The pathobiology of pediatric B-cell precursor acute lymphoblastic leukemia

Pediatric acute lymphoblastic leukemia (ALL) is a heterogeneous disease, caused by the malignant transformation of either T-cell (~15% of the cases) or B-cell progenitors (~85% of the cases). To further improve the survival of children with ALL, new targeted treatment strategies are warranted. Therefore, it is essential to gain insight in the pathobiology of childhood ALL. The scope of this thesis is on pediatric B-cell precursor ALL (BCP-ALL). We studied: 1) the occurrence of tyrosine kinase fusion genes (i.e. ABL and JAK class) and JAK2 mutations in pediatric BCP-ALL cases; 2) the efficacy of JAK inhibitors in JAK2 aberrant (translocations and point mutations) leukemic cells; 3) the potential of STAP1 as therapeutic target for DUX4-rearranged ALL cases; 4) the association between copy number aberrations in B-cell development genes (e.g. IKZF1, PAX5), long‑term prognosis, and cellular drug resistance; 5) the supportive properties and gene expression profiles of mesenchymal stromal cells derived from pediatric BCP-ALL patients and healthy pediatric donors. Our results show efficacy of new precision medicines, i.e. JAK inhibitors, but we also identified important limitations that should be overcome. Moreover, we show that the genetic context matters and that the effect of anti-cancer drugs should be studied in the proper genetic context. Lastly, we show that mesenchymal stromal cells are not actively involved in BCP-ALL leukemogenesis. Instead leukemic cells actively modulate signaling pathways in MSCs to support BCP-ALL cell survival. Targeting this interaction between BCP‑ALL cells and MSCs might be an attractive alternative treatment strategy

Copy number alterations in B-cell development genes, drug resistance, and clinical outcome in pediatric B-cell precursor acute lymphoblastic leukemia

Pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is associated with a high frequency of copy number alterations (CNAs) in IKZF1, EBF1, PAX5, CDKN2A/B, RB1, BTG1, ETV6, and/or the PAR1 region (henceforth: B-cell development genes). We aimed to gain insight in the association between CNAs in these genes, clinical outcome parameters, and cellular drug resistance. 71% of newly diagnosed pediatric BCP-ALL cases harbored one or more CNAs in these B-cell development genes. The distribution and clinical relevance of these CNAs was highly subtype-dependent. In the DCOG-ALL10 cohort, only loss of IKZF1 associated as single marker with unfavorable outcome parameters and cellular drug resistance. Prednisolone resistance was observed in IKZF1-deleted primary high hyperdiploid cells (~1500-fold), while thiopurine resistance was detected in IKZF1-deleted primary BCR-ABL1-like and non-BCR-ABL1-like B-other cells (~2.7-fold). The previously described risk stratification classifiers, i.e. IKZF1plus and integrated cytogenetic and CNA classification, both predicted unfavorable outcome in the DCOG-ALL10 cohort, and associated with ex vivo drug cellular resistance to thiopurines, or L-asparaginase and thiopurines, respectively. This resistance could be attributed to overrepresentation of BCR-ABL1-like cases in these risk groups. Taken together, our data indicate that the prognostic value of CNAs in B-cell development genes is linked to subtype-related drug responses

High STAP1 expression in DUX4-rearranged cases is not suitable as therapeutic target in pediatric B-cell precursor acute lymphoblastic leukemia

textabstractApproximately 25% of the pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cases are genetically unclassified. More thorough elucidation of the pathobiology of these genetically unclassified ('B-other') cases may identify novel treatment options. We analyzed gene expression profiles of 572 pediatric BCP-ALL cases, representing all major ALL subtypes. High expression of STAP1, an adaptor protein downstream of the B-cell receptor (BCR), was identified in BCR-ABL1-like and non-BCR-ABL1-like B-other cases. Limma analysis revealed an association between high expression of STAP1 and BCR signaling genes. However, STAP1 expression and pre-BCR signaling were not causally related: cytoplasmic Igμ levels were not abnormal in cases with high levels of STAP1 and stimulation of pre-BCR signaling did not induce STAP1 expression. To elucidate the role of STAP1 in BCP-ALL survival, expression was silenced in two human BCP-ALL cell lines. Knockdown of STAP1 did not reduce the proliferation rate or viability of these cells, suggesting that STAP1 is not a likely candidate for precision medicines. Moreover, high expression of STAP1 was not predictive for an unfavorable prognosis of BCR-ABL1-like and non-BCR-ABL1-like B-other cases. Remarkably, DUX4-rearrangements and intragenic ERG deletions, were enriched in cases harboring high expression of STAP1