Paietta, Elisabeth

Abstract Cytokine receptor–like factor 2 rearrangement (CRLF2r), an aberration causing a Philadelphia chromosome–like gene expression profile and a poor prognostic marker in B-cell acute lymphoblastic leukemia (B-ALL), endows relative chemotherapeutic resistance. Extramedullary disease (EMD), including both central nervous system (CNS) and non-CNS involvement, can also be associated with worse outcomes. The relationship between CRLF2r and EMD is unknown. Based on an initial observation of patients with relapsed/refractory (R/R) CRLF2r B-ALL and EMD, a single-center retrospective review was conducted to evaluate the incidence of EMD in patients with CRLF2r B-ALL. Across 177 children, adolescents, and young adults with R/R B-ALL, 21 (11.9%) harbored CRLF2r, of whom 19 (90.5%) had EMD at some point during their treatment course. In contrast, only 78 of the 156 patients (50%) without CRLF2r ever had EMD (P = .0003). In the CRLF2r cohort, 8 (38.1%) presented with EMD at diagnosis: 7 with CNS and 1 with non-CNS EMD. At relapse, 17 (80.9%) had EMD: 4 (19%) had CNS EMD, 9 (42.9%) had non-CNS EMD, and 4 (19%) had both. Isolated EMD was observed in 2 patients (11.8%) at first relapse and in 3 (17.6%) with multiple relapses. Given these findings, further study to evaluate this potential association between EMD and CRLF2r in R/R B-ALL is indicated.

Abstract Copy Number Alterations (CNAs), including chromosomal gains and losses, shape the genetics and clinical management of acute myeloid leukemia (AML), particularly in complex karyotypes (e.g. CK-AML). Traditionally, AML associated CNAs have been studied using cytogenetic approaches, i.e., karyotyping, that are limited in resolution and sensitivity. Here, low-coverage, sparse whole genome sequencing followed by machine learning applied to over 600 AML patient samples (ECOG-ARCIN trials: E1900, E3999) reveals novel genetic, biologic, and clinical correlates in AML disease. We find that multi-variate Cox-regression analysis applied to the data identifies select patients exhibiting focal and cryptic hemizygous deletions at 17q, 21q, and 3p, in otherwise diploid genomes, associate with inferior survival compared to other patients (median overall survival; OS = 65.5 compared to 421 days, Chi-square test pval=6x10-11), independent of factors such as age, treatment, and karyotype complexity status. In addition, we confirm that amplifications at 11q23, encoding the KM2TA gene, are associated with inferior outcome, and further identify unique breakpoint event features as well as transcriptional signatures suggestive of distinctive KM2TA-translocation independent biology. Applying machine learning approaches to the data, more specifically Non-negative Matrix Factorization (NMF), we develop a prognostic model that captures clinically adverse, cryptic variation such as focal 5q deletions, missed by conventional chromosome analysis and thereby, adds novel, complementary information to traditional, cytogenetic based risk-stratification (e.g. ELN). The model also associates gain of chromosome 8 in Intermediate risk patients with worse outcome compared to other Intermediate risk patients (median OS = 186 compared to 446 days, Chi-square test pval=0.005) and identifies a subgroup of patients within the adverse risk category that lack deletions on chromosomes 5, 7, and 17, and that fare better than the rest of the adverse risk patients (median OS = 188 compared to 97.5 days, Chi-square test pval=0.02), likely reflecting previously identified “atypical” CK-AML patients. Last, we develop a prognostic classifier based on a combination of Neural-Network and Random-Forest based learning, that predicts disease outcome with high accuracy and is based on a three genomic feature list on chromosome bands 5q31.2, 7q31.33, and 8q24, suggesting potential for clinical implementation. Altogether, our results show that low coverage, sparse whole genome sequencing combined with advanced learning methods can be applied clinically to support the diagnosis and clinical management of AML disease as well as serve as a powerful tool to further a basic understanding of the genetics and biology of CNAs in myeloid neoplasms and other cancers.

Abstract Background: Relapsed or refractory (R/R) acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LL) remain challenging to treat, particularly in older patients and those with a T-cell phenotype. Venetoclax (VEN), a selective BCL-2 inhibitor, has shown preclinical synergy with vincristine (VCR) in multiple preclinical ALL models. Following the previously reported establishment of the recommended Phase II dose (RP2D), we now report the results of the Phase II (Ph2) portion of EA9152 (VEN 600 mg daily with weekly L-VCR 2.25 mg/m² IV or VCR 1.5 mg/m2 IV capped at 2 mg), evaluating efficacy and safety in this high-risk population. Methods: This open-label, multicenter Phase II study enrolled adults (≥18 years) with R/R B- or T-cell ALL or LL. The phase II portion of this trial was a single-arm, open-label study evaluating the combination of VEN (600 mg po D1–28) with either L-VCR (2.25 mg/m² IV weekly x4) or vincristine sulfate (VCR) (1.4 mg/m² IV weekly x4). Following the market withdrawal of L-VCR in the United States in April 2022, no new patients were initiated on this formulation and patients already receiving L-VCR were transitioned to VCR at the start of their next treatment cycle or sooner if necessitated by drug availability. Prior VCR but not VEN exposure was permitted in Ph2. The primary endpoint was achievement of a complete response or complete response with incomplete count recovery CR + CRi rate by end of cycle 3. Secondary endpoints included measurable residual disease (MRD) response, progression free survival (PFS), overall survival (OS), and safety. The association of phenotype with response and time-to-event were evaluated using Fisher's exact test and the Cox proportional hazards model, respectively. Results: Twenty-one eligible patients were treated (B-cell ALL/LL: n=12; T-cell ALL/LL: n=9). The trial was terminated early after 22/56 patients were accrued on account of withdrawal of sponsor support. Median age was 50 years and 76.2% were male. Performance status was 0–1 in 85.7%. All patients had received prior chemotherapy; 47.6% had undergone prior transplant. Median number of treatment cycles was 1 (2 for B-cell, 1 for T-cell). By end of cycle 3, no patients in the B-cell cohort (0/12; 90% CI, 0.00–0.22) achieved CR or CRi, 8 had stable disease (SD). In the T-cell cohort, 1 of 9 patients (11.1%; 90% CI, 0.01–0.43) achieved CR, 1 achieved PR and 1 had SD. There was no statistically significant difference in CR + CRi rate between phenotypes (p=0.43). None of the patients achieved an MRD-negative CR/CRi by flow cytometry or molecular methods. At the time of this analysis, 16 of 21 patients had died. Median overall survival (OS) was 4.3 months (95% CI, 1.5–22.0) for B-cell and 10.2 months (95% CI, 2.0–16.4) for T-cell patients (HR 1.32, p=0.60). Median PFS was 2.9 months (95% CI, 1.7–3.7) for B-cell and 1.2 months (95% CI, 0.7–4.6) for T-cell cohorts (HR 2.18, p=0.18). Grade 3–5 treatment-related adverse events occurred in most patients. One T-cell patient experienced grade 5 respiratory failure. Among 16 patients enrolled under the revised protocol using VCR, only 1 experienced grade 3 peripheral motor neuropathy, and no peripheral sensory neuropathy was reported (combined AE rate 0.06; 90% CI, 0.00–0.26). Tumor lysis syndrome was not observed in this cohort. Conclusions: The combination of VEN at the established RP2D and L-VCR/VCR was feasible and had an acceptable safety profile in heavily pretreated patients with R/R ALL/LL. However, response rates, including CR/CRi and MRD negativity, were limited, particularly in the B-cell cohort. Median OS and PFS remain poor in both subtypes, highlighting the need for improved strategies in this high-risk population. Venetoclax, in combination with other chemotherapy regimens, has shown encouraging response rates warranting continued exploration of its benefit in ALL.

Abstract Background We performed a prospective study evaluating a baseline GA battery and clinical outcomes in fit older adults (age ≥60 years) with AML and normal cardiac and renal function in the recent E-A NCTN E2906 phase 3 study. A patient-reported outcomes (PRO) assessment of Depression, Activities of Daily Living (ADL), Cognitive Function, Social Support (SS) domains, and comorbidity was performed at study registration to evaluate the prevalence of vulnerabilities and their impact on overall survival (OS) and 30-day induction mortality rates (IM) in this cohort selected for fitness to receive IC. Methods E2906 study design and results have been presented previously [n=727, age ≥60 years, randomized 1:1 to ‘standard 7&3‘ & high dose cytarabine (Arm A) vs. single agent clofarabine (CLO, Arm B), as remission induction (Step 1) and consolidation (Step 2)]. There was no difference in composite complete remission (CCR, 50%) or IM (8.5%), and CLO was inferior for OS. A baseline GA was a key secondary protocol objective, offered to all patients, and n=532 (73%) participated. We assessed Geriatric Depression Scale (GDS, none vs. any depressive symptoms, n=524); cognitive screen using Mini-Mental Exam Section (MMES, score 8/8 vs. <8, n=516); ADL & Instrumental ADL (iADL), (need for assistances vs. not n=526); a Medical Outcomes Study SS Survey (MOS-SS, measured as per unit increase, n=527); a Comorbidity survey ( ≤4 vs. ≥5 patient-reported comorbidities, n=530), patient-reported prescription medications use (PM, 0-3 vs. ≥4, n=519); and a survey of Sexual Desire (n=491) and Sexual Activity (n=477) within 4 weeks of AML diagnosis. Association of GA domains with OS, IM, and achievement of CCR was evaluated using the Chi-squared, Fisher's exact, and Wilcoxon rank sum test. Survival analysis was performed using the Cox proportional hazards models, adjusted for treatment arm. All p-values are 2-sided. Results The median age among those participating in GA battery was 67 yrs (range 60-85), including 38% age ≥70. There were 42% females, and ECOG performance status was 0 (28%), 1 (54%), 2 (16%), or 3 (2%). Central Cytogenetic review was classified (ELN2017) as Favorable (3%), Intermediate (66%), and Adverse (31%) risk. There was a notable rate of GA scores outside ‘normal’ clinical cutoff, including Depression (GDS 31%), cognitive and functional impairment [MMSE (37%), ADL (25%) and iADL (32%)], ≥5 Comorbidities (23%), and ≥4 PM's (44%). 81% & 76%, respectively, reported no sexual activity and low/none sexual desire. MOS-SS tended to be high in this cohort [mean (SD) score 87 (17)]. We observed a significant association of GA domains with OS & IM. For OS, absence of depressive symptoms [GDS, Hazard Ratio (HR) 0.79, 95% confidence Intervals (CI) 0.64-0.97, p=0.025)], MMES 8/8 (HR 0.78, 95%CI 0.64-0.96, p=0.016), requiring no assistance with ADLs (HR 0.65, 95%CI 0.52-0.82, p<0.001) and iADLs (HR 0.69, 95%CI 0.57-0.85, p<0.001), and ≤4 Comorbidities (HR 0.68, 95%CI 0.54-0.84, p=0.001) were significant for superior OS; use of ≥4 PM's was associated with inferior OS (HR 1.32, 95%CI 1.09-1.61, p=0.005). There was no association of sexual activity/desire, BMI ≥30 kg/m2, or MOS-SS with OS. IM was significantly higher among those with any depression symptoms (GDS, p=0.005), any ADL (p=0.010) or iADL (p=0.013) impairment, ≥5 comorbidities (p=0.037) and ≥4 PM's (p=0.001); there was no association with MOS-SS or MMES. There was no significant association of GA scores with cytogenetic risk group or with CCR rates. Only ADL independence (p=0.048), and possibly Comorbidity ≤4 (p=0.071), were associated with proceeding to Step 2. Conclusions In this large prospective cohort of fit older adults with AML selected to receive IC, we observed high rates of PRO-assessed GA vulnerability, which was significantly associated with inferior OS and higher IM rates, and (for ADL impairment) lower rates of proceeding to consolidation therapy. This suggests that functional and cognitive impairments are prevalent and can significantly impact outcome even in fit older adults. Despite potential long-term OS advantages of IC previously observed in E2906, efforts to systematically recognize those at higher risk based on GA PROs are needed to help identify patients who may be more appropriate for study of lower intensity treatment options to mitigate impact on IM and OS. SImilarly we plan to evaluate the potential benefit of GA-driven supportive care to improve patients' outcomes.

Abstract 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.

Abstract Inotuzumab ozogamicin (InO) is an antibody-calicheamicin conjugate with high efficacy in lymphoid malignancies. It targets the B-cell surface protein CD22, which is expressed in most B-cell acute lymphoblastic leukemia (B-ALL) cases, albeit with variable intensity. However, factors governing CD22 expression and thus leukemia sensitivity to InO remain incompletely understood. Using multiomic characterization of 196 human B-ALL samples, coupled with ex vivo InO sensitivity profiling, we showed that early leukemia differentiation arrest at the pre–pro-B stage is associated with resistance to InO. Screening of 1639 transcription factor genes identified early B-cell factor 1 (EBF1) as a key regulator of CD22 expression (false discovery rate of 7.1 × 10−4). When comparing the assay for transposase-accessible chromatin with sequencing profiling results of the most InO-sensitive and -resistant cases (50% lethal concentration <10th vs >90th percentile, n = 18), the binding motif for EBF1 was strikingly enriched in regions with differential open chromatin status (P = 8 × 10−174). CRISPR interference targeting EBF1 binding sites at the CD22 locus led to an ∼50-fold reduction in cell surface CD22 expression and, consequently, an ∼22-fold increase in InO resistance in ALL cell lines. Interestingly, within BCR::ABL1 ALL, we observed intrasubtype heterogeneity linked to EBF1 transcriptional downregulation (P = 1.1 × 10−15) and/or somatic alteration (P = .004), which led to reduced CD22 expression (P = 8.3 × 10−11) and ex vivo and in vivo resistance to InO. Collectively, these findings point to the direct impact of EBF1 on CD22 expression during B-cell development, which, in turn, contributes to interpatient variability in InO response, even within the same subtype of B-ALL.

Abstract Inotuzumab ozogamicin (InO) is an antibody-calicheamicin conjugate with striking efficacy in B-cell acute lymphoblastic leukemia (B-ALL). However, there is wide interpatient variability in treatment response, and the genetic basis of this variation remains largely unknown. Using a genome-wide CRISPR screen, we discovered that the loss of DNA nucleotidylexotransferase (DNTT) is a primary driver of InO resistance. Mechanistically, the downregulation of DNTT attenuated InO–induced DNA damage response, cell cycle arrest, and mitochondrial apoptotic priming, thereby ultimately leading to leukemia resistance to InO. Ex vivo leukemia InO sensitivity was highly associated with DNTT expression in ALL blasts with substantial intraleukemia heterogeneity as revealed by single-cell RNA sequencing. Among patients with B-ALL enrolled in the Children's Oncology Group trial AALL1621, we observed consistent DNTT downregulation in residual blasts following InO treatment. The selection of DNTT-low blasts by InO therapy was also recapitulated in vivo using patient-derived xenograft models. Collectively, our data indicate that DNTT is a key regulator of calicheamicin response in leukemia and thus a potential biomarker for individualizing InO therapy in B-ALL.

Introduction: Based on a donor versus no-donor analysis, UKALLXII/E2993 showed a survival benefit for adults with acute lymphoblastic leukemia (ALL) who underwent allogeneic hematopoietic cell transplantation (alloHCT) in first complete remission (CR1) compared to consolidation/maintenance chemotherapy alone. The follow-up phase 3 E1910 trial (NCT02003222) randomized BCR::ABL1-negative B-lineage ALL patients (pts) aged 30-70 years in measurable residual disease (MRD)-negative CR1 after intensification to conventional chemotherapy (CC) +/- blinatumomab (blin) and demonstrated significantly improved overall survival (OS) with blin (Litzow, NEJM 2024). The current exploratory subgroup analysis evaluates outcomes of MRD-negative pts randomized on E1910 who underwent alloHCT on trial. Methods: Among pts enrolled on E1910, pts in MRD-negative CR1 by 6-color flow cytometry after intensification who were randomized to CC +/- blin and subsequently underwent alloHCT were identified. We compared baseline characteristics, MRD status post induction, relapse-free survival (RFS) and OS using the Kaplan-Meier method and the two-sided log-rank test and Cox model. A multivariable analysis was performed with alloHCT included as a time-varying covariate as well as a landmark analysis comparing the outcome of pts with unfavorable risk on the CC + blin arm who underwent alloHCT versus those who did not. Results: Of 224 MRD-negative randomized pts, 44 underwent alloHCT on trial: 22 in each arm. The median time from randomization to transplant was 3.2 months (mos). The median follow-up from initial registration was 57.8 mos. Baseline demographics including age (median 55 years), gender (53% male), race (89% white) and ethnicity (89% non-Hispanic/Latino) were equally distributed. Compared to CC + blin, the median peripheral blood white cell (WBC) count and blast percentage at diagnosis were higher in the CC arm at 6,640 vs 3,740/uL and 55 vs 9%, respectively, while median marrow blast percentage and overall unfavorable risk as defined in E1910 (55% vs 64%) were similar. Of the 44 MRD-negative pts who proceeded to alloHCT on study, 77% in the CC arm and 64% in the CC+ blin arm were MRD-negative after induction. Myeloablative conditioning was given to the majority of pts (68% CC arm and 73% CC+blin arm) and the most common graft versus host disease prophylaxis was tacrolimus-based on both arms. Among the 44 pts who underwent alloHCT, the observed hazard ratio (HR) comparing relative risk of death between pts randomized to CC+blin or CC only was 0.59 (95% CI: 0.12-2.11) with a 3-year OS rate of 82% versus 71% and the HR comparing relative risk of relapse/death was 0.52 (CI: 0.15-1.79) with a 3-year RFS rate of 82% versus 67%. For patients with unfavorable risk, 3-year OS and 3-year RFS in each treatment arm were both 71% versus 65%. Among 50 pts with unfavorable risk in MRD-negative CR after intensification who were randomized to CC + blin, a landmark analysis performed at 5 mos post randomization showed 3-year OS and RFS rates of 71% versus 90% and 71% versus 86% between the 14 pts who underwent alloHCT and those who did not, respectively. Receipt of alloHCT was a time-varying covariate in a multivariable analysis with gender, WBC count, platelets, hemoglobin, peripheral blood blasts, bone marrow blasts, performance status, and combined molecular risk category. Age, CD20 status, rituximab use, and intention to receive alloHCT were used as stratification factors. In the entire cohort of MRD-negative pts who were randomized, there was a significant association between improved OS and the receipt of CC+blin vs CC alone (HR 0.46, 95% CI: 0.26 - 0.82; p=0.009), better performance status of 0-1 vs ≥2 and favorable vs unfavorable risk ALL. In contrast, the receipt of alloHCT had no significant effect on OS (HR 1.00, 95% CI: 0.49 - 2.01). Conclusions: Within the constraints of small numbers, this exploratory subgroup analysis demonstrates that in pts with newly diagnosed BCR::ABL1-negative B-ALL treated on E1910 who achieved MRD-negativity after intensification, alloHCT outcomes did not appear to be different with or without blin in consolidation. In a multivariate analysis of all MRD-negative pts, receipt of blin but not alloHCT was associated with improved OS. Further investigation is warranted to characterize the relative benefit of blinatumomab in pts receiving alloHCT in frontline consolidation.