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.

DOI: 10.1002/ijc.33320.

Leeman A, Jenkins D, Del Pino M, Ordi J, Torné A, Doorbar J, Meijer CJLM, van Kemenade FJ, Quint WGV. Cancer Med. 2020 Apr;9(7):2454-2461. doi: 10.1002/cam4.2855. Epub 2020 Feb 5.

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.

DOI: 10.1002/cam4.2855.

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. Clin Infect Dis. 2020 Apr 8:ciaa397. doi: 10.1093/cid/ciaa397. Online ahead of print.

Cancer risk stratification of anal intraepithelial neoplasia in HIV-positive men by validated methylation markers associated with progression to cancer.

DOI: 10.1093/cid/ciaa397.

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. Int J Cancer. 2016 Jan 15;138(2):463-71. doi: 10.1002/ijc.29706. Epub 2015 Aug 14.

CADM1 and MAL methylation status in cervical scrapes is representative of the most severe underlying lesion in women with multiple cervical biopsies.

DOI: 10.1002/ijc.29706

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. Clin Infect Dis. 2019 Mar 19;68(7):1110-1117. doi: 10.1093/cid/ciy601.

Host Cell Deoxyribonucleic Acid Methylation Markers for the Detection of High-grade Anal Intraepithelial Neoplasia and Anal Cancer.

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. Int J Cancer. 2019 Jan 1;144(1):160-168. doi: 10.1002/ijc.31787. Epub 2018 Nov 18.

Reliable identification of women with CIN3+ using hrHPV genotyping and methylation markers in a cytology-screened referral population.

DOI: 10.1002/ijc.31787

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. J Clin Lab Anal. 2019 May;33(4):e22854. doi: 10.1002/jcla.22854. Epub 2019 Feb 13.

Intra- and inter-laboratory agreement of the FAM19A4/mir124-2 methylation test: Results from an international study.

DOI: 10.1002/jcla.22854

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. Int J Cancer. 2020 Aug 15;147(4):1215-1221. doi: 10.1002/ijc.32614. Epub 2019 Sep 9.

FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.

DOI: 10.1002/ijc.32614

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. Gynecol Oncol. 2018 Nov;151(2):311-318. doi: 10.1016/j.ygyno.2018.09.006. Epub 2018 Sep 13.

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.

DOI: 10.1016/j.ygyno.2018.09.006.