Comprehensive characterization of 11q amplicons in AML/MDS

The cytogenetic and molecular genetic techniques are already routinely used for the classification of acute leukaemias, assessment of the patient`s prognosis, as well as for the selection of disease specific therapeutic approaches. A further step forward in this field has been brought about by the microarray technology. It has led to the detection of new biological and clinical subtypes of leukaemia characterized by specific expression profile and thus additionally guided treatment decisions. However, we are still far from a good understanding of all the mechanisms triggering and influencing the progression of the disease that would, nevertheless, be a crucial prerequisite for the selection of successful treatment strategy in the patients. In this respect, each recurring aberration in leukaemia should be studied in detail since it might bring more understanding in the field. A growing number of publications support the evidence that the amplification within chromosome arm 11q involving the MLL gene is an important negative prognostic factor in acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). In our previous study we uncovered that this amplicon studied in 13 AML/MDS patients is rather complex. In addition to a maximally 700kb sequence around the MLL gene, the sequences from two additional 11q regions, namely 11q13.5 and 11q23-24, are frequently co-amplified in 8/13 (60%) and 10/11 (90%) patients respectively [1]. Both regions harbour a number of genes with possible oncogenic potential. Through numerous collaborations of one of the applicants, Dr. Christa Fonatsch, who is the lead participant of the Work Package 11-CYTOGENETICS within the European Leukaemia Net, we have collected in the recent year a number of additional AML/MDS samples that were not included in our initial study. Thus, we currently hold a collection of 41 AML/MDS patients identified on the basis of MLL gene amplification, which is probably one of the largest collections of patients with 11q amplification world-wide and we expect even to collect further 10-15 samples. Therefore, we propose here to continue characterizing 11q-amplicons in AML/MDS with the ultimate goal to identify target genes with biological and clinical significance for this and possibly also other tumour entities. By employing the chromosome 11 tiling path array-CGH to a large cohort of AML/MDS patients we expect to further define the borders of amplicons identified in our previous study, as well as to identify possible new regions of 11q amplification. We will then correlate the amplification status of the genes contained in the defined regions with their expression status in order to identify candidate genes that play a role in leukemogenesis. For expression studies we propose to use Affymetrix GeneChip technology and/or real time RT-PCR based analysis. Possible implications of expression deregulation of particular genes for the leukemogenesis and/or therapy selection will be evaluated.

The cytogenetic and molecular genetic techniques are already routinely used for the classification of acute leukaemias, assessment of the patient`s prognosis, as well as for the selection of disease specific therapeutic approaches. A further step forward in this field has been brought about by the microarray technology. It has led to the detection of new biological and clinical subtypes of leukaemia characterized by specific expression profile and thus additionally guided treatment decisions. However, we are still far from a good understanding of all the mechanisms triggering and influencing the progression of the disease that would, nevertheless, be a crucial prerequisite for the selection of successful treatment strategy in the patients. In this respect, each recurring aberration in leukaemia should be studied in detail since it might bring more understanding in the field. A growing number of publications support the evidence that the amplification within chromosome arm 11q involving the MLL gene is an important negative prognostic factor in acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). In our previous study we uncovered that this amplicon studied in 13 AML/MDS patients is rather complex. In addition to a maximally 700kb sequence around the MLL gene, the sequences from two additional 11q regions, namely 11q13.5 and 11q23-24, are frequently co-amplified in 8/13 (60%) and 10/11 (90%) patients respectively [1]. Both regions harbour a number of genes with possible oncogenic potential. Through numerous collaborations of one of the applicants, Dr. Christa Fonatsch, who is the lead participant of the Work Package 11-CYTOGENETICS within the European Leukaemia Net, we have collected in the recent year a number of additional AML/MDS samples that were not included in our initial study. Thus, we currently hold a collection of 41 AML/MDS patients identified on the basis of MLL gene amplification, which is probably one of the largest collections of patients with 11q amplification world-wide and we expect even to collect further 10-15 samples. Therefore, we propose here to continue characterizing 11q-amplicons in AML/MDS with the ultimate goal to identify target genes with biological and clinical significance for this and possibly also other tumour entities. By employing the chromosome 11 tiling path array-CGH to a large cohort of AML/MDS patients we expect to further define the borders of amplicons identified in our previous study, as well as to identify possible new regions of 11q amplification. We will then correlate the amplification status of the genes contained in the defined regions with their expression status in order to identify candidate genes that play a role in leukemogenesis. For expression studies we propose to use Affymetrix GeneChip technology and/or real time RT-PCR based analysis. Possible implications of expression deregulation of particular genes for the leukemogenesis and/or therapy selection will be evaluated.