Pamela S. Becker

Clonal acquisition of multiple chromosomal abnormalities in hematopoietic stem and progenitor cells (HSPCs) is a hallmark of high-risk acute myeloid leukemias with complex karyotype (AML-CK). AML-CK is associated with TP53 mutations and chromosome 5q deletions (del5q); however, the drivers and clonal trajectories of aneuploid evolution in HSPCs remain unknown. We have developed a patient-derived induced pluripotent stem cell (iPSC) model in which preleukemic HSPCs clonally evolve to distinct, highly aneuploid states following transient mitotic inhibition. By tracking chromosome evolution at single cell resolution, we show that TP53-mutant HSPCs with del5q, but not TP53­ mutation alone, evolved complex chromosomal changes. Clonal evolution was marked by stepwise acquisition of numerical and structural chromosome changes seen in AML-CK patients, with individual abnormalities conferring fitness advantage. iPSC-derived aneuploid HSPCs and primary AML-CK patient samples exhibited a conserved gene expression signature marked by upregulation of PTEN, cohesins, and anti-apoptotic factor BCL2, indicative of a shared aneuploid cell state in HSPCs. Clinical BCL2 inhibitor venetoclax eradicated BCL2-dependent aneuploid clones, with resistant clones undergoing a lineage switch to upregulate alternative BCL2 factors. In summary, we demonstrate that mutant TP53 and del5q drive chromosome evolution marked by stepwise acquisition of individual abnormalities. Moreover, aneuploid HSPCs exhibit a shared gene expression state which confers unique targetable therapeutic vulnerabilities in AML-CK.

Intratumor heterogeneity fundamentally challenges cancer treatment, as coexisting, molecularly distinct cell states with non-overlapping drug sensitivities can drive therapeutic resistance. We establish and validate a generalizable, network-based framework to systematically identify combination therapies targeting complementary tumor cell states. Applied to diffuse midline glioma (DMG)—a universally fatal pediatric malignancy—this approach identified master regulator protein dependencies in seven coexisting cell states, confirmed by pooled CRISPR–Cas9 assays. Perturbational transcriptional profiles for 372 clinically relevant drugs prioritized candidates predicted to invert state-specific master regulator activity. State-selective drug sensitivity was validated for eight out of nine (89%) drugs in vivo, including avapritinib, ruxolitinib and larotrectinib. Compared with monotherapy, co-administering drugs targeting complementary states significantly prolonged survival across virtually all combinations, with avapritinib plus ruxolitinib extending median survival nearly threefold versus vehicle and 1.5-fold versus avapritinib alone. These findings establish clinically actionable DMG combinations and a tumor-agnostic and mutation-agnostic framework for rational combination therapy design.

Allogeneic hematopoietic cell transplantation (allo-HCT) is increasingly offered as a consolidation strategy for older/infirm patients with acute myeloid leukemia (AML). Fludarabine/melphalan (Flu/Mel) conditioning is associated with effective disease control but results in significant toxicity and non-relapse mortality (NRM) when combined with calcineurin-inhibitors plus methotrexate or mycophenolate mofetil. Flu/Mel with alternative graft-versus-host disease (GVHD) prophylaxis may be better tolerated and result in superior outcomes in patients with AML. In this single-center retrospective analysis, we analyzed long-term outcomes of patients with AML (n = 342) who underwent allo-HCT with Flu/Mel conditioning and tacrolimus/sirolimus (Tac/Sir)-based GVHD prophylaxis from 2008-2019 at City of Hope. Patient median age was 63 years (range: 23–78), with 37% having high-very high Disease Risk Index (DRI) and 42% with HCT-Comorbidity Index (CI) ≥ 3. Five-year overall survival (OS: primary objective) was 55% (95% CI: 49–61%) among all patients and 70% (95% CI: 55–81%) in patients ≥70 years old. Only presence of active disease correlated with lower 5-year OS on multivariate analysis (HR = 1.95; p < .001). Five-year NRM was 24% (95% CI: 19–29%) among all patients and 21% (95% CI: 11–34%) in those ≥70 years old. In conclusion, Flu/Mel conditioning with Tac/Sir GVHD prophylaxis is associated with favorable OS and acceptable NRM, even in older/infirm patients with AML.

This editorial describes the current status of FMS‐like tyrosine kinase 3 (FLT3) inhibitors in the treatment of acute myeloid leukemia (AML) and reviews a retrospective study of single‐institution data for the use of FLT3 inhibitors with both intensive and low‐intensity treatment of AML. For patients who received low‐intensity regimens, there was benefit to the combined inclusion of an FLT3 inhibitor and venetoclax in triple‐drug regimens as well as improved outcomes with allogeneic transplant for all patients who had FLT3‐mutated AML.

Despite the success of the CD19 × CD3 T-cell engager blinatumomab in B-cell acute lymphoblastic leukemia (B-ALL), treatment failure is common and can manifest with antigen loss and extramedullary disease (EMD) relapse. To understand the impact of leukemia genetics on outcomes, we reviewed 267 adult patients with B-ALL treated with blinatumomab and used next-generation sequencing to identify molecular alterations. Patients received blinatumomab for relapsed/refractory (R/R) disease (n = 150) and minimal residual disease (MRD; n = 88), upfront as induction (n = 10) or as consolidation in MRD-negative state (n = 19). In the overall cohort, 50 patients (19%) had Philadelphia chromosome (Ph)–positive ALL, 80 (30%) had Ph-like ALL, 35 (13%) had TP53 mutations (TP53m), 7 (3%) had KMT2A rearrangement, and 8 (3%) had PAX5 alterations. For patients treated for R/R ALL, the overall complete remission (CR)/CR with incomplete hematological recovery (CRi) rate was 59%. Only pretreatment high disease burden (P < .01) and active EMD (P < .01) were associated with inferior CR/CRi rate. Of 169 patients in CR/CRi after blinatumomab, 79 (47%) patients relapsed, including 22 (28%) with CD19– and 54 (68%) with CD19+ relapse. In multivariable analysis, TP53m was associated with an increased risk of CD19– relapse (hazard ratio [HR], 6.84; 95% confidence interval [CI], 2.68-17.45; P < .01). Post-blinatumomab allogeneic stem cell transplantation consolidation was associated with a lower risk of CD19– relapse (HR, 0.10; 95% CI, 0.03-0.37; P < .01) and EMD relapse (HR, 0.36; 95% CI, 0.18-0.73; P < .01). In conclusion, leukemia genetics may predict patterns of blinatumomab failure, with TP53m associated with CD19– relapse.

Fludarabine and melphalan (FM) conditioning offers effective disease control with an acceptable toxicity profile. Post-transplant cyclophosphamide (PTCy) for graft-versus-host disease (GVHD) prophylaxis has improved transplant outcomes. We retrospectively reviewed patients receiving FM-based transplants with PTCy at City of Hope. Of 248 patients included, 89 (35.9%) received hematopoietic cell transplant (HCT) from a matched related/unrelated donor (MRD/MUD), 118 (47.6%) from a haploidentical (HID) donor, and 49 (19.8%) from a mismatched unrelated donor (MMUD). There were no differences in acute and chronic GVHD based on donor type. The 2-year overall survival (OS) for patients receiving HID, MMUD, and MRD/MUD was 58%, 55%, and 70%; disease-free survival (DFS) was 52%, 48%, and 66%; and graft-versus-host/relapse-free survival (GRFS) were 48%, 40%, and 59%, respectively. OS, DFS, and GRFS were similar regardless of donor type on multivariable analysis. However, donor age ≥35 years was associated with lower OS and GRFS and higher 2-year non-relapse mortality (NRM) on multivariable analysis across all patients, regardless of donor type. FM with PTCy appears to produce similar outcomes between MRD/MUD, MMUD, and HID when adjusting for donors <35 years, and donor age seems to be the most important factor when selecting a donor with this regimen.

Recurrent fusions drive the pathogenesis of many hematological malignancies. Compared to routine cytogenetic/fluorescence in situ hybridization (FISH) studies, the RNA-based next-generation sequencing (NGS) fusion assay enables the identification of both known and novel fusions. In many cases, these recurrent fusions are crucial for diagnosis and are associated with prognosis, relapse prediction, and therapeutic options. The aim of this study is to investigate the application of the RNA-based NGS fusion assay in hematological malignancies. Our study included 3101 cases with available fusion results, and a fusion event was identified in 17.6% of cases. The discordant rate between the RNA-based NGS fusion assay and cytogenetic/FISH studies was 36.3%. Further analysis of discordant cases indicated that, compared to cytogenetic/FISH studies, the RNA-based NGS fusion assay significantly improved the identification of cryptic fusion genes, such as NUP98::NSD1, P2RY8::CRLF2, and KMT2A fusions involving different partners. Additionally, our study identified 24 novel fusions and 16 cases with the simultaneous presence of two fusions. These additional findings from the RNA-based NGS fusion assay resulted in improved risk stratification, disease targeting and monitoring. In conclusion, our study demonstrates the feasibility and utility of an RNA-based NGS fusion assay for patients with hematological malignancies, suggesting that it may be essential for the routine clinical workup of these patients.