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

Kai Juen Leong; Jonathan James; Kaisheng Wen; Philippe Taniere; Dion G Morton; Simon P Bach; Glenn M Matthews

doi:10.1016/j.yexmp.2013.10.007

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

Kai Juen Leong, Jonathan James, Kaisheng Wen, Philippe Taniere, Dion G Morton, Simon P Bach, Glenn M Matthews

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

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.

Original language	English
Pages (from-to)	343-9
Number of pages	7
Journal	Experimental and molecular pathology
Volume	95
Issue number	3
DOIs	https://doi.org/10.1016/j.yexmp.2013.10.007
Publication status	Published - Dec 2013

Bibliographical note

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.yexmp.2013.10.007

Development and Validation of Methylation Based Prognostic Biomakers to Stratify for Risk of Recurrence in Early Rectal Cancer
Matthews, G., Bach, S. & Morton, D.
Medical Research Council
1/03/10 → 29/07/12
Project: Research Councils

Cite this

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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}",

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doi = "10.1016/j.yexmp.2013.10.007",

language = "English",

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journal = "Experimental and molecular pathology",

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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

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

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SN - 1096-0945

VL - 95

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JO - Experimental and molecular pathology

JF - Experimental and molecular pathology

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ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

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Projects

Development and Validation of Methylation Based Prognostic Biomakers to Stratify for Risk of Recurrence in Early Rectal Cancer

Cite this