Pediatric Acute Lymphoblastic Leukemia Research Articles

A Comparative Study of B Cell Blast Isolation Methods from Bone Marrow Aspirates of Pediatric Leukemia Patients.

Density gradient centrifugation is a conventional technique widely utilized to isolate bone marrow mononuclear cells (BM-MNC) from bone marrow (BM) aspirates obtained from pediatric B-cell acute lymphoblastic leukemia (B-ALL) patients. Nevertheless, this technique achieves incomplete recovery of mononuclear cells and is relatively time-consuming and expensive. Given that B-ALL is the most common childhood malignancy, alternative methods for processing B-ALL samples may be more cost-effective. In this pilot study, we use several readouts, including immune phenotype, cell viability, and leukemia-initiating capacity in immune-deficient mice, to directly compare the density gradient centrifugation and buffy coat processing methods. Our findings indicate that buffy coat isolation yields comparable BM-MNC product in terms of both immune and leukemia cell content and could provide a viable, lower cost alternative for biobanks processing pediatric leukemia samples.

Identifying Candidate Gene Drivers Associated with Relapse in Pediatric T-Cell Acute Lymphoblastic Leukemia Using a Gene Co-Expression Network Approach.

Pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) relapses are still associated with a dismal outcome, justifying the search for new therapeutic targets and relapse biomarkers. Using single-cell RNA sequencing (scRNAseq) data from three paired samples of pediatric T-ALL at diagnosis and relapse, we first conducted a high-dimensional weighted gene co-expression network analysis (hdWGCNA). This analysis highlighted several gene co-expression networks (GCNs) and identified relapse-associated hub genes, which are considered potential driver genes. Shared relapse-expressed genes were found to be related to antigen presentation (HLA, B2M), cytoskeleton remodeling (TUBB, TUBA1B), translation (ribosomal proteins, EIF1, EEF1B2), immune responses (MIF, EMP3), stress responses (UBC, HSP90AB1/AA1), metabolism (FTH1, NME1/2, ARCL4C), and transcriptional remodeling (NF-κB family genes, FOS-JUN, KLF2, or KLF6). We then utilized sparse partial least squares discriminant analysis to select from a pool of 481 unique leukemic hub genes, which are the genes most discriminant between diagnosis and relapse states (comprising 44, 35, and 31 genes, respectively, for each patient). Applying a Cox regression method to these patient-specific genes, along with transcriptomic and clinical data from the TARGET-ALL AALL0434 cohort, we generated three model gene signatures that efficiently identified relapsed patients within the cohort. Overall, our approach identified new potential relapse-associated genes and proposed three model gene signatures associated with lower survival rates for high-score patients.

Evaluation of less treatment interruption of 6-Mercaptopurine by co-administration of ursodeoxycholic acid with chemotherapy in pediatric acute lymphoblastic leukemia

Background: Ursodeoxycholic acid, a bile acid, protects the liver through various mechanisms, including bile composition modulation and enhanced secretion. In ALL chemotherapy, 6MP is hepatotoxic, requiring dose reduction. UDCA is used to alleviate liver toxicity in ALL and other chronic cholestatic conditions. The study aims to evaluate the effectiveness of UDCA with chemotherapy in reducing 6MP treatment interruptions and its impact on treatment continuity in pediatric ALL. Methods: This randomized controlled trial study conducted at the Department of Pediatric Hematology and Oncology, BSMMU in pediatric ALL patients during chemotherapy from September 2018 to August 2019. Fifty children aged 1 to 18 years with ALL were enrolled, half receiving UDCA alongside chemotherapy and the rest forming the control group. Serum hepatic transaminases, total bilirubin, and CBC were monitored every 14 days. Statistical analysis was performed using SPSS, with significance set at p<0.05. Results: In this study of 50 pediatric ALL patients, there were no statistically significant age or gender differences between the "Case" (UDCA-treated) and "Control" groups. However, the UDCA group showed a significant decrease in abnormal liver function tests (32.0%) compared to controls (60.0%). Moreover, 6MP dose reduction was significantly lower in cases (4.0%) than controls (40.0%), indicating UDCA's potential hepatoprotective effects. Multivariate logistic regression revealed male gender and mean AST levels as significant factors associated with hepatotoxicity in pediatric ALL patients. Conclusions: Co-administration of UDCA with chemotherapy reduces hepatotoxicity in pediatric ALL patients on 6 MP, but more research is needed for dosage optimization and to assess impact on survival.

Caregiver perceptions of child heath behaviors and weight during treatment for acute lymphoblastic leukemia.

Changes in health behaviors and weight are common during the early phases of pediatric acute lymphoblastic leukemia treatment, and may negatively impact treatment tolerability. Given that ALL is most prevalent in children, caregivers play an essential role in shaping health behaviors during treatment. This study presents a qualitative analysis of semi-structured interviews with caregivers of youth in the early phases of ALL treatment. Caregivers (N=17, 95% female) of a child (M age=6.76years) diagnosed with ALL and on treatment for less than 1year (M=8.7months since diagnosis) completed a semi-structured interview about perceptions of their child's nutrition, physical activity, sedentary time, and weight during ALL treatment. Thematic analysis followed Braun and Clark's six-step framework (2006). Two coders established reliability (alpha=.88) and used a multi-pass coding system to extract themes. Caregivers' concerns around their child's weight during ALL treatment primarily centered around avoiding malnutrition. Weight gain during treatment was less of a concern and often viewed as protective. Caregivers reported encouraging their child to eat palatable, calorie-dense foods to mitigate risk for weight loss. Caregivers also expressed concern that children were less active and more sedentary due to treatment-related pain. Caregivers discussed health behaviors during treatment as being child-directed, rather than parent- or provider-directed. Future interventions may consider strategies to engage in joint parent-child decisions and caregiver education around risks of excessive weight gain during treatment. Interventions should include anticipatory guidance and aim to support parents in developing skills to support their child's health behaviors during treatment.

CD9 shapes glucocorticoid sensitivity in pediatric B-cell precursor acute lymphoblastic leukemia.

Resistance to glucocorticoids (GC), the common agents for remission induction in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL), poses a significant therapeutic hurdle. Therefore, dissecting the mechanisms shaping GC resistance could lead to new treatment modalities. Here, we showed that CD9- BCP-ALL cells were preferentially resistant to prednisone and dexamethasone over other standard cytotoxic agents. Concordantly, we identified significantly more poor responders to the prednisone prephase among BCP-ALL patients with a CD9- phenotype, especially for those with adverse presenting features including older age, higher white cell count and BCR-ABL1. Furthermore, gain- and loss-offunction experiments dictated a definitive functional linkage between CD9 expression and GC susceptibility, as demonstrated by the reversal and acquisition of relative GC resistance in CD9low and CD9high BCP-ALL cells, respectively. Despite physical binding to the GC receptor NR3C1, CD9 did not alter its expression, phosphorylation or nuclear translocation but potentiated the induction of GC-responsive genes in GC-resistant cells. Importantly, the MEK inhibitor trametinib exhibited higher synergy with GC against CD9- than CD9+ lymphoblasts to reverse drug resistance in vitro and in vivo. Collectively, our results elucidate a previously unrecognized regulatory function of CD9 in GC sensitivity, and inform new strategies for management of children with resistant BCP-ALL.

IKZF1plus is a frequent biomarker of adverse prognosis in Mexican pediatric patients with B-acute lymphoblastic leukemia.

Recurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. IKZF1plus is a complex biomarker associated with a poor prognosis. It is characterized by IKZF1 deletion coexisting with PAX5, CDKN2A/2B, or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL. Here, we report the frequency of the IKZF1plus profile and the mutational spectrum of IKZF1, PAX5, CDKN2A/2B, and ERG genes and evaluate their impact on overall survival (OS) in a group of patients with B-ALL. A total of 206 pediatric patients with de novo B-ALL were included. DNA was obtained from bone marrow samples at diagnosis before treatment initiation. A custom-designed next-generation sequencing panel was used for mutational analysis. Kaplan-Meier analysis was used for OS estimation. We identified the IKZF1plus profile in 21.8% of patients, which was higher than that previously reported in other studies. A significantly older age (p=0.04), a trend toward high-risk stratification (p=0.06), and a decrease in 5-year Overall Survival (OS) (p=0.009) were observed, although heterogeneous treatment protocols in our cohort would have impacted OS. A mutation frequency higher than that reported was found for IKZF1 (35.9%) and CDKN2A/2B (35.9%) but lower for PAX5 (26.6%). IKZF1MUT group was older at diagnosis (p=0.0002), and most of them were classified as high-risk (73.8%, p=0.02), while patients with CDKN2A/2BMUT had a higher leukocyte count (p=0.01) and a tendency toward a higher percentage of blasts (98.6%, >50% blasts, p=0.05) than the non-mutated patients. A decrease in OS was found in IKZF1MUT and CDKN2A/2BMUT patients, but the significance was lost after IKZF1plus was removed. Our findings demonstrated that Mexican patients with B-ALL have a higher prevalence of genetic markers associated with poor outcomes. Incorporating genomic methodologies into the diagnostic process, a significant unmet need in low- and mid-income countries, will allow a comprehensive identification of relevant alterations, improving disease classification, treatment selection, and the general outcome.

The RAS-signaling-pathway-mutation-related prognosis in B-cell acute lymphoblastic leukemia: A report from South China children's leukemia group.

The next-generation sequencing technologies application discovers novel genetic alterations frequently in pediatric acute lymphoblastic leukemia (ALL). RAS signaling pathway mutations at the time of relapse ALL frequently appear as small subclones at the time of onset, which are considered as the drivers in ALL relapse. Whether subclones alterations in the RAS signaling pathway should be considered for risk group stratification of ALL treatment is not decided yet. In this work, we investigate the RAS signaling pathway mutation spectrum and the related prognosis in pediatric ALL. We employed an NGS panel comprising 220 genes. NGS results were collected from 202 pediatric ALL patients. 155 patients (76.7%) harbored at least one mutation. The incidences of RAS signaling pathway mutations are different significantly between T-ALL and B-ALL. In B-ALL, the RAS pathway is mostly involved, and NRAS (17.6%), KRAS (22.7%), and PTPN11 (7.7%) were the three most frequently mutated genes. Co-occurring mutations of CREBBP and NRAS, FLT3, or PTPN11 (p=0.002, p=0.009, and p=0.003, respectively) were found in this cohort. The 3-year RFS rates for the RAS signaling pathway mutation-positive and negative cases was 76.5 % versus 89.7 % (p=0.012). Four cases relapsed in the lately 3years were RAS signaling pathway mutation-positive. RAS signaling pathway mutation is an important biomarker for poorer relapse-free survival in pediatric B-ALL patients despite good early MRD levels.

Genetic polymorphisms as predictors of methotrexate toxicity: literature review

Background. A significant advancement in the treatment of high-grade aggressive non-Hodgkin’s lymphomas and acute lymphoblastic leukemia is the inclusion of high-dose (1000–5000 mg/m2) methotrexate in the treatment protocol. This approach has significantly increased the long-term survival rate, but it has been associated with toxicity, requiring supportive care. Factors that predict toxicity were identified, including genes involved in the metabolism (MTHFR) or transport (SLCO1B1) of methotrexate. The analysis of methotrexate metabolism has identified additional genes responsible for the elimination of this drug, allowing for more effective prevention and treatment of methotrexate-associated toxicity.Aim. To study the genetic polymorphisms of enzymes involved in the methotrexate metabolism and associated toxicity in the treatment of pediatric acute lymphoblastic leukemia and non-Hodgkin’s lymphomas.Materials and methods. Data were analyzed in specialized medical databases such as Pubmed, Scopus, Web of Science, Frontiers, and Google Scholar from 2001 to 2024.Results. The main predictors of high-dose methotrexate-associated toxicity are gene polymorphisms in MTHFR, SLCO1B1, ARID5B.Conclusion. Despite the contradictory data presented in the literature, it is important to consider the detection of polymorphisms during high-dose methotrexate treatment in order to administer timely supportive care and prevent significant toxicity.

Terminal deoxynucleotidyl transferase expression in different subtypes of childhood B-cell acute lymphoblastic leukemia

The lack of expression of terminal deoxynucleotidyl transferase (TdT) is frequently associated with KMT2A-rearranged subtype of pediatric acute lymphoblastic leukemia (ALL). However, this association has not been investigated extensively in the Asian population. A retrospective analysis of TdT expression in pediatric B-cell ALL (B-ALL) was performed in patients treated using the Taiwan Pediatric Oncology Group (TPOG) ALL 2002 and 2013 protocols. Among the 331 patients with B-ALL, 12 patients showed TdT negativity at initial diagnosis. Among these, eight patients showed KMT2A rearrangement (66.7%). Other patients showing negative TdT expression had ETV6::RUNX1, MEF2D-rearranged, and other B-ALL subtypes. However, in the context of KMT2A-rearranged B-ALL (n = 20), only eight patients showed TdT negativity. The 5-year event-free survival and overall survival of patients with and without TdT expression were 83.8% versus 46.8% (P <0.001) and 86.3% versus 55.4% (P = 0.004), respectively. Moreover, several aberrant markers, such as CD2, CD56, CD7, and CD117, were rarely expressed in the B-ALL samples, and if expressed, they were enriched in specific genetic subtypes. The results of this study indicate that immunophenotypic features are correlated with specific genetic subtypes of childhood B-ALL.

A Study to Evaluate the Effectiveness and Safety of Prephase Steroid Treatment before Remission Induction Chemotherapy in Patients with Pediatric Acute Lymphoblastic Leukemia Using Common Data Model-Based Real-World Data: A Retrospective Observational Study.

Rapid reduction of leukemic cells in the bone marrow during remission induction chemotherapy (RIC) can lead to significant complications such as tumor lysis syndrome (TLS). We investigated whether prephase steroid treatment before RIC could decrease TLS incidence and improve overall survival in pediatric patients with acute lymphoblastic leukemia (ALL). Data were extracted from the Common Data Model databases in two tertiary-care hospitals in Seoul, South Korea. Patients were classified into the treated or untreated group if they had received RIC with prephase steroid treatment ≥7 days before RIC in 2012-2021 or not, respectively. Stabilized Inverse Probability of Treatment Weighting (sIPTW) was applied to ensure compatibility between the treated and untreated groups. The incidence of TLS within 14 days of starting RIC, overall survival (OS), and the incidence of adverse events of special interest were the primary endpoints. Multiple sensitivity analyses were performed. Baseline characteristics were effectively balanced between the treated (n=308.4) and untreated (n=246.6) groups after sIPTW. Prephase steroid treatment was associated with a significant 88% reduction in the risk of TLS (OR 0.12, 95% CI: 0.03-0.41). OS was numerically greater in the treated group than in the untreated group although the difference was not statistically significant (HR 0.64, 95% CI 0.25-1.64). The treated group experienced significantly elevated risks for hyperbilirubinemia and hyperglycemia. The reduction in TLS risk by prephase steroid treatment was maintained in all of the sensitivity analyses. Prephase steroid treatment for ≥7 days before RIC in pediatric patients with ALL reduces the risk of TLS, while careful monitoring for toxicities is necessary. If adequately analyzed, real-world data can provide crucial effectiveness and safety information for proper management of pediatric patients with ALL, for whom prospective randomized studies may be difficult to perform for ethical and practical reasons.

Expert recommendations for pancreatitis/pancreatic necrosis treatment after L-asparaginase in children with acute lymphoblastic leukemia

L-asparaginase is one of the most effective drugs in pediatric and adult acute lymphoblastic leukemia treatment. But drug side effects are an important problem. pancreatitis and pancreatic necrosis are not common (2–18 %) complication, but high chance of severe disease with fatal outcome make to bring in careful attention of pediatric oncologists-hematologists, surgeons, intensivists, radiologists. Recognizing multidisciplinary importance of this problem, at June 21st, 2023 at Morozov Children’s Clinical hospital a Round table on pancreatitis/pancreatic necrosis after L-asparaginase use was organized. This article presents expert recommendations from federal and regional clinics in diagnosis and treatment of such severe complication.

Evaluation of FOXP3 and IL10 as immunosuppressant markers in pediatric acute lymphocytic leukemia patients in Iraq

Background. Increased FOXP3+ Treg levels in the TME were positively correlated with a worse prognosis in certain cancer patients. FOXP3 was significantly overexpressed in pediatric B-ALL patients, and this overexpression was associated with a worse prognosis and increased risk of disease relapse. It is unknown if children that have the condition would have different prenatal immune development. This study investigates the relationship between IL10, and immunological development in pediatric ALL. Methods. The 70 blood samples from children between the ages of 2 and 14 for both sexes were obtained from patients with Acute lymphoblastic leukemia. Furthermore, this study comprised 54 healthy controls. Included in this study, FOXP3 expression on leukemic blast cells were assessed using flow cytometry. And IL10 were assessed using ELISA test. Results. Increase of FOXP3 cells was noticed in children with ALL compared to healthy individuals with significant increase of FOXP3 (mean ± SD, 91.156 ± 12.255 vs. 14.88 ± 7.897pg/ml (p &lt;0.05). In light of these findings, significant differences in the levels of FOXP3, which was higher in induction than consolidation stage of chemotherapy (mean ± SD, 91.24± 11.078vs. 86.35±5. 16.66) pg/ml (p &lt;0.05). Additionally, it was found that the prevalence of lymphoblast that express FOXP3 was notably higher in the HR group in contrast to the SR group (mean ± SD, 95.52± 5.79 vs. 42.88± 31.38) pg/ml (p &lt;0.05). Following these findings, significant differences in the levels of FOXP3 was higher in relapse than new diagnosis chemotherapy stage (mean ± SD, 95.66± 5.167 vs. 91.035±5. 13.177) pg/ml (p&lt;0.05). On the other hand, children with ALL were also found to have significantly higher levels of IL10 in the current study when compared to healthy controls (mean ± SD, 0.146 ± 0.145 vs. 0.076 ± 0.10 pg/ml (P &lt;0.05). Following these findings, significant differences in the levels of IL10 was higher in consolidation than induction chemotherapy stage (mean ± SD, 0.165± 0.084 vs.0 .0720±.018) pg/ml (p &lt;0.05), the serum levels of IL-10 were evaluated in the two groups: new diagnosis and relapse cases. As in the description profile, serum levels are higher in the relapse group with a highly significant difference. For the parameter IL10 (P ≤0.05). As for he mean level, it was as follows: of IL10 (0.130) pg/ml and (0.216) pg/ml, with (P-value =0.0001) in new diagnosis and relapse receptivity. Conclusions. According to our findings, B-ALL patients have significant amounts of both FOXP3 and IL10. This pilot study provides a novel way to look into the process mediating the appearance of these markers in a greater number of B-ALL patients at various stages of their treatment.

Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling

Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling.

Pharmacokinetics of PEGasparaginase in Infants with Acute Lymphoblastic Leukemia.

PEGasparaginase is known to be a critical drug for treating pediatric acute lymphoblastic leukemia (ALL), however, there is insufficient evidence to determine the optimal dose for infants who are less than one year of age at diagnosis. This international study was conducted to identify the pharmacokinetics of PEGasparaginase in infants with newly diagnosed ALL and gather insight into the clearance and dosing of this population. Infants with ALL who received treatment with PEGasparaginase were included in our population pharmacokinetic assessment employing non-linear mixed effects modelling (NONMEM). 68 infants with ALL, with a total of 388 asparaginase activity samples, were included. PEGasparaginase doses ranging from 400 to 3,663IU/m2 were administered either intravenously or intramuscularly. A one-compartment model with time-dependent clearance, modeled using a transit model, provided the best fit to the data. Body weight was significantly correlated with clearance and volume of distribution. The final model estimated a half-life of 11.7days just after administration, which decreased to 1.8days 14days after administration. Clearance was 19.5% lower during the post-induction treatment phase compared to induction. The pharmacokinetics of PEGasparaginase in infants diagnosed under one year of age with ALL is comparable to that of older children (1-18years). We recommend a PEGasparaginase dosing at 1,500IU/m2 for infants without dose adaptations according to age, and implementing therapeutic drug monitoring as standard practice.

Pneumocystis jirovecii pneumonia in paediatric acute lymphoblastic leukaemia: A report from the multi-international clinical trial AIEOP-BFM ALL 2009.

Pneumocystis jirovecii can cause life-threatening pneumonia (PjP), and patients with haematological malignancies are at high risk of this infection. Prophylactic measures have significantly decreased morbidity and mortality, but there is a paucity of contemporary data on the incidence and clinical course of PjP in well-defined and homogenous patient populations, such as children suffering from acute lymphoblastic leukaemia (ALL). In the multi-international trial AIEOP-BFM ALL2009, PjP was diagnosed in six children (incidence 1/1000) and was associated with insufficient prophylaxis in five of them. Although none of the patients died of PjP, the long-term impact of the infection is unclear.

Metabolic Fingerprint in Childhood Acute Lymphoblastic Leukemia.

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood malignancy. Despite high cure rates, several questions remain regarding predisposition, response to treatment, and prognosis of the disease. The role of intermediary metabolism in the individualized mechanistic pathways of the disease is unclear. We have hypothesized that children with any (sub)type of ALL have a distinct metabolomic fingerprint at diagnosis when compared: (i) to a control group; (ii) to children with a different (sub)type of ALL; (iii) to the end of the induction treatment. In this prospective case-control study (NCT03035344), plasma and urinary metabolites were analyzed in 34 children with ALL before the beginning (D0) and at the end of the induction treatment (D33). Their metabolic fingerprint was defined by targeted analysis of 106 metabolites and compared to that of an equal number of matched controls. Multivariate and univariate statistical analyses were performed using SIMCAP and scripts under the R programming language. Metabolomic analysis showed distinct changes in patients with ALL compared to controls on both D0 and D33. The metabolomic fingerprint within the patient group differed significantly between common B-ALL and pre-B ALL and between D0 and D33, reflecting the effect of treatment. We have further identified the major components of this metabolic dysregulation, indicating shifts in fatty acid synthesis, transfer and oxidation, in amino acid and glycerophospholipid metabolism, and in the glutaminolysis/TCA cycle. The disease type and time point-specific metabolic alterations observed in pediatric ALL are of particular interest as they may offer potential for the discovery of new prognostic biomarkers and therapeutic targets.

Abstract 5662: PDCD1 and CD48 significantly impact cancer recurrence and survival in pediatric acute lymphoblastic leukemia

Abstract Introduction: Immune checkpoints (ICPs) play a critical role in modulating the immune response, maintaining self-tolerance, and preventing excessive immune system activation. Dysregulation of immune checkpoints has been implicated in cancer progression and treatment resistance. In this study, we aimed to screen for dysregulated immune checkpoint genes that might be associated with cancer recurrence in pediatric acute lymphoblastic leukemia (ALL) following a course of cancer treatment. We hypothesized that certain ICPs would be significantly dysregulated in relapsed ALL patients, potentially providing insights into the underlying mechanisms driving therapy resistance and disease recurrence. Methods: 51 ICP genomic data (gene expression, copy number alterations (CNAs), and mutation) of133 patients with relapse information [relapse-free (n=29) and relapsed (n=104)] extracted from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) were examined in the study. Patient’s t-test (p-value &amp;lt; 0.05) was used to identify significant genetic factors between relapse-free and relapsed patients. Free and overall survival analyses were performed using log-rank test (p-value &amp;lt; 0.05) based on patient gene expression profiles. Results: Among the 51 genes examined, PDCD1, PVR, CD70, and CD48 were significantly upregulated in relapsed patients compared with relapse-free patients (P &amp;lt; 0.05). No significant CNAs nor mutations were detected in these four genes. Patients with high expression profiles of PDCD1 and CD48 at diagnosis were 1.71 and 1.47 more likely to relapse compared to patients with low expression profiles, respectively (P &amp;lt; 0.05). Furthermore, the upregulation of PDCD1 (P= 0.0004, HR= 1.972) and CD48 (P= 0.0344, HR= 1.533) demonstrated significantly increased mortality rates in patients following treatment, as indicated by overall survival analyses. Conclusion: The upregulation of PDCD1 and CD48 was significantly associated with relapse and survival of ALL patients. Promisingly, these two ICPs can potentially be used as prognostic biomarkers for relapse risk and rationale for alternative therapeutic strategies. Our study suggests that targeting PDCD1 and CD48 might be beneficial in enhancing the treatment efficiency and thereby reducing the recurrence risk. The study was funded by the Deputyship for Research and Innovation, Ministry of Education, Saudi Arabia (DRI-KSU-1273). Citation Format: Shatha Fawaz Alotaibi, Lames Abuhadi, Noura Alolyani, Moureq R. Alotaibi, Ali R. Alhoshani, Homood As Sobeai. PDCD1 and CD48 significantly impact cancer recurrence and survival in pediatric acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5662.

Abstract 1905: The ROR1 antibody-drug conjugate, MK-2140, enhances the efficacy of established drugs in preclinical models of pediatric acute lymphoblastic leukemia

Abstract Introduction: Children diagnosed with acute lymphoblastic leukemia (ALL) experience ~90% likelihood of cure. However, the outcome for high-risk ALL and children who relapse remains poor. Receptor tyrosine kinase like orphan 1 receptor (ROR1) is a cell surface antigen primarily expressed in embryonic tissue, but also overexpressed in hematological malignancies. UC961 is a humanized IgG monoclonal antibody with high affinity for ROR1. MK-2140 (Zilovertamab vedotin/VLS-101) and VLS-211 are antibody-drug conjugates (ADCs) of UC961 with monomethyl auristatin-E or PNU payloads, respectively. This study evaluated the in vivo efficacy of MK-2140 and VLS211 against pediatric ALL patient derived xenografts (PDXs). Methods: PDXs were selected based on ROR1 mRNA (RNA-seq) and cell surface (flow cytometry) expression and grown as orthotopic disease in immune-deficient NSG mice. Engraftment and drug responses were assessed by flow cytometric enumeration of the proportion of human versus mouse CD45+ cells in peripheral blood (%huCD45+). Events were defined a priori as the %huCD45+ exceeding 25% or leukemia-related morbidity. MK-2140 (2.5 and 5.0 mg/kg) and VLS-211 (0.25 and 0.5 mg/kg) were administered intravenously, weekly x 3 weeks. Vincristine (0.15 mg/kg once weekly), dexamethasone (5 mg/kg daily x 5) and Lasparaginase (1,250 U/kg daily x 5) (VXL) were administered intraperitoneally for 3 weeks, followed by MK-2140 (5 mg/kg weekly x 3 weeks). Drug efficacy was assessed by event-free survival of treated (T) and control (C) groups and by stringent objective response criteria. In receptor occupancy/pharmacokinetic studies, a single dose of MK-2140 was administered and samples collected for analysis at discrete timepoints thereafter. Results: ROR1 mRNA and cell surface expression showed a significant correlation (R=0.83, P=0.021). MK-2140 significantly delayed disease progression in 4/7 PDXs compared to vehicle control (T-C, -2.6 to 20.0 days). At the highest dose, MK-2140 elicited objective responses (remissions) in two PDXs. VLS-211 significantly delayed disease progression in 5/7 PDXs (TC, -1.8 to 70.5 days), including 3 objective responses. Prior treatment with VXL followed by MK-2140 significantly delayed disease progression compared to VXL alone (T-C, 56.8 versus 35.2 days). MK-2140 bound to ROR1+ cells with near 100% occupancy within two hours of treatment, which was sustained for up to 96 h. Consistent with the receptor occupancy data, plasma levels of MK-2140 were maintained at &amp;gt;100 nM for at least 96 h after a single dose (5 mg/kg). Conclusions: MK-2140 and VLS-211 exerted significant single-agent in vivo activity against a panel of pediatric ALL PDXs. MK-2140 significantly enhanced the efficacy of an induction-type regimen and should be considered for further evaluation in a minimal residual disease setting. Citation Format: Richard B. Lock, Kathryn Evans, Ben Watts, Edward P. Bowman, Steven Neuhauser, Timothy Stearns, Jeffrey H. Chuang, Vivek M. Phillip, Katti A. Jessen, Emily L. Jocoy, Carol J. Bult, Beverly A. Teicher, Malcolm A. Smith. The ROR1 antibody-drug conjugate, MK-2140, enhances the efficacy of established drugs in preclinical models of pediatric acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1905.

Abstract 3952: Multiomic single-cell tumor evolution models of minimal residual disease in pediatric B-cell acute lymphoblastic leukemia

Abstract Detection of minimal residual disease (MRD) after initial diagnosis (IDX) and therapy is a strong prognostic marker for relapse in pediatric B-cell acute lymphoblastic leukemia (B-ALL). Previous studies have explored clonal genetic and gene expression changes between initial diagnosis and relapse. However, studying tumor cells present at MRD is challenging due to their low abundance. Examining the genomic profiles of leukemia cells that resist induction chemotherapy and understanding their evolutionary relationship to cells present at diagnosis may lead to a better understanding of the cells that eventually seed relapse. We analyzed somatic point mutations, indels, and copy number variants from 41 pediatric B-ALL patients with high-risk B-ALL. We specifically focused on patients from the following four common high-risk subtypes: KMT2A-rearranged, Ph+, Ph-like, and iAMP21, who had detectable disease at the end of induction. Leukemic burden at end-induction (day 29) ranged from 0.03% to 66.00%. Data were generated in partnership with the National Cancer Institute’s Human Tumor Atlas Network and the Children’s Oncology Group. Our data set of 41 patients includes 39 with paired initial diagnostic and end-induction samples that we used to create tumor evolution models based on single cells across disease stages. We produced single-cell multiome gene expression (scRNA) and chromatin accessibility (scATAC) profiles (10x Genomics) with a median of 7428 leukemic blast cells at IDX (range: 2490-14219) and 1907 at MRD (range: 240-10167) after filtering. We called somatic mutations from scRNA and scATAC using SComatic and Monopogen, and we detected copy number changes using Numbat and EpiAneufinder. We also designed a targeted DNA sequencing panel including 335 variants based on B-ALL literature and database searches to produce scDNA (Mission Bio) for 24 patients (16 IDX-MRD pairs) with a median of 2346 cells profiled at IDX (range: 340-8849) and 1828 at MRD (range: 596-5133). We built tumor phylogenies based on somatic SNVs and CNVs with COMPASS. Using multiple tools and complementary single-cell omics data types to detect somatic changes improved our confidence in the events used for tumor evolution tree construction. Our approach allowed us to define recurrent genomic events and patterns across pediatric B-ALL subtypes and to describe the clonal evolution of cells measured at initial diagnostic and end-induction disease stages. We were also able to link cell-specific mutation events to their transcriptional and epigenomic signatures, including mapping mutation events along the B-cell development trajectory and within differentially expressed gene pathways. Some cases showed dramatic shifts in subclonal structure between IDX and MRD that may be related to therapy-induced clonal selection, such as a loss of NRAS hotspot mutation. Citation Format: Steven M. Foltz, Avi Loren, Changya Chen, Rushabh Mehta, Elizabeth Li, Jason Xu, Fatemeh Alikarami, Kathrin M. Bernt, Kai Tan. Multiomic single-cell tumor evolution models of minimal residual disease in pediatric B-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3952.

Abstract 45: Driving AMPK signaling in CD4+ CART cells enhances metabolic capacity, memory formation, and anti-leukemia activity

Abstract Background: While Chimeric Antigen Receptor (CAR)T cell therapy has seen great success in pediatric and young adult acute lymphoblastic leukemia, up to 50% of patients will relapse following treatment. Increased memory formation and mitochondrial capacity, particularly in the CD4+ subset, have been linked to improved CART cell function and enhanced in vivo persistence, leading to long-term relapse-free survival. AMP-activated protein kinase (AMPK) is a cellular energy sensor responsible for promoting metabolic efficiency and T cell memory formation. We have previously demonstrated AMPK activity can be increased in human T cells via overexpression of the AMPKγ2 domain. We hypothesized that overexpression of AMPKγ2 in CART cells would enhance their metabolic capacity and improve their anti-leukemia function. Methods: Human CART cells bearing a CD19-CAR utilizing a 41BB costimulatory domain were generated from healthy human donors via lentiviral transduction and co-transduced with AMPKγ2 (AMPK) or an empty vector (EV) control. Flow sorting for the co-transduced populations yielded &amp;gt;95% CD4+ CART cells. CARTs were expanded in IL-2 for approximately 2 weeks, followed by overnight stimulation and subsequent metabolic analysis using the Seahorse Metabolic Analyzer. Memory status was assessed by CD62L and CCR7 co-expression. In vitro CART function was assessed using Zs-green+ NALM6 targets, with loss of green fluorescence over time measured on the Incucyte analyzer. Where indicated, tumor conditioned media was harvested from 72-hour NALM6 cultures. For in vivo experiments, immunodeficient NOD-scid IL2Rγnull (NSG) mice were injected with luciferase+ NALM6 targets, followed one week later by AMPK- or EV-CARTs. Leukemia burden, via IVIS imaging, and survival were followed over time. Results: CD4+ CARTs co-transduced with AMPKγ2 (AMPK-CARTs) increased oxygen consumption, maximal respiration, and spare respiratory capacity following overnight stimulation by ~20% compared to CARTs co-transduced with the EV (EV-CARTs) (p&amp;lt;0.05). Following expansion, CD62L+CCR7+ central memory cells were 4.5-fold more abundant in the AMPK-CART group (2.4-6.2-fold, p&amp;lt;0.01). In vitro, while AMPK-CARTs demonstrated similar cytotoxicity against NALM6 targets as EV-CARTs in standard media, they mediated faster killing of NALM6 targets when challenged in tumor conditioned media (p&amp;lt;0.001). In vivo, recipients of AMPK-CARTs showed a consistent decrease in tumor burden as measured by median radiance values, translating to a significant survival advantage (p&amp;lt;0.05). Conclusions: Increasing AMPK signaling in CD4+ CARTs via overexpression of AMPKγ2 improved metabolic profile, increased memory generation, and enhanced toxicity against leukemia targets both in vitro and in vivo. Together, these features make elevating AMPK signaling an attractive method to increase the efficacy of CART therapy. Citation Format: Erica Braverman, Herbert Schuler, Mengtao Qin, Craig Byersdorfer. Driving AMPK signaling in CD4+ CART cells enhances metabolic capacity, memory formation, and anti-leukemia activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 45.