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Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients.

Sigalotti L, Covre A, Fratta E, Parisi G, Sonego P, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M - J Transl Med (2012)

Bottom Line: A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0) in stage IIIC patients on the basis of distinct methylation-defined groups was also identified.A discrete whole-genome methylation signature has been identified as molecular marker of prognosis for stage IIIC CM patients.Its use in daily practice is foreseeable, and promises to refine the comprehensive clinical management of stage III CM patients.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy. lsigalotti@cro.it

ABSTRACT

Background: The clinical course of cutaneous melanoma (CM) can differ significantly for patients with identical stages of disease, defined clinico-pathologically, and no molecular markers differentiate patients with such a diverse prognosis. This study aimed to define the prognostic value of whole genome DNA methylation profiles in stage III CM.

Methods: Genome-wide methylation profiles were evaluated by the Illumina Human Methylation 27 BeadChip assay in short-term neoplastic cell cultures from 45 stage IIIC CM patients. Unsupervised K-means partitioning clustering was exploited to sort patients into 2 groups based on their methylation profiles. Methylation patterns related to the discovered groups were determined using the nearest shrunken centroid classification algorithm. The impact of genome-wide methylation patterns on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analyses.

Results: Unsupervised K-means partitioning by whole genome methylation profiles identified classes with significantly different OS in stage IIIC CM patients. Patients with a "favorable" methylation profile had increased OS (P = 0.001, log-rank = 10.2) by Kaplan-Meier analysis. Median OS of stage IIIC patients with a "favorable" vs. "unfavorable" methylation profile were 31.5 and 10.4 months, respectively. The 5 year OS for stage IIIC patients with a "favorable" methylation profile was 41.2% as compared to 0% for patients with an "unfavorable" methylation profile. Among the variables examined by multivariate Cox regression analysis, classification defined by methylation profile was the only predictor of OS (Hazard Ratio = 2.41, for "unfavorable" methylation profile; 95% Confidence Interval: 1.02-5.70; P = 0.045). A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0) in stage IIIC patients on the basis of distinct methylation-defined groups was also identified.

Conclusions: A discrete whole-genome methylation signature has been identified as molecular marker of prognosis for stage IIIC CM patients. Its use in daily practice is foreseeable, and promises to refine the comprehensive clinical management of stage III CM patients.

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Groups of stage IIIC CM patients identified by whole-genome methylation profiling. Genome-wide DNA methylation profile was evaluated by Illumina HumanMethylation27 Bead-Chip whole-genome assay in short-term cultures of CM cells generated from neoplastic lesions of 45 stage IIIC CM patients. Cells were analyzed at 6th in vitro passage. Patients were divided into 2 classes (LM and HM) based on the whole genome methylation profile of their tumor cells through the k-means algorithm. Panel a, the whole genome methylation profiles in the patients’ population have been reported as a heatmap. Patient identifier numbers and the k-means-defined groups have been reported on top of the heatmap. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1). Panel b, the genome-wide methylation profile of each patient was summarized by the “methylation score”, where “methylation scores” > and < 0 represent methylation above and below the population’s mean, respectively. Separate box plots have been generated for the LM and HM whole methylome defined patients’ groups. Black horizontal bars represent the median values of “methylation score” for each group. *, P = 0.001 as evaluated by Student’s T test.
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Figure 1: Groups of stage IIIC CM patients identified by whole-genome methylation profiling. Genome-wide DNA methylation profile was evaluated by Illumina HumanMethylation27 Bead-Chip whole-genome assay in short-term cultures of CM cells generated from neoplastic lesions of 45 stage IIIC CM patients. Cells were analyzed at 6th in vitro passage. Patients were divided into 2 classes (LM and HM) based on the whole genome methylation profile of their tumor cells through the k-means algorithm. Panel a, the whole genome methylation profiles in the patients’ population have been reported as a heatmap. Patient identifier numbers and the k-means-defined groups have been reported on top of the heatmap. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1). Panel b, the genome-wide methylation profile of each patient was summarized by the “methylation score”, where “methylation scores” > and < 0 represent methylation above and below the population’s mean, respectively. Separate box plots have been generated for the LM and HM whole methylome defined patients’ groups. Black horizontal bars represent the median values of “methylation score” for each group. *, P = 0.001 as evaluated by Student’s T test.

Mentions: Genome-wide gene methylation profiles were evaluated in the 45 short-term CM cell cultures under study using the Illumina HumanMethylation27 Bead-Chip whole-genome assay, which interrogates 27,578 CpG sites, corresponding to 14,495 genes. Patients were divided into 2 subgroups, according to their whole genome methylation profile, by the k-means clustering method (Figure1). The subgroups generated included 33 and 12 patients (Figure1).


Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients.

Sigalotti L, Covre A, Fratta E, Parisi G, Sonego P, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M - J Transl Med (2012)

Groups of stage IIIC CM patients identified by whole-genome methylation profiling. Genome-wide DNA methylation profile was evaluated by Illumina HumanMethylation27 Bead-Chip whole-genome assay in short-term cultures of CM cells generated from neoplastic lesions of 45 stage IIIC CM patients. Cells were analyzed at 6th in vitro passage. Patients were divided into 2 classes (LM and HM) based on the whole genome methylation profile of their tumor cells through the k-means algorithm. Panel a, the whole genome methylation profiles in the patients’ population have been reported as a heatmap. Patient identifier numbers and the k-means-defined groups have been reported on top of the heatmap. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1). Panel b, the genome-wide methylation profile of each patient was summarized by the “methylation score”, where “methylation scores” > and < 0 represent methylation above and below the population’s mean, respectively. Separate box plots have been generated for the LM and HM whole methylome defined patients’ groups. Black horizontal bars represent the median values of “methylation score” for each group. *, P = 0.001 as evaluated by Student’s T test.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539917&req=5

Figure 1: Groups of stage IIIC CM patients identified by whole-genome methylation profiling. Genome-wide DNA methylation profile was evaluated by Illumina HumanMethylation27 Bead-Chip whole-genome assay in short-term cultures of CM cells generated from neoplastic lesions of 45 stage IIIC CM patients. Cells were analyzed at 6th in vitro passage. Patients were divided into 2 classes (LM and HM) based on the whole genome methylation profile of their tumor cells through the k-means algorithm. Panel a, the whole genome methylation profiles in the patients’ population have been reported as a heatmap. Patient identifier numbers and the k-means-defined groups have been reported on top of the heatmap. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1). Panel b, the genome-wide methylation profile of each patient was summarized by the “methylation score”, where “methylation scores” > and < 0 represent methylation above and below the population’s mean, respectively. Separate box plots have been generated for the LM and HM whole methylome defined patients’ groups. Black horizontal bars represent the median values of “methylation score” for each group. *, P = 0.001 as evaluated by Student’s T test.
Mentions: Genome-wide gene methylation profiles were evaluated in the 45 short-term CM cell cultures under study using the Illumina HumanMethylation27 Bead-Chip whole-genome assay, which interrogates 27,578 CpG sites, corresponding to 14,495 genes. Patients were divided into 2 subgroups, according to their whole genome methylation profile, by the k-means clustering method (Figure1). The subgroups generated included 33 and 12 patients (Figure1).

Bottom Line: A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0) in stage IIIC patients on the basis of distinct methylation-defined groups was also identified.A discrete whole-genome methylation signature has been identified as molecular marker of prognosis for stage IIIC CM patients.Its use in daily practice is foreseeable, and promises to refine the comprehensive clinical management of stage III CM patients.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy. lsigalotti@cro.it

ABSTRACT

Background: The clinical course of cutaneous melanoma (CM) can differ significantly for patients with identical stages of disease, defined clinico-pathologically, and no molecular markers differentiate patients with such a diverse prognosis. This study aimed to define the prognostic value of whole genome DNA methylation profiles in stage III CM.

Methods: Genome-wide methylation profiles were evaluated by the Illumina Human Methylation 27 BeadChip assay in short-term neoplastic cell cultures from 45 stage IIIC CM patients. Unsupervised K-means partitioning clustering was exploited to sort patients into 2 groups based on their methylation profiles. Methylation patterns related to the discovered groups were determined using the nearest shrunken centroid classification algorithm. The impact of genome-wide methylation patterns on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analyses.

Results: Unsupervised K-means partitioning by whole genome methylation profiles identified classes with significantly different OS in stage IIIC CM patients. Patients with a "favorable" methylation profile had increased OS (P = 0.001, log-rank = 10.2) by Kaplan-Meier analysis. Median OS of stage IIIC patients with a "favorable" vs. "unfavorable" methylation profile were 31.5 and 10.4 months, respectively. The 5 year OS for stage IIIC patients with a "favorable" methylation profile was 41.2% as compared to 0% for patients with an "unfavorable" methylation profile. Among the variables examined by multivariate Cox regression analysis, classification defined by methylation profile was the only predictor of OS (Hazard Ratio = 2.41, for "unfavorable" methylation profile; 95% Confidence Interval: 1.02-5.70; P = 0.045). A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0) in stage IIIC patients on the basis of distinct methylation-defined groups was also identified.

Conclusions: A discrete whole-genome methylation signature has been identified as molecular marker of prognosis for stage IIIC CM patients. Its use in daily practice is foreseeable, and promises to refine the comprehensive clinical management of stage III CM patients.

Show MeSH
Related in: MedlinePlus