Refractory Philadelphia-positive acute lymphoblastic leukemia carrying an IKZF1plus profile. A case report

Introduction. The introduction of tyrosine kinase inhibitors (TKIs) greatly improved outcome in adult Philadelphia-positive acute lymphoblastic leukemia (Ph+ALL). Nonetheless, the rare patients failing novel frontline approaches with 2nd-3rd generation TKIs and immunotherapy have poor survival, underlying unknown mechanisms of disease persistence. Case-report. A 49-year-old male with hyperleukocytosis (217.4 x 109/L) was diagnosed with Ph+ALL (p190) in November 2021 and enrolled in the experimental arm of the phase-3 GIMEMALAL 2820 frontline trial, based on the 3rd generation TKI ponatinib in induction followed by blinatumomab as consolidation. At diagnosis, copy number aberration analysis by Multiplex Ligation Probe-dependent Amplification (MLPA) showed an IKZF1plus signature. The patient started induction with ponatinib (45 mg/daily), steroids and CNS prophylaxis. Ponatinib dose was reduced to 15 mg/daily due to liver and cardiovascular toxicity. End of induction assessment showed a complete hematologic remission and persistence of measurable residual disease (MRD) (0.24 BCR::ABL1/ABL1 x 100). Sanger sequencing (SS) demonstrated the occurrence of the T315I ABL1 mutation, confirmed by digital droplet PCR (ddPCR). The presence of the mutation at diagnosis and/or at previous time-points was excluded by ddPCR. ABL1 compound mutations and TP53 involvement were also excluded. Consolidation with blinatumomab was administered and a MRD improvement was observed after cycle 1. Unfortunately, a full-blown hematologic relapse occurred after the 2nd blinatumomab cycle. Salvage therapy with inotuzumab was associated with a complete molecular response, enabling an allogeneic stem cell transplantation (allo-SCT) from a matched sibling donor following a myeloablative conditioning. However, a second hematologic relapse with a hyperleukocytosis (71.4 x 109/L) occurred 38 days after the allo-SCT. The patient was therefore eligible for anti-CD19 CAR-T cell salvage therapy, but lymphapheresis proved successful only at the third attempt, because of an uncontrolled disease progression that required immediate treatment with high dose chemotherapy. Given the highly chemorefractory disease, the association of ponatinib and venetoclax was used as bridging-therapy during the CAR-T cell turn-around time, but the patient eventually died due to disease progression and infectious complications. Results. Despite the presence of the IKZF1plus signature, the extremely high proliferation rate and the resistance to ponatinib prompted an extensive molecular investigation. Conventional cytogenetics failed, but we could predict patient’s karyotype by digitalMLPA analysis that showed chromosomal deletions at 7p, 9p and 14q32.33, together with a gain within Xp(PAR) (Fig. 1a). Moreover, immunoglobulin/T-cell receptor (IG/TR) clonal gene rearrangement screening showed a TR rearrangement at diagnosis and relapses, confirming the persistence of the same leukemic clone throughout the course of the disease. Targeted RNA-sequencing on diagnostic and 1st relapse samples revealed a pathogenic stop-gained mutation on the SDHA gene (R352*) involved in mitochondrial oxidative phosphorylation, validated by SS also at the 2nd relapse (Fig. 1b). SDHA mutation was absent on germinal DNA. Conclusions. Given the patient's highly proliferative disease and the fact that the SDHA mutation was the only “unconventional“ lesion, screening and expression analysis on additional Ph+ALL patients will clarify its role as potential novel risk-factor. Overall, this study highlights the need of an in-depth molecular characterization at diagnosis/relapse to better understand key drivers of leukemia resistance/progression.