Despite the impressive success in cure rates of approximately 80%, leukaemia is still one of the leading causes of death in childhood and adolescence. Moreover, a substantial proportion of surviving children experiences severe treatment-related side and late effects. Therefore, it is of paramount importance to further improve risk stratification, identify relapse-prone cases and to implement targeted therapies. To do this, we explore genome-wide alterations and study the molecular and cellular mechanisms that contribute to leukaemia development, drug resistance and relapses.

Childhood acute lymphoblastic Leukaemia (ALL) results from the acquisition of genetic alterations in a stem/progenitor cell population that undergoes complex processes of diversification and selection. We use a variety of genome-wide screening approaches, including the latest cutting-edge technologies, to identify copy number and sequence alterations that i) are likely to contribute to leukaemia emergence, ii) cause resistance and relapse and iii) qualify as biomarkers. The molecular mechanisms by which various oncogenic proteins exert their function as well as the respective effects are being investigated in various in vitro and in vivo models. 

Current projects include the following:

Clonal heterogeneity and evolution of ALL

Acute lymphoblastic leukaemia (ALL) is the prevalent cancer in children and adolescents and a heterogeneous disease entity with only half of it being genetically characterized by either a recurrent chromosomal translocation or a hyperdiploid karyotype. Additionally, and contrary to the previously notion, the individual leukaemia comprises various cell populations, which differ with regard to their patterns of secondary alterations whereby the initiating or founder mutation represents sometimes the only common one. Relapses usually evolve from small subclones that are present at initial diagnosis and their selection during chemotherapy suggests that they harbour mutations likely to confer drug resistance (Konrad et al. 2003). Therefore, these alterations or the founder mutation, if in fact still required for disease maintenance, represent ideal targets for novel treatment strategies. We have recently addressed these issues in three major subgroups of childhood ALL carrying ETV6-RUNX1 (ER) (Kuster et al. 2011), P2RY8-CRLF2 (Morak et al. 2012) or a high hyperdiploid (HD) karyotype (Inthal et al. 2012). Our data suggest that the majority of ER-positive and HD ALL relapses evolve from a clone that is ancestral to both the relapse and the initial leukaemia and that particular relapse-associated genetic alterations may confer resistance to glucocorticoids in both ALL subgroups, albeit with different underlying mechanisms. Moreover, the P2RY8-CRLF2 fusion does not seem to be an early or crucial mutation for relapse emergence because initially small clones do not progress and relapses frequently do not harbour the fusion present at initial diagnosis. Current studies, also employing NGS, are aiming to complement and extend these initial findings and to identify the respective founder mutation in the latter ALL subgroup.

Molecular and functional consequences of ETV6-RUNX1 expression in leukaemia 
While the role of the ETV6-RUNX1 fusion gene in leukaemia initiation is well established, its function in leukaemia is still poorly understood. We recently discovered by an shRNA approach that the expression of the chimeric transcription factor is required for survival, proliferation and maintenance of the malignant phenotype, implying that the leukaemia cell is “addicted” to this oncogene (Fuka et al. 2012; Diakos et al. 2007). These cellular functions concur with a heavily deranged transcriptional program that appears mainly derived from ETV6-RUNX1-mediated gene repression (Fuka et al. 2011). Among the perturbed specific functions and signaling pathways, we identified the mitotic checkpoint (Krapf et al. 2010), the p53 pathway (Kaindl et al. 2013) and the critical pro-survival PI3K/Akt pathway. These data therefore suggest that ETV6-RUNX1 itself, or its downstream pathways, would represent perfect drug targets for this particular subtype of leukaemia because the clonal variegation of secondary aberrations need not be taken into account. Further research includes the in-depth analysis of particular pathways and interactions and the mode of downstream target regulation by ETV6-RUNX1.

Translational research into development and validation of biomarkers

Focusing primarily on the intermediate risk group of childhood ALL, where the vast majority of relapses occur, we are testing the most promising genetic alterations for their qualification as useful biomarkers in current treatment protocols.

Selected Articles

Kuster L, Grausenburger R, Fuka G, Kaindl U, Krapf G, Inthal A, Mann G, Kauer M, Rainer J, Kofler R, Hall A, Metzler M, Meyer LH, Meyer C, Harbott J, Marschalek R, Strehl S, Haas OA, Panzer-Grümayer R. (2011) ETV6/RUNX1-positive relapses evolve from an ancestral clone and frequently acquire deletions of genes implicated in glucocorticoid signaling. Blood. 117(9):2658-67.

Morak M, Attarbaschi A, Fischer S, Nassimbeni C, Grausenburger R, Bastelberger S, Krentz S, Cario G, Kasper D, Schmitt K, Russell LJ, Pötschger U, Stanulla M, Eckert C, Mann G, Haas OA, Panzer-Grümayer R. (2012) Small sizes and indolent evolutionary dynamics challenge the potential role of P2RY8-CRLF2-harboring clones as main relapse-driving force in childhood ALL. Blood 2012 Dec 20;120(26):5134-42. doi: 10.1182/blood-2012-07-443218. Epub 2012 Oct 22. Erratum in: Blood. 2013 Aug 15;122(7):1328.

Inthal A, Zeitlhofer P, Zeginigg M, Morak M, Grausenburger R, Fronkova E, Fahrner B, Mann G, Haas OA, Panzer-Grümayer R.  (2012) CREBBP HAT domain mutations prevail in relapse cases of high hyperdiploid childhood acute lymphoblastic leukemia. Leukemia. doi:10.1038/leu.2012.60 

Fuka G, Kauer M, Kofler R, Haas OA, Panzer-Grümayer R. (2011) The leukemia-specific fusion gene ETV6/RUNX1 perturbs distinct key biological functions primarily by gene repression. PLoS One. 6(10):e26348

Fuka G, Kantner HP, Grausenburger R, Inthal A, Bauer E, Krapf G, Kaindl U, Kauer M, Dworzak MN, Stoiber D, Haas OA, Panzer-Grümayer R. (2012) Silencing of ETV6/RUNX1 abrogates PI3K/AKT/mTOR signaling and impairs reconstitution of leukemia in xenografts. Leukemia. doi: 10.1038/leu.2011.322.