Evaluating Methotrexate Toxicity and Its Association with ABCB1 Genetic Polymorphism in Children with Acute Lymphoblastic Leukemia

Background: Acute lymphoblastic leukemia (ALL) is among the most prevalent type of hematologic malignancy in children. The Children’s Oncology Group protocol recognizes methotrexate (MTX) as a therapy for this problem in children, despite its several complications. The relationship between MTX toxicity and ATP-binding cassette subfamily B member 1 (ABCB1) SNPs in ALL children patients has been investigated in many studies. Objectives: Regarding the controversial findings reported by these studies, the present work aims to evaluate Methotrexate toxicity and its association with ABCB1 Genetic Polymorphism in ALL pediatric patients. Methods: Blood samples were collected from pediatric ALL patients. Next, DNA was extracted and polymerase chain reaction (PCR) was conducted using 300 μMol/μL of direct primers in 50 µL as the ultimate volume. ABCB1 gene was amplified using the PCR technique, and 0.5% agarose gel electrophoresis was used to identify reaction products. Afterward, the PCR fragments’ length was proved by observing through UV-transilluminator. Finally, liver and blood toxicity was studied in all cases under treatment with MTX. Results: In the present study, 81 children with ALL (36 females and 45 males) with a mean age of 6.32 ± 3.08 years old were examined. The ABCB1 1199 G->A gene mutation frequency and the ABCB1 3435 C->T gene mutation frequency was 4.9 and 70.4%, respectively. The results showed no statistically significant difference between leukopenia, gastrointestinal toxicity, renal toxicity, hepatotoxicity, anemia, thrombocytopenia, and neutropenia in cases having homozygous heterozygous ABCB1 3435 C->T and ABCB1 1199 G->A mutant polymorphisms than those having ordinary polymorphism. Conclusions: Overall, it seems that C3435 T, G1199A, and ABCB1 are not significant MTX toxicity markers in pediatric ALL cases.

Transcriptional and Mutational Profiling of B-Other Acute Lymphoblastic Leukemia for Improved Diagnostics

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common cancer in children, and significant progress has been made in diagnostics and the treatment of this disease based on the subtypes of BCP-ALL. However, in a large proportion of cases (B-other), recurrent BCP-ALL-associated genomic alterations remain unidentifiable by current diagnostic procedures. In this study, we performed RNA sequencing and analyzed gene fusions, expression profiles, and mutations in diagnostic samples of 185 children with BCP-ALL. Gene expression clustering showed that a subset of B-other samples partially clusters with some of the known subgroups, particularly DUX4-positive. Mutation analysis coupled with gene expression profiling revealed the presence of distinctive BCP-ALL subgroups, characterized by the presence of mutations in known ALL driver genes, e.g., PAX5 and IKZF1. Moreover, we identified novel fusion partners of lymphoid lineage transcriptional factors ETV6, IKZF1 and PAX5. In addition, we report on low blast count detection thresholds and show that the use of EDTA tubes for sample collection does not have adverse effects on sequencing and downstream analysis. Taken together, our findings demonstrate the applicability of whole-transcriptome sequencing for personalized diagnostics in pediatric ALL, including tentative classification of the B-other cases that are difficult to diagnose using conventional methods.

Genomic Heterogeneity Contributed To The Different Survival Between Adult and Pediatric Acute Lymphoblastic Leukemia

Prognosis of acute lymphoblastic leukemia (ALL) in adults is inferior to children. Hence, ALL is still a challenging disease to be cured in adult population. Aberrant genetic alterations have been observed previously in ALL, while the patterns of differential gene alteration have not much been comprehensively determined in the adult and pediatric ALL on a genome-wide scale. This study was attempted to investigate the biological differences in genomic profiling between the adults and children with ALL, and the relationship between the genomic heterogeneity and prognosis. The results showed the similar common mutation types in two populations but the increased prevalence of genetic alterations in adult ALL. The median number of detected gene mutations was 17 (range: 1–53) per sample in adult ALL and 4.5 (range: 1–19) in pediatric ALL(P<0.001). A significant correlation between the increased number of gene mutations and age was found (R2 = 0.5853, P<0.001). 122 and 53 driver genes were identified in adult and pediatric ALL samples, respectively. The IKZF1, IDH1 and TTN mutations were significantly enriched in adult ALL. The incidence of relapse was 40.0% and 9.6% in the adult and pediatric ALL, respectively(P=0.0003). The overall survival (OS) and relapse free survival (RFS) of adult ALL were poorer than pediatric ALL (P=0.0002, P<0.001, respectively). This genomic landscape enhanced the understanding of the biological differences of ALL between the two populations and provided a clue for novel therapeutic approaches.

Characteristics in gut microbiome is associated with chemotherapy-induced pneumonia in pediatric acute lymphoblastic leukemia

Background Children with acute lymphoblastic leukemia (ALL) undergoing chemotherapy experience a relatively high risk of infection. And the disturbance of gut microbiota is generally believed to impair intestinal barrier function and may induce bacterial infections and inflammation. The study aimed to investigate the alterations in the gut microbiota and assess its relationship with chemotherapy-induced pneumonia in pediatric ALL patients. Methods We conducted a case–control study with 14 cases affected by pneumonia and 44 unaffected subjects and characterized the physiological parameters and gut microbiota by microarray-based technique. Results There were significant differences in α- and β-diversity in the affected group compared with the control group. At species level, the LEfSe analysis revealed that Enterococcus malodoratus, Ochrobactrum anthropi and Actinomyces cardiffensis were significantly abundant in the affected subjects. A receiver operating characteristic (ROC) curve yielded the area under the curve (AUC) of 0.773 for classification between the two groups. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in the bacterial secretion system were more enriched in the affected group than in the control group. Conclusions Gut microbiota alteration was associated with chemotherapy-induced pneumonia in pediatric ALL patients, which provided a new perspective on the personalized clinical care of pediatric ALL.

Evaluation of DNA Methylation at Birth in Monozygotic Twin Pairs Discordant for Acute Lymphoblastic Leukemia

Background: Aberrant patterns of DNA methylation constitute a key feature of pediatric acute lymphoblastic leukemia (ALL) at diagnosis, however its role as a predisposing or early contributor to the development of ALL remains unknown. We employed a discordant monozygotic twin model to identify epigenetic variation associated with future development of pediatric ALL through evaluation of DNA methylation at birth. Methods: Twin pairs discordant for the development of pediatric ALL were identified using linked data from the California Cancer Registry and California Birth Statistical Master File spanning from 1989 to 2015. Archived dried neonatal blood spots were obtained from 86 same-gender twin pairs with available materials from the California Biobank Program. Following isolation of genomic DNA from DBS samples, monozygosity was confirmed in 43 of 86 twin pairs through an identity-by-descent analysis from a genome-wide SNP-array. Epigenome-wide DNA methylation assessment of the 43 discordant monozygotic twin pairs was conducted using the Illumina Infinium MethylationEPIC BeadChip kit (Illumina, San Diego, CA, USA). Data preprocessing and quality control measures were conducted in R, using SeSAMe for data normalization. Two twin pairs were omitted due to failure to pass quality control measures. Within-pair analysis was conducted through identification of array probes with absolute differences in methylation beta values greater than 15% between case and control siblings of a twin pair unit. Differentially methylated probes (DMP) were identified using a conditional logistic regression model accounting for array-specific variation, nucleated cell proportions, and appropriate control for the paired nature of the dataset. Differentially methylated regions (DMR) were defined by regional correlation of p-values from the conditional logistic regression model. Gene set enrichment analysis was conducted on significant probes identified through the within pair and regression analysis. Results: The discordant twin cohort (n = 41 pairs) included 24 female and 17 male pairs. Median gestational age was 258 days, ranging from 184 to 306 days. Age of diagnosis in the case twin ranged from &lt;1 to 23 years (median = 5). There was no significant association between birthweight and case status (paired Wilcoxon signed rank test p = 0.22). No significant differences in nucleated cell proportions were identified in deconvolution analysis. Within-pair analysis identified a total of 18,001 probes with absolute methylation variation greater than 15% across the 41 twin pairs, with 3,984 recurrently variable across more than one pair. Gene ontology analysis of these recurrently variable sites revealed an enrichment of immune-related processes in 7 of the top 15 terms with nominal p-value &lt;0.05, though no terms were significant after correction for multiple comparisons. Conditional logistic regression was conducted on 37 twin pairs, with T-cell cases (n=4) omitted to improve data resolution. This resulted in 240 significant DMPs with p-values below an FDR threshold of 0.05. Of these significant probes, 20 associate with genes previously reported to have altered DNA methylation in ALL at diagnosis. Regional analysis identified 10 significant DMRs with adjusted p-values below 0.05, with the top association encompassing a 454bp region on chromosome 6 located near TRIM39-RPP21 (adjusted p-value 2.39e-05). Notably, conditional regression analysis revealed a significant negative bias in coefficients (409,812 of 710,010 probes, binomial exact test p &lt;2.2e-16), indicating a global tendency toward hypomethylation in cases compared to unaffected siblings (Figure 1). The strength of this bias was greater in probes associated with open sea regions compared to those in island regions, as well as promoter-associated probes. Conclusions: This novel analysis of DNA methylation at birth in ALL-discordant monozygotic twins identified sites of differential methylation associated with immune regulation. In addition, these results provide evidence of an association between global DNA hypomethylation and future development of ALL in one member of a genetically identical twin pair. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Clostridioides Difficile Carriage Rate Increases during Pediatric ALL Treatment

Background Clostridioides difficile infection (CDI) is frequent in pediatric patients with acute lymphoblastic leukemia (ALL). Studies have shown upwards of 20% positivity rate in CDI testing among pediatric oncology patients, and up to several percent in pediatric ALL patients in the first 180 days of diagnosis. Antibiotic usage has been variably linked to CDI positivity in these populations. As CDI testing is usually done in symptomatic patients, the question of C. difficile carriage versus CDI has not been addressed. We and others have shown that microbiome is altered in pediatric ALL patients and survivors. We conducted a longitudinal stool microbiome study in pediatric ALL patients and tested the hypothesis that alteration of the microbiome during ALL treatment promotes C. difficile carriage. Methods Children with ALL were prospectively recruited on a rolling basis and stool samples were collected at diagnosis (Dx) and at the end of induction (EOI), consolidation (EOC), interim maintenance I (IMI), delayed intensification (DI), interim maintenance II (IMII), as well as approximately 3 months and 6 months into maintenance (M3, M6). Stool samples from healthy siblings were used as controls. TaqMan-based quantitative-PCR (qPCR) was performed on DNA extracted from stool samples to detect C. diff 16S rRNA, tcdA, (Toxin A) and tcdB (Toxin B) genes . Samples positive or either tcdA or tcdB, or both, were designated positive for toxigenic C. difficile. 16S rRNA hypervariable region V4 was sequenced and analyzed for microbiome diversity and relative abundance of microbiota. Results 32 ALL patients age 3 months-19 years were included. The diagnoses were 12 standard risk and 14 high risk pre-B ALL, 5 T-ALL, and 1 relapsed pre-B ALL. Stool samples were collected from 18 healthy siblings. The numbers of samples tested at each treatment phase were: 29 Dx, 24 EOI, 23 EOC, 25 IMI, 21 DI, 6 IMII, 14 M3, 7 M6. No patient had symptoms suggestive of CDI, and no patient was clinically tested or treated for CDI. Total number of stool samples tested was 149, of which 43 (29%) were positive for toxigenic C. difficile (Figure 1). At diagnosis, 2/29 (7%) patients were positive, compared to 2/18 (11%) in healthy siblings. At EOI, positivity rate increased to 17%, then up to 40% - 52% at EOC, IMI, and DI. C. difficile positivity were lower around 30% at M3 and M6, although few patients reached maintenance to contribute samples for analysis. Twenty-five patients (78%) were positive at some phase. Longitudinal analysis of individual patients showed that C. difficile positivity was intermittent through treatment phases; only 3 patients remained persistently positive. Seven patients (22%) were never positive. Multivariate analysis showed that EOC, IMI, and DI treatment phases were significant risk factors for C. difficile carriage. Neither the number of antibiotics nor the number of antibiotic courses administered was significant. Leukemia risk stratification (high risk versus standard risk) also did not correlate with C. difficile positivity. Microbiome analysis showed statistically significant differences in relative abundance of certain taxa between C. diff positive and negative samples at the class, order, and family levels (Figure 2). Examples include depletion of the class Verrucomicrobiae, which contains protective Akkermansia, and depletion of the common taxa Bifidobacteriaceae and Ruminococcaceae. Conclusion Longitudinal PCR testing of toxigenic C. difficile in pediatric ALL patients demonstrated increased C. difficile prevalence further into treatment phases. C. difficile carriage correlated significantly with depletion of several bacterial taxa, as microbiome diversity decreased overall with successive treatment phases. Our data lend support to the hypothesis that altered microbiome in ALL treatment allows permissibility for C. difficile carriage. In addition, no C. difficile positive patient had symptoms of CDI, therefore, caution must be taken in clinical testing, as there is a high asymptomatic carriage rate. Further longitudinal testing during maintenance and off-therapy is needed to see if C. difficile carriage rate returns to baseline and correlates with recovery of gut microbiome. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Physical Therapy Utilization Among Hospitalized Patients with Pediatric Acute Lymphoblastic Leukemia

Background: Pediatric acute lymphoblastic leukemia (ALL) patients have excellent survival outcomes, yet remain at increased risk for impaired physical function due to multiple chemotherapy-associated conditions including myopathy, peripheral neuropathy, bone toxicities, and fatigue. While initiating physical therapy (PT) early in treatment is likely to improve physical function and overall health of children with ALL, there are no published recommendations to guide PT service delivery for this population. In fact, utilization of PT and factors associated with utilization during planned and unplanned hospitalizations are not known. We sought to determine patterns of inpatient PT utilization in pediatric ALL patients, and its association with patient and hospital factors. Methods: Leveraging the Premier Healthcare Database, we conducted a cohort study that included participants hospitalized with ALL at 0-21 years of age from January 1, 2010 through March 31, 2017. Patients who underwent bone marrow transplant or had traumatic injuries unrelated to ALL therapy were excluded. The primary outcome was receipt of inpatient PT, identified by billing claims, within one year of first hospitalization. A multivariable logistic regression model was used to estimate odds ratios (OR) and 95% confidence intervals (CI) of sociodemographic and clinical variables associated with PT. Results: Our cohort included 5,488 pediatric ALL patients admitted to 330 hospitals (42.3% female, 56.0% White, median age 7 years). Among these patients, 1,491 (27.2%) received PT within one year of their first admission, with 840 (15.3%) receiving PT during their first admission (Figure). For inpatient hospital stays in which participants received PT, the median length of stay was 9 (interquartile range [IQR] 4-18) days, and the median number of PT encounters per stay was 2 (IQR 1-4). Of 426 patients who had a diagnosis of peripheral neuropathy (n=334), myopathy (n=35), or avascular necrosis (n=74), 251(58.9%) received PT within a year of their first ALL admission. Compared with patients 0-4 years old, those aged 5-9 were less likely to receive PT (OR=0.71, 95% CI: 0.60-0.84), while those aged 10-14 (OR=1.38, 95% CI: 1.15-1.66) and 15-21 (OR=1.44, 95% CI: 1.20-1.73) were more likely to receive PT (Table). Patient factors associated with receiving PT included Hispanic ethnicity (OR=1.22, 95% CI: 1.01-1.46) and a history of an intensive care unit stay (OR=2.67, 95% CI: 2.28-3.11). Patients at teaching hospitals (OR= 1.64, 95% CI 1.39-1.89) were more likely to receive PT than those at non-teaching hospitals, while patients at rural hospitals (OR=0.39, 95% CI: 0.27-0.56) were less likely to receive PT than those at urban hospitals. Compared to patients treated by a pediatric hematologist/oncologist, patients treated by a non-hematology/oncology pediatric (OR=0.53, 95% CI:0.44-0.63) or adult (OR=0.46, 95% CI:0.37-0.57) specialist were less likely to receive PT. PT utilization also varied significantly by geographic region, and hospital size, while patient sex and insurance coverage did not appear to impact PT utilization (Table). Conclusions: Less than 30% of pediatric ALL patients receive inpatient PT within a year of their first hospitalization. Interventions to increase inpatient PT services to pediatric ALL patients and address disparities in PT utilization would be desirable to improve the physical function and long-term health of survivors. Figure 1 Figure 1. Disclosures Ma: Celgene/Bristol Myers Squibb: Consultancy, Research Funding.

A Phase I Open Label Dose Escalation Study of MB-CART19.1 in Relapsed and Refractory CD19+ B Cell Malignancies, Interim Preliminary Results in Pediatric ALL, Adult ALL Including CLL Cohorts

Introduction This phase I first-in-human clinical study assesses the safety and preliminary efficacy of a CD19-directed, CAR (4-1BBz) gene-modified, autologous T-cell immunotherapy (MB-CART19.1) intended for use in pediatric and adult patients with relapsed or refractory B-cell acute lymphoblastic leukemia (ALL) and Non-Hodgkin lymphoma (NHL). The study also evaluates the feasibility of a hybrid manufacturing model, combining central and academic manufacturing capabilities with central QP oversight. Methods MB-CART19.1 is evaluated in a Phase I (EudraCT 2017-002848-32) multi-center, open label, dose escalation trial enrolling 33 to 48 patients in three disease cohorts, defined by disease biology and age. Pediatric (1-17 years) and adult patients are eligible if diagnosed with relapsed/refractory (r/r) CD19-expressing B-cell ALL or B-cell high-grade and low-grade (adults) NHL, including chronic lymphocytic leukemia (CLL). Enrollment is still ongoing. The starting material, a fresh patient leukapheresis product, is enriched for CD4/CD8 T-cells, transduced with a lentiviral vector (LV) and expanded using the CliniMACS Prodigy System allowing a high degree of control and consistency of the manufacturing process in both a central and decentralized facilities. MB-CART19.1 is presented as fresh cellular dispersion for single infusion and undergoes central release. Subjects undergo lymphodepletion with fludarabine (25 mg/m 2 daily for 3 days) and cyclophosphamide (1000 mg/m 2 on day -3). Dose escalation includes 3 dose levels (DL) 5x10 5 (DL I), 1x10 6 (DL II), 3x10 6 (DL III) CAR T cells/kg BW, respectively, and a safety dose level 0. The primary objective is to determine the recommended dose of MB-CART19.1. Secondary objectives are preliminary efficacy parameters evaluation of as well as CART persistence. Results Disease cohort I: pediatric ALL and aggressive NHL, 1-17 years. Up to the data lock point for interim analysis (DLP, 02 June 2021), 9 pediatric ALL patients were treated, 6 at DL I and 3 at DL II. All 9 patients completed the 28 days safety follow-up. At DL I, 5 of 6 patients experienced CRS (4 grade I-II, 1 grade III,) starting 5 to 7 days after IMP infusion. Two CRS cases were managed with tocilizumab and resolved within 1-2 weeks. 1 patient developed signs of neurotoxicity (grade IV seizure) concurrently with grade II CRS, which was effectively managed and fully resolved within 48 hours. The event was evaluated as DLT and led to the extension of the dose group from 3 to 6 patients. No further neurotoxicities occurred. Four of 6 patients treated at DL I finished the active part of the trial (12 months after administration of IMP) in CR-MRD and entered the long term follow-up. Two patients had CD19-negative relapses 4 and 10 months post MB-CART19.1 infusion. At DL II, 1 patient completed the 6 months follow up in ongoing CR, and 2 patients relapsed. Disease cohort II adult ALL: Up to the DLP, 4 adult ALL patients were treated at DL I. 1 patient died due to progression of disease on day 20 after the IMP infusion. All 4 adult patients experienced a grade I or II CRS all cases were reversible within 1-2 weeks , 1 patient received tocilizumab One patient developed neurologic symptoms (grade III visual impairment and grade III muscle weakness right-sided) with onset 41 and 72 days after administration of MB-CART19.1, respectively. 2 of the 3 patients who completed the safety follow-up finished the active part of the trial and entered the long-term follow-up, both in molecular CR up to Month 6. Disease cohort III adult NHL/CLL: 4 patients were enrolled with the starting dose of 1x10 6 CAR+ cells/kg (DL II). 1 patient experienced grade III CRS and was treated with tocilizumab. 3 patients completed the 28 days safety follow up. One patient with CLL achieved a CR, which is maintained at 6 months. Another CLL patient was in PR at the assessment visit Day 28. Data from the 2 other patients, 1 with MCL and 1 with DLBCL were in PR at month 3. Later data is not yet available. Conclusions 18 of 19 patients completed the follow-up safety period of 28 days defined as observation period for dose limiting toxicity (DLT). One DLT was observed as well as 3 grade III CRS events and 1 grade III neurological event. Early efficacy results are very encouraging. Longer follow-up will establish whether treatment results in durable responses. The hybrid manufacturing model provides flexibility and a timely delivery of the fresh drug product to the patients Disclosures Hanssens: Miltenyi Biomedicine GmbH: Current Employment. Stelljes: MSD: Consultancy, Speakers Bureau; Novartis: Consultancy, Speakers Bureau; Celgene/BMS: Consultancy, Speakers Bureau; Kite/Gilead: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; Medac: Speakers Bureau; Pfizer: Consultancy, Research Funding, Speakers Bureau. Bethge: Novartis: Consultancy, Honoraria, Speakers Bureau; Kite-Gilead: Consultancy, Honoraria, Speakers Bureau; Miltenyi Biotec: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau. Yakushina: Miltenyi Biomedicine GmbH: Current Employment. Holtkamp: Miltenyi Biomedicine GmbH: Current Employment. Assenmacher: Miltenyi Biotec: Current Employment. Jurk: Miltenyi Biotec: Current Employment. Rauser: Miltenyi Biomedicine GmbH: Current Employment. Schneider: Employee of Lentigen Technology, a Miltenyi Biotec Company: Current Employment. Rossig: AdBoards by Amgen: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; BMS and Celgene: Honoraria.

Dysregulation of Epigenetic Landscape Uncovered the Mechanisms Underlying the Relapse of Pediatric Acute Lymphoblastic Leukemia with NSD2 Mutation

Background: Relapse from acute lymphoblastic leukemia (ALL) is one of the most common causes of pediatric cancer-related death. Early relapse of ALL is associated with recurrent mutations of histone methyltransferase NSD2 (nuclear receptor binding SET domain protein 2), which is specific for H3K36me2, suggesting a link to therapy resistance or other mechanisms underlying relapse such as central neural system (CNS) infiltration. NSD2 p.E1099K affects gene expression through disturbing the balance of H3K36me2/H3K27me3. Using CRISPR/Cas9-edited isogenic ALL cell lines and PDX cells, we found that NSD2 p.E1099K drives oncogenic programming, CNS infiltration and glucocorticoid (GC) resistance. However, the molecular mechanisms underlying the relapse of this subtype of ALL are still under investigation. Aim: To elucidate the epigenetic landscape underlying the mechanism of the relapse of pediatric ALL with NSD2 mutation. Methods: We performed in vivo experiments to observe tumor burden, leukemia cell infiltration and survival of the NOD/SCID mice injected with a NSD2 p.E1099K mutation knock-out SEM cell line and knock-in CEM cell line. We determined transcriptome (RNA-Seq), chromatin accessibility (ATAC-Seq) in isogenic RCH-ACV, SEM, RPMI-8402 and CEM cell lines, transcription factor binding and histone modification (ChIP-Seq) and 3D organization (Hi-C) in RCH-ACV cells. Finally, we integrated analysis of RNA-Seq, ATAC-Seq, ChIP-Seq and Hi-C to comprehensively disclose the epigenetic landscape in ALL with NSD2 mutation. Results: NOD/SCID mice xenografted with NSD2 mutant cells developed high tumor burden and infiltration to spleen, liver and brain while the mice injected with WT cells accumulated significant less tumor cells and had extended survival. RNA-Seq analysis showed that reversion of NSD2 mutation to WT caused more genes downregulated while insertion of NSD2 mutation to WT cells led to more genes upregulated (Mutant vs WT: RCH-ACV 838 vs 494, SEM 1567 vs 1158, RPMI-8402 1922 vs 1745, CEM 1809 vs 1031). 50 upregulated genes and 3 downregulated genes were in common in B-ALL and T-ALL with NSD2 mutation. Most of the upregulated genes correlated with neural development and adhesion which might contribute to CNS infiltration (e.g., NCAM1 and NEO1). A few genes were associated with GC resistance such as decreased NR3C1 and increased NR3C2. Accordingly, ATAC-Seq showed that NSD2 mutant cells had more open chromatin peaks than those of WT (RCH-ACV 4853 vs 3212, SEM 10052 vs 7595, RPMI-8402 20392 vs 12133, CEM 10155 vs 6437). ChIP-Seq revealed general large gains of H3K36me2 in intergenic regions in NSD2 mutant cells. Importantly, genes upregulated with NSD2 mutation (e.g., NCAM1 and NEO1) lost H3K27me3 at promoters but gained H3K36me2 at promoters and whole gene bodies, accompanied with increased H3K27ac at enhancers. Conversely, a small subset of genes gained H3K27me3 and lost H3K36me2 in their promoters. Concentrated H3K36me2 in gene bodies diffused and broadened was less prominent and H3K27me3 accumulation became dominant. This for example was associated with repression of NR3C1 to drive GC resistance of NSD2 mutant cells. Genes upregulated in NSD2 mutant cells were enriched for binding sites for lymphoid transcriptional activators such as EBF1 and IRF2. The promoters of the downregulated genes had motifs for transcription factors poorly expressed in lymphoid cells and were enriched for binding sites for the BCL6 transcriptional repressor. Hi-C analysis revealed 430 topologically associated domains (TADs) with increased loop interactions while 136 TADs with decreased interactions were in NSD2 mutant cells compared to WT cells. Overall, 491 regions switched from compartment A to B and 444 regions switched from B to A in NSD2 mutant cells compared to WT cells. Compartment switching from inactive B to active A correlated with upregulated gene expression levels while the reverse was true for switching from A to B. Increased intra-TAD interactions were linked to upregulated genes while decreased intra-TAD interactions were linked to downregulated genes. Conclusions: The NSD2 mutation led to increased tumor burden, CNS infiltration and glucocorticoid resistance due to dysregulation of epigenetic patterns and 3D chromatin architecture, indicating mechanisms underlying the relapse of pediatric ALL and potential therapeutic targets in ALL with NSD2 mutation. Disclosures Licht: Epizyme: Research Funding.