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Identification of novel high-frequency DNA methylation changes in breast cancer.

Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA - PLoS ONE (2007)

Bottom Line: Recent data have revealed that epigenetic alterations, including DNA methylation and chromatin structure changes, are among the earliest molecular abnormalities to occur during tumorigenesis.The power of the global approach for discovery is underscored by the identification of a single differentially methylated locus, associated with the GHSR gene, capable of distinguishing infiltrating ductal breast carcinoma from normal and benign breast tissues with a sensitivity and specificity of 90% and 96%, respectively.Notably, the frequency of these molecular abnormalities in breast tumors substantially exceeds the frequency of any other single genetic or epigenetic change reported to date.

View Article: PubMed Central - PubMed

Affiliation: Orion Genomics, St. Louis, Missouri, United States of America. jordway@oriongenomics.com

ABSTRACT
Recent data have revealed that epigenetic alterations, including DNA methylation and chromatin structure changes, are among the earliest molecular abnormalities to occur during tumorigenesis. The inherent thermodynamic stability of cytosine methylation and the apparent high specificity of the alterations for disease may accelerate the development of powerful molecular diagnostics for cancer. We report a genome-wide analysis of DNA methylation alterations in breast cancer. The approach efficiently identified a large collection of novel differentially DNA methylated loci (approximately 200), a subset of which was independently validated across a panel of over 230 clinical samples. The differential cytosine methylation events were independent of patient age, tumor stage, estrogen receptor status or family history of breast cancer. The power of the global approach for discovery is underscored by the identification of a single differentially methylated locus, associated with the GHSR gene, capable of distinguishing infiltrating ductal breast carcinoma from normal and benign breast tissues with a sensitivity and specificity of 90% and 96%, respectively. Notably, the frequency of these molecular abnormalities in breast tumors substantially exceeds the frequency of any other single genetic or epigenetic change reported to date. The discovery of over 50 novel DNA methylation-based biomarkers of breast cancer may provide new routes for development of DNA methylation-based diagnostics and prognostics, as well as reveal epigenetically regulated mechanism involved in breast tumorigenesis.

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Related in: MedlinePlus

Differential DNA methylation relative to tumor stage.(A) Comparison of the frequency of differential DNA methylation of 16 loci in stage I breast tumors relative to stage II–III breast tumors. (B) DNA methylation density of 3 selected loci relative to tumor stage. The percent depletion by McrBC for each sample in which a given locus scored as methylated was calculated [1-(1/2̂delta Ct (McrBC digested – Mock treated)) * 100] to provide a measure of the load of methylated molecules within the sample. The % depletion is plotted (from left to right) for normal and benign samples, stage I tumors, stage IIA tumors, stage IIB tumors and stage III tumors.
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pone-0001314-g004: Differential DNA methylation relative to tumor stage.(A) Comparison of the frequency of differential DNA methylation of 16 loci in stage I breast tumors relative to stage II–III breast tumors. (B) DNA methylation density of 3 selected loci relative to tumor stage. The percent depletion by McrBC for each sample in which a given locus scored as methylated was calculated [1-(1/2̂delta Ct (McrBC digested – Mock treated)) * 100] to provide a measure of the load of methylated molecules within the sample. The % depletion is plotted (from left to right) for normal and benign samples, stage I tumors, stage IIA tumors, stage IIB tumors and stage III tumors.

Mentions: Fig. 4A shows a plot of the frequency of hypermethylation of the 16 loci in the 8 Stage I tumors (i.e. the percentage of Stage I tumors scoring as intermediately to densely methylated) versus the Stage II and III tumors. The directly proportional relationship between the two sensitivity calculations (R2 = 0.887; slope = 0.9815) indicates that the frequency of hypermethylation of these loci is similar regardless of tumor stage. Therefore, for the majority of loci, the differential methylation events are just as likely to be present in a Stage I tumor as they are in later stage tumors. The proportion of methylated molecules in tumors at each stage was then analyzed for three selected loci (Fig. 4B). While there was a trend for increased methylation density at these loci with increasing tumor stage, methylation density of Stage I tumors was not significantly different than Stage II–III tumors, yet dramatically different than normal samples. Therefore, differential methylation of these loci is independent of tumor stage in regards to both frequency and density of hypermethylation.


Identification of novel high-frequency DNA methylation changes in breast cancer.

Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA - PLoS ONE (2007)

Differential DNA methylation relative to tumor stage.(A) Comparison of the frequency of differential DNA methylation of 16 loci in stage I breast tumors relative to stage II–III breast tumors. (B) DNA methylation density of 3 selected loci relative to tumor stage. The percent depletion by McrBC for each sample in which a given locus scored as methylated was calculated [1-(1/2̂delta Ct (McrBC digested – Mock treated)) * 100] to provide a measure of the load of methylated molecules within the sample. The % depletion is plotted (from left to right) for normal and benign samples, stage I tumors, stage IIA tumors, stage IIB tumors and stage III tumors.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2117343&req=5

pone-0001314-g004: Differential DNA methylation relative to tumor stage.(A) Comparison of the frequency of differential DNA methylation of 16 loci in stage I breast tumors relative to stage II–III breast tumors. (B) DNA methylation density of 3 selected loci relative to tumor stage. The percent depletion by McrBC for each sample in which a given locus scored as methylated was calculated [1-(1/2̂delta Ct (McrBC digested – Mock treated)) * 100] to provide a measure of the load of methylated molecules within the sample. The % depletion is plotted (from left to right) for normal and benign samples, stage I tumors, stage IIA tumors, stage IIB tumors and stage III tumors.
Mentions: Fig. 4A shows a plot of the frequency of hypermethylation of the 16 loci in the 8 Stage I tumors (i.e. the percentage of Stage I tumors scoring as intermediately to densely methylated) versus the Stage II and III tumors. The directly proportional relationship between the two sensitivity calculations (R2 = 0.887; slope = 0.9815) indicates that the frequency of hypermethylation of these loci is similar regardless of tumor stage. Therefore, for the majority of loci, the differential methylation events are just as likely to be present in a Stage I tumor as they are in later stage tumors. The proportion of methylated molecules in tumors at each stage was then analyzed for three selected loci (Fig. 4B). While there was a trend for increased methylation density at these loci with increasing tumor stage, methylation density of Stage I tumors was not significantly different than Stage II–III tumors, yet dramatically different than normal samples. Therefore, differential methylation of these loci is independent of tumor stage in regards to both frequency and density of hypermethylation.

Bottom Line: Recent data have revealed that epigenetic alterations, including DNA methylation and chromatin structure changes, are among the earliest molecular abnormalities to occur during tumorigenesis.The power of the global approach for discovery is underscored by the identification of a single differentially methylated locus, associated with the GHSR gene, capable of distinguishing infiltrating ductal breast carcinoma from normal and benign breast tissues with a sensitivity and specificity of 90% and 96%, respectively.Notably, the frequency of these molecular abnormalities in breast tumors substantially exceeds the frequency of any other single genetic or epigenetic change reported to date.

View Article: PubMed Central - PubMed

Affiliation: Orion Genomics, St. Louis, Missouri, United States of America. jordway@oriongenomics.com

ABSTRACT
Recent data have revealed that epigenetic alterations, including DNA methylation and chromatin structure changes, are among the earliest molecular abnormalities to occur during tumorigenesis. The inherent thermodynamic stability of cytosine methylation and the apparent high specificity of the alterations for disease may accelerate the development of powerful molecular diagnostics for cancer. We report a genome-wide analysis of DNA methylation alterations in breast cancer. The approach efficiently identified a large collection of novel differentially DNA methylated loci (approximately 200), a subset of which was independently validated across a panel of over 230 clinical samples. The differential cytosine methylation events were independent of patient age, tumor stage, estrogen receptor status or family history of breast cancer. The power of the global approach for discovery is underscored by the identification of a single differentially methylated locus, associated with the GHSR gene, capable of distinguishing infiltrating ductal breast carcinoma from normal and benign breast tissues with a sensitivity and specificity of 90% and 96%, respectively. Notably, the frequency of these molecular abnormalities in breast tumors substantially exceeds the frequency of any other single genetic or epigenetic change reported to date. The discovery of over 50 novel DNA methylation-based biomarkers of breast cancer may provide new routes for development of DNA methylation-based diagnostics and prognostics, as well as reveal epigenetically regulated mechanism involved in breast tumorigenesis.

Show MeSH
Related in: MedlinePlus