IMPRESS: Improved methylation profiling using restriction enzymes and smMIP sequencing, combined with a new biomarker panel, creating a multi-cancer detection assay.
Journal
British journal of cancer
ISSN: 1532-1827
Titre abrégé: Br J Cancer
Pays: England
ID NLM: 0370635
Informations de publication
Date de publication:
24 Aug 2024
24 Aug 2024
Historique:
received:
12
02
2024
accepted:
24
07
2024
revised:
19
07
2024
medline:
26
8
2024
pubmed:
26
8
2024
entrez:
24
8
2024
Statut:
aheadofprint
Résumé
Despite the worldwide progress in cancer diagnostics, more sensitive diagnostic biomarkers are needed. The methylome has been extensively investigated in the last decades, but a low-cost, bisulfite-free detection method for multiplex analysis is still lacking. We developed a methylation detection technique called IMPRESS, which combines methylation-sensitive restriction enzymes and single-molecule Molecular Inversion Probes. We used this technique for the development of a multi-cancer detection assay for eight of the most lethal cancer types worldwide. We selected 1791 CpG sites that can distinguish tumor from normal tissue based on DNA methylation. These sites were analysed with IMPRESS in 35 blood, 111 tumor and 114 normal samples. Finally, a classifier model was built. We present the successful development of IMPRESS and validated it with ddPCR. The final classifier model discriminating tumor from normal samples was built with 358 CpG target sites and reached a sensitivity of 0.95 and a specificity of 0.91. Moreover, we provide data that highlight IMPRESS's potential for liquid biopsies. We successfully created an innovative DNA methylation detection technique. By combining this method with a new multi-cancer biomarker panel, we developed a sensitive and specific multi-cancer assay, with potential use in liquid biopsies.
Sections du résumé
BACKGROUND
BACKGROUND
Despite the worldwide progress in cancer diagnostics, more sensitive diagnostic biomarkers are needed. The methylome has been extensively investigated in the last decades, but a low-cost, bisulfite-free detection method for multiplex analysis is still lacking.
METHODS
METHODS
We developed a methylation detection technique called IMPRESS, which combines methylation-sensitive restriction enzymes and single-molecule Molecular Inversion Probes. We used this technique for the development of a multi-cancer detection assay for eight of the most lethal cancer types worldwide. We selected 1791 CpG sites that can distinguish tumor from normal tissue based on DNA methylation. These sites were analysed with IMPRESS in 35 blood, 111 tumor and 114 normal samples. Finally, a classifier model was built.
RESULTS
RESULTS
We present the successful development of IMPRESS and validated it with ddPCR. The final classifier model discriminating tumor from normal samples was built with 358 CpG target sites and reached a sensitivity of 0.95 and a specificity of 0.91. Moreover, we provide data that highlight IMPRESS's potential for liquid biopsies.
CONCLUSIONS
CONCLUSIONS
We successfully created an innovative DNA methylation detection technique. By combining this method with a new multi-cancer biomarker panel, we developed a sensitive and specific multi-cancer assay, with potential use in liquid biopsies.
Identifiants
pubmed: 39181941
doi: 10.1038/s41416-024-02809-1
pii: 10.1038/s41416-024-02809-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Universiteit Antwerpen (University of Antwerp)
ID : BOF/TOP 39705
Organisme : Universiteit Antwerpen (University of Antwerp)
ID : IOF/SBO 43782
Organisme : Universiteit Antwerpen (University of Antwerp)
ID : BOF/Methusalem grant 40790
Organisme : Universiteit Antwerpen (University of Antwerp)
ID : BOF/TOP 39705
Organisme : Universiteit Antwerpen (University of Antwerp)
ID : IOF/SBO 43782
Organisme : Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
ID : IS67523N
Organisme : Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
ID : 11B5220N
Informations de copyright
© 2024. The Author(s).
Références
Globocan I Cancer Today. Data visualisation tools for exploring the global cancer burden in 2020. 2020.
WHO. Cancer - Screening and early detection. 2010.
National Cancer Institute. Stage at Diagnosis. 2022.
Kulis M, Esteller M. Chapter 2 - DNA Methylation and Cancer. Epigenet Cancer, Part A. 2010;70:27–56.
doi: 10.1016/B978-0-12-380866-0.60002-2
Constâncio V, Nunes SP, Moreira-Barbosa C, Freitas R, Oliveira J, Pousa I, et al. Early detection of the major male cancer types in blood-based liquid biopsies using a DNA methylation panel. Clin Epigenet. 2019;11:175–93.
Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G, Genome-wide DNA. methylation profiling and identification of potential pan-cancer and tumor-specific biomarkers. Mol Oncol. 2022;16:2432–47.
doi: 10.1002/1878-0261.13176
pubmed: 34978357
pmcid: 9208075
Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA methylation in solid tumors: Functions and methods of detection. Int J Mol Sci. MDPI; 2021; 22:4247–69.
Liu Z, Wang Z, Jia E, Ouyang T, Pan M, Lu J, et al. Analysis of genome-wide in cell free DNA methylation: progress and prospect. Analyst. 2019;144:5912–22. 2019/08/23
doi: 10.1039/C9AN00935C
pubmed: 31436778
Sun Z, Vaisvila R, Hussong LM, Yan B, Baum C, Saleh L, et al. Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res. 2021;31:291–300.
doi: 10.1101/gr.265306.120
pubmed: 33468551
pmcid: 7849414
Liu Y, Siejka-Zielińska P, Velikova G, Bi Y, Yuan F, Tomkova M, et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol. 2019;37:424–9.
doi: 10.1038/s41587-019-0041-2
pubmed: 30804537
Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, Kakhki MP, Raine A, Needhamsen M, et al. Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Epigenetics. 2021.
Vaisvila R, Chaithanya Ponnaluri VK, Sun Z, Langhorst BW, Saleh L, Guan S, et al. EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA. Available from: https://doi.org/10.1101/2019.12.20.884692 .
Thermes C. Ten years of next-generation sequencing technology.Trends in genetics: TIG. 2014;30:418–26.
Beikircher G, Pulverer W, Hofner M, Noehammer C, Weinhaeusel A. Multiplexed and sensitive DNA methylation testing using methylation-sensitive restriction enzymes “MSRE-qPCR”. In: Methods in Molecular Biology. Humana Press Inc.; 2018. p. 407–24.
Hiatt JB, Pritchard CC, Salipante SJ, O’Roak BJ, Shendure J. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res. 2013;23:843–54.
doi: 10.1101/gr.147686.112
pubmed: 23382536
pmcid: 3638140
Steeghs EMP, Kroeze LI, Tops BBJ, Van Kempen LC, Ter Elst A, Kastner-Van Raaij AWM, et al. Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material. BMC Cancer. 2020;20:291–306.
Bekers EM, Eijkelenboom A, Rombout P, Van Zwam P, Mol S, Ruijter E, et al. Identification of novel GNAS mutations in intramuscular myxoma using next-generation sequencing with single-molecule tagged molecular inversion probes. Diagn Pathol. 2019; 8:14.
Köster J, Rahmann S. Snakemake—a scalable bioinformatics workflow engine. Bioinforma [Internet]. 2012;28:2520–2. https://doi.org/10.1093/bioinformatics/bts480 .
doi: 10.1093/bioinformatics/bts480
Li H. zaSQ Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013;00:1–3. Available from: http://arxiv.org/abs/1303.3997 .
Broad Institute. Picard Toolkit [Internet]. 2019. Available from: https://broadinstitute.github.io/picard/ .
Boyle EA, O’Roak BJ, Martin BK, Kumar A, Shendure J. MIPgen: Optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics 2014;30:2670–2.
doi: 10.1093/bioinformatics/btu353
pubmed: 24867941
pmcid: 4155255
Venables WN, Ripley BD. Modern Applied Statistics with S [Internet]. 4th ed. New York: Springer; 2002. Available from: http://www.stats.ox.ac.uk/pub/MASS4 .
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinforma [Internet]. 2005;21:3940–1. https://doi.org/10.1093/bioinformatics/bti623 .
doi: 10.1093/bioinformatics/bti623
Arts P, van der Raadt J, van Gestel SHC, Steehouwer M, Shendure J, Hoischen A, et al. Quantification of differential gene expression by multiplexed targeted resequencing of cDNA. Nat Commun. 2017;5:8.
Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, et al. Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Res. 2006;34:528–42.
doi: 10.1093/nar/gkj461
pubmed: 16428248
pmcid: 1345696
Armbruster DA, Pry T. Limit of Blank, Limit of Detection and Limit of Quantitation. Clin Biochem Rev. 2008;39:S49–52.
Harrison A, Parle-McDermott A. DNA methylation: A timeline of methods and applications. Front Genet. 2011;2:74–87.
Wu D, Waalkes A, Penewit K, Salipante SJ. Ultrasensitive detection of chimerism by single-Molecule molecular inversion probe capture and high-Throughput sequencing of copy number deletion polymorphisms. Clin Chem. 2018;64:938–49.
doi: 10.1373/clinchem.2017.284737
pubmed: 29549183
pmcid: 6263032
Weren RDA, Mensenkamp AR, Simons M, Eijkelenboom A, Sie AS, Ouchene H, et al. Novel BRCA1 and BRCA2 Tumor Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas. Hum Mutat. 2017;38:226–35.
doi: 10.1002/humu.23137
pubmed: 27767231
Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, et al. BRCA testing by single-molecule molecular inversion probes. Clin Chem. 2017;63:503–12.
doi: 10.1373/clinchem.2016.263897
pubmed: 27974384
Verkouteren BJA, Wakkee M, van Geel M, van Doorn R, Winnepenninckx VJ, Korpershoek E, et al. Molecular testing in metastatic basal cell carcinoma. J Am Acad Dermatol. 2021;85:1135–42.
doi: 10.1016/j.jaad.2019.12.026
pubmed: 31870915
Acuna-Hidalgo R, Sengul H, Steehouwer M, van de Vorst M, Vermeulen SH, Kiemeney LALM, et al. Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life. Am J Hum Genet. 2017;101:50–64.
doi: 10.1016/j.ajhg.2017.05.013
pubmed: 28669404
pmcid: 5501773
Šestáková Š, Šálek C, Remešová H. DNA Methylation Validation Methods: A Coherent Review with Practical Comparison. Biological Procedures Online. BioMed Central Ltd.; 2019; 21:19–30.
Croes L, Op de Beeck K, Pauwels P, Vanden Berghe W, Peeters M, Fransen E, et al. DFNA5 promoter methylation a marker for breast tumorigenesis [Internet]. Oncotarget. 2017; 8. Available from: www.impactjournals.com/oncotarget/ .
Cohen JD, Li L, Wang Y, Thoburn C, Afsari B, Danilova L, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test [Internet]. 17 Available from: https://www.science.org .
Liu MC, Oxnard GR, Klein EA, Swanton C, Seiden MV, Liu MC, et al. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. Ann Oncol. 2020;31:745–59.
doi: 10.1016/j.annonc.2020.02.011
pubmed: 33506766
Chen X, Gole J, Gore A, He Q, Lu M, Min J, et al. Non-invasive early detection of cancer four years before conventional diagnosis using a blood test. Nat Commun. 2020; 1;11:3475–85.
Klein EA, Richards D, Cohn A, Tummala M, Lapham R, Cosgrove D, et al. Clinical validation of a targeted methylation-based multi-cancer early detection test using an independent validation set. Ann Oncol. 2021;32:1167–77.
doi: 10.1016/j.annonc.2021.05.806
pubmed: 34176681
Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Res. 2021;49:E76.
doi: 10.1093/nar/gkab291
pubmed: 33905495
pmcid: 8287915
Liu Y, Hu Z, Cheng J, Siejka-Zielińska P, Chen J, Inoue M, et al. Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. Nat Commun. 2021;12:618.
doi: 10.1038/s41467-021-20920-2
pubmed: 33504799
pmcid: 7840749
Morrison J, Koeman JM, Johnson BK, Foy KK, Beddows I, Zhou W, et al. Evaluation of whole-genome DNA methylation sequencing library preparation protocols. Epigenet Chromatin. 2021;14:28.
doi: 10.1186/s13072-021-00401-y
Hawthorn L, Lan L, Mojica W. Evidence for field effect cancerization in colorectal cancer. Genomics 2014;103:211–21.
doi: 10.1016/j.ygeno.2013.11.003
pubmed: 24316131
Cherkezyan L, Stypula-Cyrus Y, Subramanian H, White C, Dela Cruz M, Wali RK, et al. Nanoscale changes in chromatin organization represent the initial steps of tumorigenesis: a transmission electron microscopy study. BMC Cancer. 2014;14:189.
doi: 10.1186/1471-2407-14-189
pubmed: 24629088
pmcid: 3995586
Sun K, Wang J, Wang H, Sun H. GeneCT: A generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. Bioinformatics. 2018;34:4129–30.
doi: 10.1093/bioinformatics/bty524
pubmed: 29947737