Translational Research in Childhood Acute Lymphoblastic Leukemia (TRANSCALL)

Acute lymphoblastic leukaemia (ALL) is the most common malignancy in children. Major improvements in outcome have been achieved by a risk-adapted treatment tailored to the patients` individual needs by assessing molecular response to initial treatment. As a result today cure rates of approximately 80% are achieved. While this success is encouraging, leukaemia is still one of the leading causes of death in this age group, and in particular the intermediate risk (IR) group (the majority of cases) has still a relapse risk of >20%. Moreover, a considerable proportion of cured children suffer from significant toxic side and late effects. Therefore, it is paramount to further improve risk stratification by the identification of relapse-prone cases and to implement targeted therapies. While a growing number of candidate genes, identified through the application of genome-wide or candidate gene approaches, have been suggested as potentially useful biomarkers, so far, not a single one has been implemented in current clinical protocols. We have therefore put together a consortium of internationally well-renowned scientists with particular expertise in basic and translational research. We were among the first to report on the genomic aberrations of JAK, CRLF2, and IL7R leading to constitutive activation of the JAK-STAT pathway, thus paving the way for the application of targeted therapies with JAK inhibitors. As the leading childhood cancer competence centre in Austria, The CCRI has the ideal infrastructure for this collaboration, including up-front diagnostics, a biobank, and clinical and statistical data management. To evaluate the most robust and economic approach for the identification and quantification of clinically relevant genetic alterations, we plan, on the one hand, to use conventional tools such as FISH, MLPA, and PCR, on which the initial data were created; and on the other hand, to employ cutting-edge technologies, like next generation sequencing (NGS). NGS is the method of choice to evaluate subclonal heterogeneity and to assess the potential added value of identifying relapse-prone individuals already at initial diagnosis. Based on our previous research dealing with basic and translational aspects of childhood leukaemia, we are very well positioned to design these new methods (WP1) and analyze the expected 250 cases, consecutively enrolled in the current Austrian ALL-BFM 2009 clinical trial. This will be done for selected genomic aberrations (IKZF1, CRLF2, IL7R aberrations, JAK- STAT pathway mutations; NOTCH and RAS pathway mutations) occurring in B- and T cell precursor-ALL (WPs 2+3). We will also support WP 4 pharmacogenetics (TPMT genotyping) by providing the required material and clinical information. Thus, it can be expected that this common approach in biomarker validation in the EU will finally realize our visions of future integrated strategies where leukaemia patients are treated "online" according to their mutational and host genetic profiles.

Acute lymphoblastic leukemia (ALL), the most common malignancy in children and adolescents, can nowadays be cured in approximately 80%. This progress was made possible by the use of risk-adapted treatment protocols that are tailored to the patients individual needs. Yet there is still a >20% relapse incidence in the large group of non-high-risk cases, implying that relapsing patients currently cannot be identified at diagnosis or early during treatment. In the last years, a growing number of genomic alterations have been identified that may serve as potentially useful biomarkers, and some of them may also be considered as attractive drug targets. However, so far, none of the genomic alteration has been implemented as risk-stratifying parameter in current AIEOP/BFM protocols. This consortium identified a new predictive parameter for B cell precursor (BCP) ALL termed IKZF1plus (comprising deletions of IKZF1 plus at least an additional one from a set of other genomic alterations), which was able to distinguish a new, very poor prognostic group of cases among those with an intermediate minimal residual disease (MRD) response. As current AIEOP/BFM protocols appear largely ineffective for such leukemia patients, new experimental treatment approaches will be evaluated in our upcoming new trial AIEOP/BFM ALL 2017. In another project, we focused on the relapse-prone subset of patients with a BCP ALL characterized by a P2RY8-CRLF2 fusion. Comparing relapsing and non-relapsing cases, we showed that JAK/STAT, but also RTK/Ras pathway alterations are often subclonal at initial diagnosis and unstable at relapse. The P2RY8-CRLF2 fusion behaves similarly and therefore is likely to act only as a proliferative alteration, but not as a resistance-causing one. By contrast, genomic alterations affecting lymphoid development and cell cycle regulation always remained stable. Only IKZF1 alterations predominated in relapsing cases and in fact even increased at relapse. IKZF1s critical role for leukemia and relapse development is further corroborated by its specific transcriptional signature pointing at enhanced self-renewal, homing to the bone marrow niche, and drug resistance. Consequently, reverting aberrant IKRAOS signaling or its disparate programs emerges as an attractive addition to conventional treatment protocols. ALL with a high-hyperdiploid karyotype have also an increased relapse risk in AIEOP/BFM protocols. In-depth analysis of large cohorts of relapsing and non-relapsing cases indicated that RTK/Ras pathway alterations are very heterogeneous and unstable and that inactivating alterations in CREBBP increased at relapse and then commonly co-occurred with KRAS mutations suggesting that these two alterations might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone. None of these alterations, however, qualifies as a biomarker. Infrastructure and methods for the novel strategy for ALL diagnostics are set up and running.