Abstract
DNA methylation analysis of paraffin-embedded archival tumor tissues (PEAT) is important in clinical and translational research studies. Efficient identification and isolation of homogeneous cell population, optimal DNA extraction, and sodium bisulfite modification (SBM) are essential, particularly in small tumor lesions. Laser capture microdissection (LCM) coupled with an in situ SBM improves the specificity, through histopathology accuracy, and the amount of genomic DNA modified for downstream methylation assays.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Hahn WC, Weinberg RA (2002) Rules for making human tumor cells. N Engl J Med 347(20):1593–1603
Sadikovic B, Al-Romaih K, Squire JA et al (2008) Cause and consequences of genetic and epigenetic alterations in human cancer. Curr Genomics 9(6):394–408
Greenberg ES, Chong KK, Huynh KT et al (2014) Epigenetic biomarkers in skin cancer. Cancer Lett 342(2):170–177 [Epub Ahead of Print]
van Hoesel AQ, van de Velde CJ, Kuppen PJ et al (2012) Hypomethylation of LINE-1 in primary tumor has poor prognosis in young breast cancer patients: a retrospective cohort study. Breast Cancer Res Treat 134(3):1103–1114
Lian CG, Xu Y, Ceol C et al (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150(6):1135–1146
Lister R, Pelizzola M, Dowen RH et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322
Jones PA, Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293(5532):1068–1070
Sunami E, Vu A, Nguyen SL et al (2008) Analysis of methylated circulating DNA in cancer patients’ blood. Methods Mol Biol 507:349–356
Liu A (2010) Laser capture microdissection in the tissue biorepository. J Biomol Tech 21(3):120–125
Kristensen LS, Hansen LL (2009) PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clin Chem 55(8):1471–1483
Grunau C, Clark SJ, Rosenthal A (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29(13), E65-5
de Maat MF, Umetani N, Sunami E et al (2007) Assessment of methylation events during colorectal tumor progression by absolute quantitative analysis of methylated alleles. Mol Cancer Res 5(5):461–471
Sunami E, de Maat M, Vu A et al (2011) LINE-1 hypomethylation during primary colon cancer progression. PLoS One 6(4):e18884
Umetani N, de Maat MF, Mori T et al (2005) Synthesis of universal unmethylated control DNA by nested whole genome amplification with phi29 DNA polymerase. Biochem Biophys Res Commun 329(1):219–223
Acknowledgement
This work was supported by NIH, NCI, PO1 CA029605 Project II and Core C, the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, the Associates for Breast and Prostate Cancer Studies (ABCs), and Ruth and Martin H. Weil Foundation.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2015
About this protocol
Cite this protocol
Marzese, D.M., Huang, S.K., Hoon, D.S.B. (2015). In Situ Sodium Bisulfite Modification of Genomic DNA from Microdissected Melanoma Paraffin-Embedded Archival Tissues. In: Methods in Molecular Biology. Humana Press. https://doi.org/10.1007/7651_2015_303
Download citation
DOI: https://doi.org/10.1007/7651_2015_303
Published:
Publisher Name: Humana Press