B6: Genomic and signalomic characterization of pre- and post-therapy ALL modeled in vivo
Despite the great success in treating pediatric acute lymphoblastic leukemia (ALL) with elaborated risk-stratifying protocols, resulting in cure rates of more than 80%, 20% of the patients will relapse resulting mostly in poor outcome. The majority of relapses occurs in the standard-risk group. Over the last years, molecular and functional analyses of ALL have identified mechanisms and characteristics of leukemia biol-ogy such as activating mutations, dysregulated pathways, and clonal selection at relapse opening the ave-nue for pathway-directed therapies. However, translational studies in patient-derived ALL are limited by the restricted availability of cells and the inability to culture primary ALL cells in vitro. Thus, preclinical xenograft models, using primary patient-derived ALL cells transplanted into immunodeficient mice, are used to over-come these restrictions. We have established a NOD/SCID/hu-ALL xenograft model for pediatric ALL and have built up a large biobank of ALL xenografts derived from more than 130 individual pediatric ALL pa-tients. In this model, we have identified a specific gene expression signature, which characterizes ALL sam-ples with rapid engraftment, i.e., a short-time to leukemia development (TTLshort) and poor prognosis. This TTLshort phenotype is characterized by a hyper-activated mTOR signaling pathway and in vivo treatment using combinations of mTOR-directed therapies with chemotherapy was highly effective. By genomic profiling, we have characterized mutation frequencies upon repeated transplantation and diagnostic ALL samples and obtained miRNA signatures. Using candidate genes of the TTL signature, we identified novel targets by RNA interference and obtained first evidence for an anti-CD70-directed immunotherapy as novel treatment strate-gy in B-cell precursor ALL. Lastly, we identified defective apoptosis signaling as an additional feature asso-ciated with the TTL signature which could be restored by Smac-mimetics such as BV6. Taking further ad-vantage of this xenograft model, we will perform an in-depth analysis with a particular focus on genomic alterations, functional status and clonal evolution of ALL between diagnosis and relapse. To this aim, we will characterize genomic signatures in primary ALL and at the time of relapse occurring after conventional short-term treatment in the NOD/SCID/hu-ALL system. This will include clonal analysis to address issues of heter-ogeneity and drug resistance of individual clones. Furthermore, this analysis will be extended to paired samples from patients analyzed at diagnosis and relapse. The genomic analysis will be complemented by multicolor-phosphoflow and phosphoproteomic analyses of individual leukemia cells. To this aim, we will also make use of the newly established CyTOF technology, allowing multi-marker analysis of surface and cytoplasmic molecules at the single cell level. Furthermore, we will analyze sensitivity and resistance for targeting of specific pathways involved in differentiation, survival and apoptosis such as PI3K, mTOR, pre-B-cell receptor, B-cell receptor, IL7 receptor, Bcl-2 and IAP. This approach can also be used for novel com-pound screening in the appropriate setting. Taken together, given the fact that we have established one of the largest cohorts of pediatric ALL in the NOD/SCID/hu-ALL model, we expect that our studies will not only give a more detailed insight into leukemia biology and possible prognostic markers, but will also help iden-tifying rational targets for novel therapeutic interventions.
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