Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia

Abstract

Background: Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is characterized by a gene-expression profile similar to that of BCR-ABL1-positive ALL, alterations of lymphoid transcription factor genes, and a poor outcome. The frequency and spectrum of genetic alterations in Ph-like ALL and its responsiveness to tyrosine kinase inhibition are undefined, especially in adolescents and adults.

Methods: We performed genomic profiling of 1725 patients with precursor B-cell ALL and detailed genomic analysis of 154 patients with Ph-like ALL. We examined the functional effects of fusion proteins and the efficacy of tyrosine kinase inhibitors in mouse pre-B cells and xenografts of human Ph-like ALL.

Results: Ph-like ALL increased in frequency from 10% among children with standard-risk ALL to 27% among young adults with ALL and was associated with a poor outcome. Kinase-activating alterations were identified in 91% of patients with Ph-like ALL; rearrangements involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB, PTK2B, TSLP, or TYK2 and sequence mutations involving FLT3, IL7R, or SH2B3 were most common. Expression of ABL1, ABL2, CSF1R, JAK2, and PDGFRB fusions resulted in cytokine-independent proliferation and activation of phosphorylated STAT5. Cell lines and human leukemic cells expressing ABL1, ABL2, CSF1R, and PDGFRB fusions were sensitive in vitro to dasatinib, EPOR and JAK2 rearrangements were sensitive to ruxolitinib, and the ETV6-NTRK3 fusion was sensitive to crizotinib.

Conclusions: Ph-like ALL was found to be characterized by a range of genomic alterations that activate a limited number of signaling pathways, all of which may be amenable to inhibition with approved tyrosine kinase inhibitors. Trials identifying Ph-like ALL are needed to assess whether adding tyrosine kinase inhibitors to current therapy will improve the survival of patients with this type of leukemia. (Funded by the American Lebanese Syrian Associated Charities and others.).

Figure 1. Kaplan–Meier Estimates of Event-free and Overall Survival among Patients with Philadelphia Chromosome–like Acute Lymphoblastic Leukemia (Ph-like ALL)

Panel A shows the median (±SD) rates of event-free survival for young adults, adolescents, and high-risk children with Ph-like ALL (24.1±10.5%, 41.0±7.4%, and 58.2±5.3%, respectively). Panel B shows rates of overall survival in the three age groups (25.8±9.9%, 65.8±7.1%, and 72.8±4.8%, respectively).

Figure 2. Recurring Kinase Alterations in Ph-like ALL

Data are shown for 154 patients with Ph-like ALL who underwent detailed genomic analysis, including transcriptome sequencing (RNA-seq), whole-genome sequencing (WGS), whole-exome sequencing (WES), and reverse-transcriptase polymerase chain reaction (RT-PCR). The cohort is divided into patients with ABL-class fusions (ABL1, ABL2, CSF1R, PDGFRB) responsive to dasatinib, EPOR or JAK2 rearrangements, CRLF2 rearrangements, other JAK–STAT–activating mutations (IL7R, FLT3, SH2B3, JAK1, JAK3, TYK2, IL2RB, and TSLP), other kinase fusions (miscellaneous group, including NTRK3 and DGKH), alterations in the Ras pathway (KRAS, NRAS, PTPN11, NF1, and BRAF), and no kinase alteration. For details of specific alterations, see Tables S9 and S12 in Supplementary Appendix 1 and Table S20 in Supplementary Appendix 3.

Figure 3. Response to Tyrosine Kinase Inhibitors

Panel A shows the proliferation of interleukin-7–dependent primary Arf^−/− pre-B cells expressing the dominant negative Ikaros isoform (Ik6) with empty vector, RCSD1–ABL1, RCSD1–ABL2, SSBP2–CSF1R, or PAX5–JAK2 in the absence of cytokine. Panel B shows the growth of Arf^−/− pre-B cells in increasing concentrations of dasatinib. Panel C shows constitutive phosphorylation of STAT5 and CRKL (pSTAT5 and pCRKL, respectively). Cells expressing ABL2, CSF1R, and JAK2 fusions have enhanced STAT5 activation, which is inhibited by dasatinib in RCSD1–ABL2 and SSBP2–CSF1R and by ruxolitinib in PAX5–JAK2.