Differentially expressed genes (adjusted P <0.01 ) in STAG2/LMO2 subtype compared to other T-ALL cases.

Differentially expressed genes (adjusted P <0.05) in three TLX3 subtypes (TLX3 γδ, TLX3 immature, TLX3 DP-like) compared to other T-ALL cases.

The gene expression profiles of γδ T-ALL.

Compounds used in single-dose (10uM) drug screening.

Differential peaks of H3K27ac and differentially expressed genes in gene-edited PF382 model.

The list of drugs for the patient-derived xenografts (PDX) cell screening.

Comparison of clinical characteristics and outcomes between gamma delta T-ALL and non-gamma delta T-ALL.

Lists of T-ALL related genes for filtering tumor-only and RNAseq samples.

Patient characteristics of 24 cases of STAG2/LMO2 subtype T-ALL that were performed genomic analysis.

The clinical features of γδ T-ALL.

Patient characteristics of 76 γδ T-ALL cases performed genomic analysis.

Up-regulated pathways in STAG2/LMO2 subtype compared to other T-ALL cases for mouse leukemia initiating cells (LIC) signatures analyzed by gene-set enrichment analysis (GSEA).

Models for examining the effects of STAG2 inactivation.

Differentially expressed genes (adjusted P <0.01 ) of LMO2 γδ-like subtype vs other T-ALL.

The genomic features of LMO2::STAG2 translocations.

Introduction Nadir bone marrow biopsies (BM Bx) are routinely performed around day 14 to assess early response to AML intensive induction therapy. The presence of residual disease prompts initiation of reinduction therapy, often with another cycle of intensive chemotherapy. Whether there are characteristics of nadir BM Bx that predict for response to intensive reinduction is unknown. To evaluate this, we analyzed data from ECOG-ACRIN clinical trials in AML of intensive induction chemotherapy with nadir biopsy information available to determine predictors of outcomes after reinduction. Methods We included patients from ECOG-ACRIN E1900 (Fernandez NEJM 2009) and arm A of E2906 (Foran ASH 2015) who received induction therapy with daunorubicin and cytarabine (7+3), had residual disease (blasts ≥5% or cellularity ≥20%) at nadir BM Bx and received reinduction chemotherapy. Nadir BM Bx characteristics that were evaluated included blast percentage and cellularity as well as both absolute and relative (percentage change, e.g. 20% to 10% = -50%) differences calculated between diagnosis and nadir for each parameter. Complete remission (CR) after reinduction therapy, disease free survival (DFS) and overall survival (OS) were outcomes for all analyses. Logistic regression models were used to evaluate associations with CR, and Cox proportional hazards models were used for DFS and OS. For models evaluating changes in blast percentage or cellularity as predictors, baseline blast percentage or cellularity was included as a covariate, respectively. Results Of 1013 patients identified, 750 (74%) had a nadir biopsy, 233 (23%) had evidence of residual disease, received reinduction therapy, and were included in the primary analysis. The median age was 58 and 42% were female. Cytogenetic risk category (by ELN2017) was adverse in 31%, intermediate in 66% and favorable in 3%. The median nadir BM Bx blast was 30% (range 0 to +97%) and cellularity was 20% (0 to +100%). The median absolute difference in blast percentage between baseline and nadir BM Bx was -15% (-95% to +66%) with a median relative difference of -36% (-100% to +400%). After reinduction, 118 patients (52%) achieved a CR. Neither absolute difference in blast percentage (OR 0.99, 95%CI 0.98-1.00, p=0.20) nor relative difference (OR 1.00, 95%CI 0.99-1.00, p=0.33) predicted CR. There was similarly no association with DFS (HR = 1.00, 95%CI: 0.99-1.01, p=0.65) or OS (HR = 1.00, 95%CI 0.99-1.01, p=0.76). Blast reduction ≥50% similarly did not predict these outcomes. We also evaluated the impact of any reduction in blast percentage (responders) from baseline to nadir and again found no association with CR (OR 1.65, 95%CI 0.90-3.03, p=0.11). Similarly, there was no association with DFS (HR 0.74, 95%CI 0.51-1.09, p=0.13) or OS (HR 0.81, 95%CI 0.58-1.13, p=0.21) in responders vs nonresponders. No association with CR, DFS or OS were identified when performing the same analysis in intermediate and adverse cytogenetic subgroups. We found no association with CR when nadir cellularity was assessed as a continuous variable (OR 0.99, 95%CI 0.98-1.00, p=0.10) or by relative difference (OR 0.99, 95%CI 0.99-1.00, p=0.10). There was a trend towards association with absolute reduction in cellularity from baseline to nadir and CR (OR 0.99, 95%CI 0.98-1.00, p=0.06). No association was identified between relative difference in cellularity and DFS and OS, nor was there an association among cytogenetic risk subgroups with any outcome. Discussion In intensively treated patients with residual disease at nadir BM Bx (i.e. day 14) who received intensive reinduction, the likelihood of achieving a CR was not influenced by the magnitude of disease reduction nor the extent of disease at the time of nadir biopsy. Similarly, there were no nadir biopsy features that predicted DFS or OS after intensive reinduction therapy. Given alternative reinduction therapies such as hypomethylating agents and venetoclax are available, these results suggest that the decision to attempt a second intensive induction cycle following the unequivocal presence of residual disease should not be influenced by characteristics of the nadir BM Bx. Although patient-specific factors such as patient fitness may favor a switch to less intensive options, these results support consideration of intensive reinduction therapy in patients with residual disease at nadir biopsy, even without changes in blasts or cellularity.

Exploration of targets in STAG2/LMO2 T-ALL.

Quizartinib is a potent type II inhibitor of FMS-like tyrosine kinase 3 (FLT3) that demonstrated significant survival benefit among patients with newly diagnosed (ND) acute myeloid leukemia (AML) without FLT3-internal tandem duplication (FLT3-ITD) in the randomized, Phase II QUIWI trial. Here, we present the rationale and design of QuANTUM-Wild, a double-blind, randomized, placebo-controlled, Phase III study to confirm the efficacy and safety of quizartinib plus standard induction and consolidation chemotherapy and as maintenance monotherapy in adult patients with ND FLT3-ITD-negative AML. Eligible patients are randomized 2:2:1 to one of three treatment arms. Patients in Arm A (n ≈ 280) receive quizartinib plus chemotherapy during induction and consolidation (with option for transplant without study drug), followed by up to 36 cycles of single-agent maintenance therapy. Patients in Arm B (n ≈ 280) receive placebo in all treatment phases plus chemotherapy, then as maintenance monotherapy. Patients in Arm C (n ≈ 140) receive quizartinib plus chemotherapy in the induction and consolidation phases, then placebo during the maintenance phase, to specifically assess the utility of quizartinib maintenance. The primary endpoint is overall survival. Secondary endpoints include event-free survival, remission rate, and safety.Clinical trial registration: http://www.clinicaltrials.gov identifier is NCT06578247.

CRISPR editing construct sequences.

Fusion calls detected by RNA sequencing.