Kinome Reprogramming of G2/M Kinases and Repression of MYCN Contribute to Superior Efficacy of Lorlatinib in ALK-Driven Neuroblastoma

Mutations in the tyrosine kinase domain of the anaplastic lymphoma kinase (ALK) oncogene in neuroblastoma occur most frequently at one of three hotspot amino acid residues, with the F1174* and F1245* variants conferring de novo resistance to first- and second-generation ALK inhibitors, including crizotinib and ceritinib. Lorlatinib, a third-generation ALK/ROS1 inhibitor, overcomes de novo resistance and induces complete and sustained tumor regressions in patient-derived xenograft models unresponsive to crizotinib. Lorlatinib has now completed phase 1 testing in children and adults with relapsed/refractory ALK-driven neuroblastoma and entered pivotal phase 3 testing within the Children's Oncology Group. To define mechanisms underlying the superior activity of lorlatinib, we utilized a chemical proteomics approach to quantitatively measure functional kinome dynamics in response to lorlatinib and crizotinib in clinically relevant ALK-driven neuroblastoma patient-derived xenograft models. Lorlatinib was a markedly more potent inhibitor of ALK and preferentially downregulated several kinases implicated in G2/M cell-cycle transition compared with crizotinib. Lorlatinib treatment also led to the repression of MYCN expression and its occupancy at promoters of the same G2/M kinases. These data provide mechanistic insight into the superior efficacy of lorlatinib over crizotinib for the treatment of ALK-driven neuroblastoma.