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CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.

Hájková H, Fritz MH, Haškovec C, Schwarz J, Šálek C, Marková J, Krejčík Z, Dostálová Merkerová M, Kostečka A, Vostrý M, Fuchs O, Michalová K, Cetkovský P, Beneš V - J Hematol Oncol (2014)

Bottom Line: Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression.We discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis.Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Studying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients. The aim of this study was to identify differentially methylated genes with potential impact on AML pathogenesis based on the correlation of methylation and expression data.

Methods: The primary method of studying DNA methylation changes was targeted bisulfite sequencing capturing approximately 84 megabases (Mb) of the genome in 14 diagnostic AML patients and a healthy donors' CD34+ pool. Subsequently, selected DNA methylation changes were confirmed by 454 bisulfite pyrosequencing in a larger cohort of samples. Furthermore, we addressed gene expression by microarray profiling and correlated methylation of regions adjacent to transcription start sites with expression of corresponding genes.

Results: Here, we report a novel hypomethylation pattern, specific to CBFB-MYH11 fusion resulting from inv(16) rearrangement that is associated with genes previously described as upregulated in inv(16) AML. We assume that this hypomethylation and corresponding overexpresion occurs in the genes whose function is important in inv(16) leukemogenesis. Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression. PBX3 has been recently shown to be a key interaction partner of HOX genes during leukemogenesis and we revealed higher incidence of relapses in PBX3-overexpressing patients.

Conclusions: We discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis. Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.

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Related in: MedlinePlus

Expression of hypomethylated genes in inv(16) AML measured by TaqMan gene expression assays. Relative expression value of MN1(A), SPARC(B), ST18(C) and DHRS3(D) in inv(16) AML patients versus other AML subtypes and healthy control cells; MNC – mononuclear cells; asterisks correspond to statistically significant changes of expression, ***P < 0.0001, *P < 0.05, ns – not significant.
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Fig3: Expression of hypomethylated genes in inv(16) AML measured by TaqMan gene expression assays. Relative expression value of MN1(A), SPARC(B), ST18(C) and DHRS3(D) in inv(16) AML patients versus other AML subtypes and healthy control cells; MNC – mononuclear cells; asterisks correspond to statistically significant changes of expression, ***P < 0.0001, *P < 0.05, ns – not significant.

Mentions: Further, we evaluated expression levels of MN1, SPARC, ST18 and DHRS3 by TaqMan gene expression assays in all samples already examined by 454 pyrosequencing. As can be seen in Figure 3, inv(16) patients had higher average levels of expression for all 4 genes in comparison to other non-inv(16) AML samples, but only in ST18 when compared to healthy donors.Figure 3


CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.

Hájková H, Fritz MH, Haškovec C, Schwarz J, Šálek C, Marková J, Krejčík Z, Dostálová Merkerová M, Kostečka A, Vostrý M, Fuchs O, Michalová K, Cetkovský P, Beneš V - J Hematol Oncol (2014)

Expression of hypomethylated genes in inv(16) AML measured by TaqMan gene expression assays. Relative expression value of MN1(A), SPARC(B), ST18(C) and DHRS3(D) in inv(16) AML patients versus other AML subtypes and healthy control cells; MNC – mononuclear cells; asterisks correspond to statistically significant changes of expression, ***P < 0.0001, *P < 0.05, ns – not significant.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197269&req=5

Fig3: Expression of hypomethylated genes in inv(16) AML measured by TaqMan gene expression assays. Relative expression value of MN1(A), SPARC(B), ST18(C) and DHRS3(D) in inv(16) AML patients versus other AML subtypes and healthy control cells; MNC – mononuclear cells; asterisks correspond to statistically significant changes of expression, ***P < 0.0001, *P < 0.05, ns – not significant.
Mentions: Further, we evaluated expression levels of MN1, SPARC, ST18 and DHRS3 by TaqMan gene expression assays in all samples already examined by 454 pyrosequencing. As can be seen in Figure 3, inv(16) patients had higher average levels of expression for all 4 genes in comparison to other non-inv(16) AML samples, but only in ST18 when compared to healthy donors.Figure 3

Bottom Line: Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression.We discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis.Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Studying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients. The aim of this study was to identify differentially methylated genes with potential impact on AML pathogenesis based on the correlation of methylation and expression data.

Methods: The primary method of studying DNA methylation changes was targeted bisulfite sequencing capturing approximately 84 megabases (Mb) of the genome in 14 diagnostic AML patients and a healthy donors' CD34+ pool. Subsequently, selected DNA methylation changes were confirmed by 454 bisulfite pyrosequencing in a larger cohort of samples. Furthermore, we addressed gene expression by microarray profiling and correlated methylation of regions adjacent to transcription start sites with expression of corresponding genes.

Results: Here, we report a novel hypomethylation pattern, specific to CBFB-MYH11 fusion resulting from inv(16) rearrangement that is associated with genes previously described as upregulated in inv(16) AML. We assume that this hypomethylation and corresponding overexpresion occurs in the genes whose function is important in inv(16) leukemogenesis. Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression. PBX3 has been recently shown to be a key interaction partner of HOX genes during leukemogenesis and we revealed higher incidence of relapses in PBX3-overexpressing patients.

Conclusions: We discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis. Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.

Show MeSH
Related in: MedlinePlus