The online version of this article (doi:10.1186/s13045-014-0094-0) contains supplementary material, which is available to authorized users.
The authors declare that they have no competing interests.
KSK performed majority of the sample processing and analyses and wrote the manuscript. KR was responsible for the qPCR analyses, and KF performed the statistical analyses. EM defined the crucial characteristics of the sorted subpopulations of the healthy BM cells and designed all of the FACS sorting experiments. MZ was responsible for the molecular characterization of the AML patients. HD and JT revised the manuscript and provided critical intellectual feedback. JaS was responsible for the clinical management of the patients. As a senior author, JuS coordinated all of the experiments, revised the manuscript and is the principal investigator of the whole study. CMZ, MvdHE and MF contributed by providing datasets and performing the gene expression profiling analyses of the replication sets. All authors read and approved the final manuscript.
Although distinct patterns of homeobox (HOX) gene expression have been described in defined cytogenetic and molecular subsets of patients with acute myeloid leukemia (AML), it is unknown whether these patterns are the direct result of transcriptional alterations or rather represent the differentiation stage of the leukemic cell.
To address this question, we used qPCR to analyze mRNA expression of HOXA and HOXB genes in bone marrow (BM) samples of 46 patients with AML and sorted subpopulations of healthy BM cells. These various stages of myeloid differentiation represent matched counterparts of morphological subgroups of AML. To further study the transcriptional alterations of HOX genes in hematopoiesis, we also analyzed gene expression of epigenetic modifiers in the subpopluations of healthy BM and leukemic cells.
Unsupervised hierarchical clustering divided the AMLs into five clusters characterized by the presence of prevalent molecular genetic aberrations. Notably, the impact of genotype on HOX gene expression was significantly more pronounced than that of the differentiation stage of the blasts. This driving role of molecular aberrations was best exemplified by the repressive effect of the PML-RARa fusion gene on HOX gene expression, regardless of the presence of the FLT3/ITD mutation. Furthermore, HOX gene expression was positively correlated with mRNA levels of histone demethylases (JMJD3 and UTX) and negatively correlated with gene expression of DNA methyltranferases. No such relationships were observed in subpopulations of healthy BM cells.
Our results demonstrate that specific molecular genetic aberrations, rather than differentiation per se, underlie the observed differences in HOX gene expression in AML. Moreover, the observed correlations between epigenetic modifiers and HOX ex pression that are specific to malignant hematopoiesis, suggest their potential causal relationships.
Additional file 1: Table S1.: Patients’ characteristics. (DOC 44 KB)13045_2014_94_MOESM1_ESM.doc
Additional file 2: Figure S1.: mRNA expression of particular HOXA and HOXB genes in subpopulations of healthy BM. (DOC 92 KB)13045_2014_94_MOESM2_ESM.doc
Additional file 3: Figure S2.: Correlation of HOXA, HOXB and chromatin modifier gene expression in subpopulations of healthy BM. (DOC 58 KB)13045_2014_94_MOESM3_ESM.doc
Additional file 4: Figure S3.: mRNA expression of particular HOXA and HOXB genes in morphological subgroups of AML patients. (DOC 168 KB)13045_2014_94_MOESM4_ESM.doc
Additional file 5: Figure S4.: mRNA expression of particular HOXA and HOXB genes in subgroups of AML patients defined according to molecular genetics. (DOC 152 KB)13045_2014_94_MOESM5_ESM.doc
Additional file 6: Figure S5.: Unsupervised HCA of AML patients based on the epxression pattern of HOX genes. (DOC 59 KB)13045_2014_94_MOESM6_ESM.doc
Additional file 7: Figure S6.: Comparison of individual HOX gene expression of SR and HR groups. (DOC 105 KB)13045_2014_94_MOESM7_ESM.doc
Additional file 8: Figure S7.: Comparison of HOX gene expression pattern between AML M5 patients and sorted subpopulation of healthy BM (A. AML M5a vs. ID = M3; B. AML M5b vs. ID = M4). (DOC 466 KB)13045_2014_94_MOESM8_ESM.doc
Additional file 9: Figure S8.: Correlation of HOX and chromatin modifier gene expression in AML patients. (DOC 68 KB)13045_2014_94_MOESM9_ESM.doc
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- Homeobox gene expression in acute myeloid leukemia is linked to typical underlying molecular aberrations
Karolina Skvarova Kramarzova
Harry A Drabkin
Marry M van den Heuvel-Eibrink
- BioMed Central
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