Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma

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Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma. / Leong, Kai Juen; James, Jonathan; Wen, Kaisheng; Taniere, Philippe; Morton, Dion G; Bach, Simon P; Matthews, Glenn M.

In: Experimental and molecular pathology, Vol. 95, No. 3, 12.2013, p. 343-9.

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@article{4684af3b7e964efea291f77bb7ef21ea,
title = "Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma",
abstract = "BACKGROUND: Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer.METHODS: 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing.RESULTS: FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues.CONCLUSION: Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.",
keywords = "Adenomatous Polyposis Coli Protein, DNA Methylation, Formaldehyde, Humans, Kidney, Laser Capture Microdissection, Long Interspersed Nucleotide Elements, Paraffin Embedding, Polymerase Chain Reaction, Rectal Neoplasms, Stromal Cells",
author = "Leong, {Kai Juen} and Jonathan James and Kaisheng Wen and Philippe Taniere and Morton, {Dion G} and Bach, {Simon P} and Matthews, {Glenn M}",
note = "{\textcopyright} 2013.",
year = "2013",
month = dec,
doi = "10.1016/j.yexmp.2013.10.007",
language = "English",
volume = "95",
pages = "343--9",
journal = "Experimental and molecular pathology",
issn = "0014-4800",
publisher = "Elsevier",
number = "3",

}

RIS

TY - JOUR

T1 - Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma

AU - Leong, Kai Juen

AU - James, Jonathan

AU - Wen, Kaisheng

AU - Taniere, Philippe

AU - Morton, Dion G

AU - Bach, Simon P

AU - Matthews, Glenn M

N1 - © 2013.

PY - 2013/12

Y1 - 2013/12

N2 - BACKGROUND: Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer.METHODS: 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing.RESULTS: FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues.CONCLUSION: Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.

AB - BACKGROUND: Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer.METHODS: 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing.RESULTS: FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues.CONCLUSION: Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.

KW - Adenomatous Polyposis Coli Protein

KW - DNA Methylation

KW - Formaldehyde

KW - Humans

KW - Kidney

KW - Laser Capture Microdissection

KW - Long Interspersed Nucleotide Elements

KW - Paraffin Embedding

KW - Polymerase Chain Reaction

KW - Rectal Neoplasms

KW - Stromal Cells

U2 - 10.1016/j.yexmp.2013.10.007

DO - 10.1016/j.yexmp.2013.10.007

M3 - Article

C2 - 24161956

VL - 95

SP - 343

EP - 349

JO - Experimental and molecular pathology

JF - Experimental and molecular pathology

SN - 0014-4800

IS - 3

ER -