Tyrosine kinase inhibitor resistance in de novo BCR::ABL1–positive BCP-ALL beyond kinase domain mutations

A better understanding of ABL1 kinase domain mutation–independent causes of tyrosine kinase inhibitor (TKI) resistance is needed for BCR::ABL1–positive B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Although TKIs have dramatically improved outcomes, a subset of patients still experiences relapsed or refractory disease. We aimed to identify potential biomarkers of intrinsic TKI resistance at diagnosis in samples from 32 pediatric and 19 adult patients with BCR::ABL1–positive BCP-ALL. Reduced ex vivo imatinib sensitivity was observed in cells derived from newly diagnosed patients who relapsed after combined TKI and chemotherapy treatment compared with cells derived from patients who remained in continuous complete remission. We observed that ex vivo imatinib resistance was inversely correlated with the amount of (phosphorylated) BCR::ABL1/ABL1 protein present in samples that were taken at diagnosis without prior TKI exposure. This suggests an intrinsic cause of TKI resistance that is independent of functional BCR::ABL1 signaling. Simultaneous deletions of IKZF1 and CDKN2A/B and/or PAX5 (IKZF1plus), as well as deletions of PAX5 alone, were related to ex vivo imatinib resistance. In addition, somatic lesions involving ZEB2, SETD2, SH2B3, and CRLF2 were associated with reduced ex vivo imatinib sensitivity. Our data suggest that the poor prognostic value of IKZF1(plus) deletions is linked to intrinsic mechanisms of TKI resistance other than ABL1 kinase domain mutations in newly diagnosed pediatric and adult BCR::ABL1–positive BCP-ALL.</p

ABL family genes in pediatric acute lymphoblastic leukemia: Molecular determinants of tyrosine kinase inhibitor response

BCR::ABL1-positive and ABL-class acute lymphoblastic leukemia (ALL) together account for approximately 5% of pediatric and 25% of adult ALL cases. ABL-class ALL is characterized by tyrosine kinases ABL1, ABL2, PDGFRB, or CSF1R fused to various partner genes, excluding the sentinel BCR::ABL1 fusion. ABL-class ALL shares several characteristics with BCR::ABL1-positive ALL, including a similar gene expression profile, poor response to chemotherapy only, and sensitivity to tyrosine kinase inhibitors. Some patients develop tyrosine kinase inhibitor resistance through ABL1 kinase domain mutations, leading to relapse or refractory disease, but not all relapsed or refractory cases are associated with these mutations. This suggests the existence of other intrinsic tyrosine kinase inhibitor resistance mechanisms that are yet to be elucidated. For ABL-class ALL, tyrosine kinase inhibitors have been introduced more recently hence there is limited knowledge on determinants of sensitivity to tyrosine kinase inhibitors. We aimed to enhance our understanding of the determinants of tyrosine kinase inhibitors sensitivity in BCR::ABL1-positive and ABL-class ALL. Ex vivo analysis of 32 pediatric and 19 adult BCR::ABL1-positive ALL samples from diagnosis revealed variable responses to imatinib, which correlated with responses to next-generation tyrosine kinase inhibitors, dasatinib and bosutinib. Notably, diagnostic samples from patients who relapsed after imatinib treatment exhibited greater ex vivo imatinib-resistance. Reduced BCR::ABL1 protein expression and phosphorylation were associated with intrinsic tyrosine kinase inhibitor resistance, indicating decreased dependence on BCR::ABL1 signaling. Imatinib resistance was also linked to deletions or mutations in B-cell development genes IKZF1 and PAX5. Similarly, ex vivo analysis of 16 diagnostic or relapsed pediatric ABL-class ALL samples showed varying sensitivity to imatinib, dasatinib, and bosutinib. The specific tyrosine kinase gene involved in ABL-class ALL determined tyrosine kinase inhibitor sensitivity. ABL1-fused ALL samples exhibited similar sensitivity to all three tyrosine kinase inhibitors, while PDGFRB-fused ALL samples displayed reduced sensitivity to dasatinib and bosutinib. Unlike in BCR::ABL1-positive ALL, no association was found between imatinib sensitivity and IKZF1 or PAX5 deletions, although these deletions were common in ABL-class ALL. Besides evaluating tyrosine kinase inhibitor sensitivity, our study aimed to optimize measurable residual disease monitoring. We compared monitoring using the genomic breakpoint of the ABL-class fusion gene with the conventional method based on the clonality of leukemia-specific rearrangements of target genes immunoglobulin and T-cell receptor. The conventional method faces limitations, as approximately 5% of patients lack suitable targets, and ongoing rearrangements or subclonal presence of the target can render the method unreliable. We found an 89% correlation between the two methods. The fusion gene method measured MRD in three patients lacking conventional targets and monitored the full leukemic clone in one patient for whom part of the leukemic cells lacked the conventional targets that were selected at diagnosis. Lastly, using the oncogenic fusion gene, we discovered a patient with multi-lineage presentation rather than ALL with implications for diagnosis and treatment. Overall, our research contributes to a deeper understanding of the biology and treatment response of ABL-family ALL, emphasizing the importance of exploring alternative treatment options and refining monitoring strategies to improve patient outcomes

Tyrosine kinase inhibitor resistance in de novo BCR::ABL1–positive BCP-ALL beyond kinase domain mutations

A better understanding of ABL1 kinase domain mutation–independent causes of tyrosine kinase inhibitor (TKI) resistance is needed for BCR::ABL1–positive B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Although TKIs have dramatically improved outcomes, a subset of patients still experiences relapsed or refractory disease. We aimed to identify potential biomarkers of intrinsic TKI resistance at diagnosis in samples from 32 pediatric and 19 adult patients with BCR::ABL1–positive BCP-ALL. Reduced ex vivo imatinib sensitivity was observed in cells derived from newly diagnosed patients who relapsed after combined TKI and chemotherapy treatment compared with cells derived from patients who remained in continuous complete remission. We observed that ex vivo imatinib resistance was inversely correlated with the amount of (phosphorylated) BCR::ABL1/ABL1 protein present in samples that were taken at diagnosis without prior TKI exposure. This suggests an intrinsic cause of TKI resistance that is independent of functional BCR::ABL1 signaling. Simultaneous deletions of IKZF1 and CDKN2A/B and/or PAX5 (IKZF1plus), as well as deletions of PAX5 alone, were related to ex vivo imatinib resistance. In addition, somatic lesions involving ZEB2, SETD2, SH2B3, and CRLF2 were associated with reduced ex vivo imatinib sensitivity. Our data suggest that the poor prognostic value of IKZF1(plus) deletions is linked to intrinsic mechanisms of TKI resistance other than ABL1 kinase domain mutations in newly diagnosed pediatric and adult BCR::ABL1–positive BCP-ALL.</p

Tyrosine kinase inhibitor response of ABL-class acute lymphoblastic leukemia:the role of kinase type and SH3 domain

Acute lymphoblastic leukemia (ALL) with fusions of ABL-class tyrosine kinase genes other than BCR::ABL1 occurs in ∼3% of children with ALL. The tyrosine kinase genes involved in this BCR::ABL1-like (Ph-like) subtype include ABL1, PDGFRB, ABL2, and CSF1R, each of which has up to 10 described partner genes. ABL-class ALL resembles BCR::ABL1-positive ALL with a similar gene expression profile, poor response to chemotherapy, and sensitivity to tyrosine kinase inhibitors (TKIs). There is a lack of comprehensive data regarding TKI sensitivity in the heterogeneous group of ABL-class ALL. We observed variability in TKI sensitivity within and among each ABL-class tyrosine kinase gene subgroup. We showed that ALL samples with fusions for any of the 4 tyrosine kinase genes were relatively sensitive to imatinib. In contrast, the PDGFRB-fused ALL samples were less sensitive to dasatinib and bosutinib. Variation in ex vivo TKI response within the subset of samples with the same ABL-class tyrosine kinase gene was not associated with the ALL immunophenotype, 5′ fusion partner, presence or absence of Src-homology-2/3 domains, or deletions of IKZF1, PAX5, or CDKN2A/B. In conclusion, the tyrosine kinase gene involved in ABL-class ALL is the main determinant of TKI sensitivity and relevant for specific TKI selection.</p

Tyrosine kinase inhibitor response of ABL-class acute lymphoblastic leukemia:the role of kinase type and SH3 domain

Acute lymphoblastic leukemia (ALL) with fusions of ABL-class tyrosine kinase genes other than BCR::ABL1 occurs in ∼3% of children with ALL. The tyrosine kinase genes involved in this BCR::ABL1-like (Ph-like) subtype include ABL1, PDGFRB, ABL2, and CSF1R, each of which has up to 10 described partner genes. ABL-class ALL resembles BCR::ABL1-positive ALL with a similar gene expression profile, poor response to chemotherapy, and sensitivity to tyrosine kinase inhibitors (TKIs). There is a lack of comprehensive data regarding TKI sensitivity in the heterogeneous group of ABL-class ALL. We observed variability in TKI sensitivity within and among each ABL-class tyrosine kinase gene subgroup. We showed that ALL samples with fusions for any of the 4 tyrosine kinase genes were relatively sensitive to imatinib. In contrast, the PDGFRB-fused ALL samples were less sensitive to dasatinib and bosutinib. Variation in ex vivo TKI response within the subset of samples with the same ABL-class tyrosine kinase gene was not associated with the ALL immunophenotype, 5′ fusion partner, presence or absence of Src-homology-2/3 domains, or deletions of IKZF1, PAX5, or CDKN2A/B. In conclusion, the tyrosine kinase gene involved in ABL-class ALL is the main determinant of TKI sensitivity and relevant for specific TKI selection.</p

Characterisation of an Adult Zebrafish Model for <i>SDHB</i>-Associated Phaeochromocytomas and Paragangliomas

Phaeochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumours arising from chromaffin cells. Pathogenic variants in the gene succinate dehydrogenase subunit B (SDHB) are associated with malignancy and poor prognosis. When metastases arise, limited treatment options are available. The pathomechanism of SDHB-associated PPGL remains largely unknown, and the lack of suitable models hinders therapy development. Germline heterozygous SDHB pathogenic variants predispose to developing PPGLs with a life-long penetrance of around 50%. To mimic the human disease phenotype, we characterised adult heterozygous sdhb mutant zebrafish as a potential model to study SDHB-related PPGLs. Adult sdhb mutant zebrafish did not develop an obvious tumour phenotype and were anatomically and histologically like their wild-type siblings. However, sdhb mutants showed significantly increased succinate levels, a major hallmark of SDHB-related PPGLs. While basal activity was increased during day periods in mutants, mitochondrial complex activity and catecholamine metabolite levels were not significantly different. In conclusion, we characterised an adult in vivo zebrafish model, genetically resembling human carriers. Adult heterozygous sdhb mutants mimicked their human counterparts, showing systemic elevation of succinate levels despite the absence of a tumour phenotype. This model forms a promising basis for developing a full tumour phenotype and gaining knowledge of the pathomechanism behind SDHB-related PPGLs