TET2 mutations are associated with specific 5-methylcytosine and 5-hydroxymethylcytosine profiles in patients with chronic myelomonocytic leukemia

Chronic myelomonocytic leukemia (CMML) has recently been associated with a high incidence of diverse mutations in genes such as TET2 or EZH2 that are implicated in epigenetic mechanisms. We have performed genome-wide DNA methylation arrays and mutational analysis of TET2, IDH1, IDH2, EZH2 and JAK2 in a group of 24 patients with CMML. 249 genes were differentially methylated between CMML patients and controls. Using Ingenuity pathway analysis, we identified enrichment in a gene network centered around PLC, JNK and ERK suggesting that these pathways, whose deregulation has been recently described in CMML, are affected by epigenetic mechanisms. Mutations of TET2, JAK2 and EZH2 were found in 15 patients (65%), 4 patients (17%) and 1 patient (4%) respectively while no mutations in the IDH1 and IDH2 genes were identified. Interestingly, patients with wild type TET2 clustered separately from patients with TET2 mutations, showed a higher degree of hypermethylation and were associated with higher risk karyotypes. Our results demonstrate the presence of aberrant DNA methylation in CMML and identifies TET2 mutant CMML as a biologically distinct disease subtype with a different epigenetic profile

Papel de la alteración de la metilación del DNA en el pronóstico de los pacientes con leucemia mielomonocítica crónica

Se ha demostrado, que varios genes alterados genética y funcionalmente en las neoplasias mieloproliferativas, como es el caso del gen TET2, están implicados en la regulación de los mecanismos epigenéticos. Teniendo en cuenta estos datos, la hipótesis que nos planteamos para este estudio consistió en que el metiloma del DNA podría estar alterado en los pacientes con LMMC y que este podría ser diferente entre los pacientes con esta neoplasia según la presencia o no de mutaciones en genes que participan en la regulación de los mecanismos epigenéticos, incluso pudiendo ser un marcador para la clasificación y pronóstico de los pacientes con esta enfermedad

Papel de la alteración de la metilación del DNA en el pronóstico de los pacientes con leucemia mielomonocítica crónica

Se ha demostrado, que varios genes alterados genética y funcionalmente en las neoplasias mieloproliferativas, como es el caso del gen TET2, están implicados en la regulación de los mecanismos epigenéticos. Teniendo en cuenta estos datos, la hipótesis que nos planteamos para este estudio consistió en que el metiloma del DNA podría estar alterado en los pacientes con LMMC y que este podría ser diferente entre los pacientes con esta neoplasia según la presencia o no de mutaciones en genes que participan en la regulación de los mecanismos epigenéticos, incluso pudiendo ser un marcador para la clasificación y pronóstico de los pacientes con esta enfermedad

TET2 mutations are associated with specific 5-methylcytosine and 5-hydroxymethylcytosine profiles in patients with chronic myelomonocytic leukemia

Chronic myelomonocytic leukemia (CMML) has recently been associated with a high incidence of diverse mutations in genes such as TET2 or EZH2 that are implicated in epigenetic mechanisms. We have performed genome-wide DNA methylation arrays and mutational analysis of TET2, IDH1, IDH2, EZH2 and JAK2 in a group of 24 patients with CMML. 249 genes were differentially methylated between CMML patients and controls. Using Ingenuity pathway analysis, we identified enrichment in a gene network centered around PLC, JNK and ERK suggesting that these pathways, whose deregulation has been recently described in CMML, are affected by epigenetic mechanisms. Mutations of TET2, JAK2 and EZH2 were found in 15 patients (65%), 4 patients (17%) and 1 patient (4%) respectively while no mutations in the IDH1 and IDH2 genes were identified. Interestingly, patients with wild type TET2 clustered separately from patients with TET2 mutations, showed a higher degree of hypermethylation and were associated with higher risk karyotypes. Our results demonstrate the presence of aberrant DNA methylation in CMML and identifies TET2 mutant CMML as a biologically distinct disease subtype with a different epigenetic profile

TET2 mutations are associated with specific 5-methylcytosine and 5-hydroxymethylcytosine profiles in patients with chronic myelomonocytic leukemia

Chronic myelomonocytic leukemia (CMML) has recently been associated with a high incidence of diverse mutations in genes such as TET2 or EZH2 that are implicated in epigenetic mechanisms. We have performed genome-wide DNA methylation arrays and mutational analysis of TET2, IDH1, IDH2, EZH2 and JAK2 in a group of 24 patients with CMML. 249 genes were differentially methylated between CMML patients and controls. Using Ingenuity pathway analysis, we identified enrichment in a gene network centered around PLC, JNK and ERK suggesting that these pathways, whose deregulation has beenrecently described in CMML, are affected by epigenetic mechanisms. Mutations of TET2, JAK2 and EZH2 were found in 15 patients (65%), 4 patients (17%) and 1 patient (4%) respectively while no mutations in the IDH1 and IDH2 genes were identified. Interestingly, patients with wild type TET2 clustered separately from patients with TET2 mutations, showed a higher degree of hypermethylation and were associated with higher risk karyotypes. Our results demonstrate the presence of aberrant DNA methylation in CMML and identifies TET2 mutant CMML as a biologically distinct disease subtype with a different epigenetic profile

Analysis of differentially methylated genes in CMML samples with and without <i>TET2</i> mutations.

<p><b>A</b>) Hierarchical cluster analysis based on abnormally methylated genes between CMML samples with <i>TET2</i> mutations and CMML samples without <i>TET2</i> mutations. B values are depicted using a pseudocolor scale (Red = Genes hypermethylated; Green = Genes hypomethylated). Samples are color coded. The top bar beneath the dendrogram refers CMML or healthy donor samples, second bar indicates CMML samples with or without <i>TET2</i> mutations and lower bar indicates cytogenetic risk of CMML patients. <b>B</b>) Box plots for hypermethylated genes in CMML samples with <i>TET2</i> mutations (<i>TET2</i>-mut) with respect to CMML <i>TET2</i> wild type (<i>TET2</i>-wt) samples. <b>C</b>) Box plots for hypermethylated genes in CMML <i>TET2</i>-wt samples respect to CMML samples with <i>TET2</i>-mut.</p

Analysis of 5 hmC and 5 mC levels in genes hypermethylated in CMML TET2-mut in comparison to TET2-wt patients.

<p>The percentage of 5 hmC, 5 mC and ratio between 5 hmC/5 mC were measured in 8 CMML <i>TET2</i>-mut and 5 <i>TET2</i>-wt patient samples using qPCR. Two CpG located 5′upstream (−38 and −244 bp respectively) to the CpG analyzed in the methylation array in the case of <i>LAX1</i>; one upstream CpG (59 bp) and another downstream CpG (58 bp) to the CpG in the case of <i>SLC22A12</i> gene and one CpG downstream (5 bp) in the case of <i>VHL</i> gene were analyzed. Median values of percentage of 5 hmC, 5 mC or ratio between 5 hmC/5 mC are indicated and P values were obtained using the 2-tailed T test or U Mann Whitney test. CG: CpG dinucleotide included in the array; CCGG: CpG dinucleotide in which 5 hmC and 5 mC have been analysed and TSS: transcriptional start site.</p