Primary B-cell Acute Lymphoblastic Leukemia Research Articles

Second primary B-ALL after exposure to lenalidomide for multiple myeloma: A US multicenter study.

7533 Background: Maintenance treatment (rx) with lenalidomide (R) improves overall survival (OS) in multiple myeloma (MM). We report a retrospective cohort of patients (pts) with second primary B-cell acute lymphoblastic leukemia (ALL) diagnosed after R-rx for MM. Methods: We included pts who were exposed to at least 1 yr of R for MM rx prior to ALL dx. After approval by institutional review board, data were collected by chart review at participating centers using Redcap. OS was the primary endpoint. We used BlueSky statistics v10.3.1 for analysis. Results: Analysis included 33 ALL pts diagnosed from 2014-2022 at 7 sites. 52% pts were female. Median follow up was 9.6 yrs (95%CI,7.6-11.8) from MM dx and 3.2 yrs (CI, 2.1-4.7) from ALL dx. Pt characteristics at MM dx are given in Table. Induction rx included: proteasome inhibitor (PI) +immunomodulatory drug (IMiD) (43%), PI+alkylator (24%), IMiD (18%) & others (15%). 50% pts received autologous stem cell transplantation (ASCT). Median OS from MM dx was 11.2 yrs (CI, 8.9-NR). Time from MM dx and initial R rx to ALL dx were 5.0 yrs (range, 2.4-18.5) and 4.4 yrs (2.2-10.6) respectively. Median duration of R exposure before ALL dx was 3.8 yrs (1.6-10.4). Table shows characteristics of pts at B-ALL dx and genetic classification based on karyotyping (n=30), ALL FISH (n=28), chromosomal microarray (n=5) and next-generation sequencing (n=5). 31 pts received ALL-directed rx while 1 pt was initially managed with close observation as the pt attained CR on stopping R ( Lakshman et al; ASH 2019 ). Rx was unknown in 1 pt. Initial rx included: hyper-CVAD+/- rituximab- 49%, pediatric inspired protocols-18%, reduced intensity rx for frail pts- 21% and others- 12%. Response to first line rx were: CR- 56%, CRi- 28%, induction failure- 16%. 32% pts attained measurable residual disease (MRD) negativity. 48% pts underwent SCT for ALL. 14 pts died during follow up. 3-yr OS from ALL-dx was 50% (CI, 33%-76%). 3 pts required rx for MM after ALL diagnosis (2 had allo-SCT for ALL before MM relapse). Conclusions: Most pts had standard risk MM and were exposed to R for several years prior to dx of B-ALL, characterized by high incidence of hypodiploid karyotype; IKZF1 loss and TP53 deletions/mutations were detected in a subset of pts.MRD-adapted timely discontinuation of R in standard risk MM may decrease risk of second primary ALL. [Table: see text]

Molecular characterization and biomarker identification in pediatric B-cell acute lymphoblastic leukemia.

6524 Background: B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent hematologic malignancy in children and a leading cause of mortality. Despite high cure rates, the management of B-ALL remains challenging due to its high heterogeneity and propensity for relapse. This study aimed to delineate molecular features of pediatric B-ALL and explore the clinical utility of circulating tumor DNA (ctDNA) as a biomarker in B-ALL. Methods: The study analyzed 146 primary pediatric B-ALL patients who were diagnosed from August 2020 to April 2023 and received systemic chemotherapy in Wuhan Children's Hospital. Baseline bone marrow (BM) and plasma samples were collected for next-generation sequencing (NGS) to profile the mutational landscape. BM samples collected on day 19 of the treatment were utilized for minimal residual disease (MRD) testing to assess treatment efficacy. Transcriptomic profiling of baseline BM samples was performed via bulk RNA sequencing. Fisher's exact test and the Wilcoxon rank sum test were utilized to compare categorical and continuous variables between groups, respectively. A two‐tailed P-value<0.05 was considered statistically significant unless indicated otherwise. Results: Transcriptomic analysis revealed that 86.3% of patients (126 out of 146) could be categorized into 13 distinct molecular subtypes, with hyperdiploidy emerging as the predominant subtype. Baseline BM NGS identified gene fusions in 61% of patients, including 37 novel fusions previously unreported in B-ALL. Specifically, the KMT2A-TRIM29 novel fusion was detected and validated in a male child diagnosed with the KMT2A-rearranged subtype. Despite initially responding well to therapy, the patient experienced disease progression after a year, indicating a poor prognosis. We also found that elevated mutant counts and maximum-variant-allele-frequency (maxVAF) in baseline BM were associated with significantly poorer response to chemotherapy ( P=0.0012 and 0.028, respectively). Additionally, MRD-negative patients exhibited upregulated expression of immune-related pathways ( P<0.01) and increased CD8+ T cell infiltration ( P=0.047), indicating a more active immune microenvironment in better responding tumors. Baseline plasma ctDNA, which exhibited high mutational concordance with paired baseline BM samples, also demonstrated significant associations with chemotherapy efficacy, highlighting its potential as a non-invasive tool for disease monitoring and treatment outcome prediction. Conclusions: This study elucidated novel gene fusions and potential biomarkers for treatment response in pediatric B-ALL. Importantly, both baseline plasma ctDNA and BM samples offer promising prognostic insights into chemotherapy responses, paving the way for non-invasive monitoring strategies in the management of pediatric B-ALL.

Abstract 5987: Targeting the spliceosome in high-risk B-cell acute lymphoblastic leukemia

Abstract The outcome for children with high-risk B-cell acute lymphoblastic leukemia (B-ALL) is poor. Disease relapse is speculated to be due to leukemia cells escaping treatment. Our group discovered a unique cell subpopulation in B-ALL that has the capacity to initiate leukemia and is resistant to treatment. Transcriptome studies of this cell population highlight a unique RNA regulation process, specifically RNA splicing. In B-ALL, dysregulated splicing is reported to be associated with drug resistance and disease relapse. SF3B1 is a core component of the spliceosome and an essential protein in the RNA splicing process. SF3B1 inhibition is therapeutic in many cancers. In our current studies, we investigated the therapeutic potential of pladienolide B (Plad-B), an SF3B1 inhibitor, in B-ALL. SF3B1 protein expression was significantly higher in cell lines (Reh and JM1) and 28 primary B-ALL samples (14 each for standard-risk and high-risk), regardless of the risk group, than in normal B-cells (NBs) and hematopoietic stem cells (HSCs). Plad-B showed significant dose-dependent cytotoxicity in the cell lines with IC50 of 1.2nM and 0.6nM, respectively, and three harvested high-risk patient-derived xenograft (PDX) samples with almost the same IC50 as the cell lines. Plad-B did not show cytotoxicity in NBs and HSCs at the same tested concentrations. In vivo efficacy of Plad-B was tested using an Reh xenograft mouse model and a high-risk PDX model. Plad-B, as a single drug treatment, significantly prolonged survival in both models (p<0.01). G2/M cell cycle arrest and apoptosis induction were observed at 24 hours after Plad-B treatment in Reh and JM1. Splicing events were examined by RNA-seq in the treated cells at different time points (15 min, 30 min, and 60 min). Plad B demonstrated rapid splicing inhibition as early as 15 min post-treatment and, at 60 min, splicing was inhibited in 1,669 genes, including apoptosis-associated genes. 2,625 differential splicing events were observed in these genes with ~96% from intron retention and exon skipping. Furthermore, 202 genes showed significant changes in their expression over this time frame. Most of the genes were rapidly downregulated in the treatment group compared to the control, and some were slowly downregulated. There were also some genes which were upregulated, either rapidly or slowly, compared to the control. We demonstrated that Plad-B induced short pro-apoptotic spliced isoforms, instead of anti-apoptotic forms, in BCL2L1 and MCL-1, as early as 60 min after treatment. In conclusion, these data demonstrated the therapeutic potential of SF3B1 inhibition in high-risk B-ALL. Plad-B rapidly inhibited splicing in many genes and downregulated the anti-apoptotic forms of apoptosis-associated genes, leading to cell apoptosis. In future studies, we will identify the downstream targets of Plad-B and further investigate the mechanism of rapid apoptosis induction by SF3B1 inhibition. Citation Format: Yuki Murakami, Hiroaki Konishi, Clifford Tepper, John McPherson, Noriko Satake. Targeting the spliceosome in high-risk 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 5987.

Transcriptome analysis of primary adult B-cell lineage acute lymphoblastic leukemia identifies pathogenic variants and gene fusions, and predicts subtypes for in depth molecular diagnosis.

B-cell acute lymphoblastic leukemia (B-ALL) is classified into subgroups based on known driver oncogenes and molecular lesions, including translocations and recurrent mutations. However, the current diagnostic tests do not identify subtypes or oncogenic lesions for all B-ALL samples, creating a heterogeneous B-ALL group of unknown subtypes. We sorted primary adult B-ALL cells and performed transcriptome analysis by bulk RNA sequencing (RNA-seq). Transcriptomic analysis of an adult B-ALL cohort allowed the classification of four patient samples with subtypes that were not previously revealed by standard gene panels. The leukemia of two patients were of the DUX4 subtype and two were CRLF2+ Ph-like B-ALL. Furthermore, single nucleotide variant analysis detected the oncogenic NRAS-G12D, KRAS-G12D, and KRAS-G13D mutations in three of the patient samples, presenting targetable mutations. Additional oncogenic variants and gene fusions were uncovered, as well as multiple variants in the PDE4DIP gene across five of the patient samples. We demonstrate that RNA-seq is an effective tool for precision medicine in B-ALL by providing comprehensive molecular profiling of leukemia cells, identifying subtype and oncogenic lesions, and stratifying patients for appropriate therapy.

Abstract C055: Distinct epigenomic regulation of gene expression in Hispanic/Latino children with high-risk B-cell acute lymphoblastic leukemia

Abstract B-Cell Acute Lymphoblastic Leukemia (B-ALL) is the most common childhood malignancy. Hispanic/Latino (H/L) children have a 40% higher death rate than non-Hispanic white (NHW) children after correcting for socioeconomic factors. Recently, we identified a 3.5-fold increased incidence of deletion of one IKZF1 allele (IKZF1-del) and over 15-fold increased incidence of deletion of one IKZF1 allele concomitant with IGH-CRLF2 translocation (IKZF1-del/IGH-CRLF2) in B-ALL of H/L children. This provided a biological rationale for the worse prognosis of B-ALL in H/L children. The very high incidence (29% in all H/L children and 60% in ≥10yr old H/L children) makes IKZF1-del the most frequent genetic alteration that confers adverse prognosis in B-ALL in H/L children. The IKZF1 gene encodes a DNA-binding protein, IKAROS, which regulates transcription of its target genes via chromatin remodeling. The purpose of the study is to analyze the global epigenomic regulation of gene expression in H/L and NHW children with B-ALL and identify biological determinants of altered gene expression that result in worse prognosis for H/L children with B-ALL. /. B-ALL primary cells from 60 H/L and NHW children were analyzed with whole genome sequencing and gene expression profiling using RNA-seq. A subset of B-ALL from each group was analyzed for epigenomic changes by Reduced Representation Bisulfite Sequencing (RRBS), ChIP-seq, CUT&RUN, and CUT&Tag. Results showed that gene expression pattern in B-ALL of H/L children is quite different from B-ALL of NHW children. GSEA and Ingenuity pathway analysis identified oncogenic drivers of B-ALL in H/L children. B-ALL of H/L children have elevated expression of genes that promotestemness, inflammation, and with antiapoptotic activity. RBBS analysis showed a distinct DNA methylation pattern in B-ALL in H/L vs NHW children at promoters of a large set of genes that are involved in cellular signaling, RNA processing, and cellular proliferation. Presence of IKZF1-del results in the alteration of global epigenomic regulation of gene expression with altered enhancer and super-enhancer landscape. Epigenomic alterations due to IKZF1-del resulted in profound redistribution of enhancers and super-enhancers in B-ALL of both H/L vs. NHW children. This was associated with a distinct alteration in gene expression and uncovered that IKAROS regulates different sets of genes in B-ALL in H/L vs. NHW children. These data identified a unique oncogenic signaling that are responsible for aggressive course of B-ALL in H/L children. In conclusion, the multiomics analysis of primary B-ALL cells revealed a distinct global epigenomic regulation of gene expression between B-ALL from H/L and NHW children. This was demonstrated by alterations in DNA methylation and enhancer landscape. Presence of IKZF1-del has a different effect on gene expression in B-ALL of H//L vs NHW children. Results of the study provide a biological rationale for the worse prognosis of B-ALL in H/L children and identified novel therapeutic targets for this disease. Citation Format: Laura Budurlean, Bing He, Yali Ding, Diwakar Bastihalli Tukaramrao, Chingakham Singh, Joseph Schramm, Daniel Bogush, James Broach, Sinisa Dovat. Distinct epigenomic regulation of gene expression in Hispanic/Latino children with high-risk B-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C055.

Mitochondrial dsRNA from B-Precursor Acute Lymphoblastic Leukemia Cells Induce Formation of Cancer Associated Fibroblast in the Bone Marrow Leading to Formation of a Chemoprotective Bone Marrow Niche

Precursor B-cell Acute Lymphoblastic Leukemia (B-ALL) is typically a highly chemosensitive malignancy with the majority of children being cured by chemotherapy alone. Adult ALL is often chemosensitive at initial treatment, but long term disease free survival is less common. It is widely accepted that outcome in ALL closely relates to underlying genetic lesion (Moorman, Hematologica 2016) but no specific mechanisms by which ALL genetics influence outcome have been identified. We have previously demonstrated that an ‘activated mesenchymal stromal cell (MSC) niche’ develops in response to reactive oxygen species (ROS) -inducing chemotherapy in which mitochondria are actively transferred along tunnelling nanotubes to ‘rescue’ B-ALL cells from chemotherapy (Burt, et al Blood 2019). According to recent evidence that chemotherapy resistant ALL sub-clones may exist at diagnosis (Dobson et al Cancer Discovery 2020), we hypothesised that B-ALL cells may themselves directly activate bone marrow stromal cells to generate cancer associated fibroblasts (CAF) from MSC. To test this hypothesis, we first used our previously described in vitro niche model wherein either the HS27a MSC cell line or healthy donor (HD) MSCs are co-cultured with either B-ALL cell lines or primary patient B-ALL cells. Three of five B-ALL cell lines and 3 of 4 primary B-ALL samples tested, induced activation of the MSCs, as characterised by cytomorphological changes identified by confocal microscopy, up-regulation of CAF-relevant gene expression and increased IL6, IL8 and CCL2 protein secretion. The ability of the B-ALL cell lines to induce CAF correlated directly with the intrinsic ROS levels of the cell as determined by CellROX assay. In vivo, the CAF-inducing ALL cell lines also activated murine MSCs when established as xenografts in NOD-SCID gamma (NSG) mice. Immunohistochemistry of NSG murine femora revealed a very significant expansion in nestin+ cells after exposure to CAF-induing ALL cells compared to non-CAF-inducing controls. We established that the ALL cells activated MSC without contact, both from exposure of MSC to ALL cells in transwell and from exposure to B-ALL cell conditioned media (CM). RNA sequencing of HS27a stromal cells exposed to CAF-inducing B-ALL cell CM compared with non-CAF inducing controls unexpectedly showed that the most highly upregulated pathways were those involved in RNA sensing. Using a smaller gene panel selected from among the RNA-sensing pathway genes, we confirmed that this was also the case for primary, HD MSCs upon exposure to primary ALL patient samples. As a result, we sought evidence for the role of mitochondrial dsRNA, which has been shown to activate the anti-viral signalling pathway (Dhir et al, Nature 2018). Using the J2 anti-dsRNA monoclonal antibody in both confocal and flow cytometric assays, we observed very significantly higher levels of dsRNA in MSC which had been exposed to CAF inducing B-ALL cell CM than in non-CAF inducing B-ALL or MSC alone controls. We confirmed by RT-PCR for mitochondrial genes on dsRNA immunoprecipitated from CAF inducing B-ALL cell CM that the dsRNA was of mitochondrial origin. Using ELISA, we quantified dsRNA from total cell RNA extracted from paired primary B-ALL patient samples at diagnosis and in remission. We found significantly higher levels of dsRNA at diagnosis than in remission, with it being undetectable in most remission samples. Moreover, we confirmed by flow cytometry the presence of dsRNA in 6 B-ALL patient derived xenografts which was absent in the control NSG mice without leukemia. We used DMSO to degrade dsRNA from CAF inducing B-ALL cell CM, as is often done in Sanger sequencing and confirmed the degradation by ELISA. We then quantified gene expression of a selection of stromal cell activation marker genes, as well as genes in the RNA sensing pathway after exposure to either DMSO-treated B-ALL cell CM or non-treated control. There was a 2 to 4-fold reduction in expression of IL6, IL8 as well as of RIG-I, MX2, IFIH1, MAVS and OAS1 expression in DMSO-treated condition compared to control. We confirmed that IL6, IL8 and CCL2 protein secretion was also significantly abrogated in the test but not the control condition. We propose a model in which ROS-induced mitochondrial dysfunction in ALL cells leads to release of dsRNA which in turn activates bone marrow stromal cells leading to protective niche formation, despite lack of prior exposure to cytotoxic agents.

Oncogenic RAS Signaling Promotes an Immunosuppressive Niche in Acute Lymphoblastic Leukemia

Emerging evidence suggests that genomic aberrations in cancer cells may impact the composition of the tumor microenvironment leading to a tumor-specific supporting niche. Previous genomic profiling studies have identified somatic alterations in RAS pathway genes that drive treatment resistance in B-cell acute lymphoblastic leukemia (B-ALL): yet it is unknown whether such genetic events may specifically hijack the leukemic niche. Here, we analyzed bulk RNA-sequencing data of bone marrow mononuclear cells from 185 pediatric B-ALL patients entering our center and performed mutation calling of RAS pathway genes, namely KRAS, NRAS, BRAF and PTPN11. Transcriptomic analysis revealed attenuated immune responses and decreased T cell activation in samples harboring RAS mutations (n= 62) compared with wild type cases (n= 123). To further explore this finding at single-cell resolution, we sorted bone marrow mononuclear cells from 8 primary B-ALL pediatric patient samples (4 RAS mutant and 4 wild type), enriching on the hematopoietic and non-hematopoietic compartments, followed by single-cell RNA-sequencing using the 10x Genomics platform. Twelve cell populations were identified by the expression of bona fide markers, mapping different immune and stromal cells in the ALL landscape. Specifically, the RAS-mutant microenvironment was defined by dysfunctional CD8+ T-cells, characterized by high expression of TIM-3, TIGIT and LAG-3, as well as regulatory T cells, displaying expression of CTLA-4, ICOS and FOXP3, suggesting a RAS-mediated immunosuppressive mechanism. In light of these changes, we examined flow cytometry data of bone marrow mononuclear cells collected at diagnosis from our cohort of 185 patient samples. Whereas the overall proportion of lymphoid subsets (T, B and NK cells) was not significantly changed among RAS mutant and wild type groups, we detected a decrease in myeloid subsets (neutrophils, eosinophils, and monocytes) in RAS mutant ALL, which was more prominent in monocytes. Cross comparison of the transcriptional state of monocytes in our single-cell data unravel that monocytes in the RAS mutant niche displayed a non-classical phenotype, characterized with high expression of the immune checkpoint TIM-3, which is a major driver of T cell exhaustion. Taken together, the bone marrow microenvironment of ALL patients harbouring oncogenic RAS lymphoblasts is defined by dysfunctional immune cell populations. Further studies on the cellular dynamics in the niche will provide the basis for the development of therapeutic opportunities to target the immune micro-environment in RAS mutant ALL.

Unraveling the Mechanism of Action of Bispecific T-Cell Engagers in B-Cell Acute Lymphoblastic Leukemia Using Advanced Single-Cell Multiomics

Background Bispecific T-cell engagers (BiTEs) stimulate T lymphocytes proximate to tumor cells, inducing T-cell stimulation and tumor killing. Blinatumomab, an anti CD3-CD19, was the first to be approved with overall response rates of up to 80% in refractory B-cell Acute Lymphoblastic Leukemia (B-ALL). To overcome resistance and to develop next-generation BiTEs, we need to build on blinatumomab's success and better understand BiTEs mode of action and interaction with the tumor microenvironment (TME). Here, we apply advanced multiomics to examine blinatumomab's activation signatures and the sustained dynamics in the tumor and bone marrow (BM) immune TME. Methods Physically interacting Cells sequencing (PIC-seq) is an advanced multiomics technology deciphering the crosstalk between the cellular components of an immunological synapse (Cohen et al., 2022; Giladi et al., 2020). To assess Immediate activation signatures, we applied PIC-seq on a model of B-ALL cell lines (RS4;11, NALM-6) and lymphocytes obtained from healthy subjects, activated by blinatumomab, compared to no-treatment and activation with anti CD3-CD28 antibodies. To examine the Sustained effects on the immune TME, we performed a longitudinal single-cell RNA sequencing of the bone BM of adult B-ALL patients, before and after treatment with blinatumomab in the Division of Hematology in the Tel Aviv Sourasky Medical Center in 2021-22. Results Immediate activation Applying PIC-seq on n=16,543 CD3 and CD19+ cells, we identified the distinct gene expression of ‘blinatumomab-activated lymphocytes’ (Figure 1). Blinatumomab induced cellular synapses composed of specific T lymphocytes subsets along the activation continuum, namely: effector T cells (CCL5, GNLY, NKG7), early IFN-G activation (IRF1, GBP5), activated cytotoxic (Xcl1-2, IFN-G) and proliferating T cells (CD69, CCND2) . ‘Blinatumomab-activated lymphocytes’ were characterized by a unique activation signature: upregulation of cytotoxicity (Xcl1, IFN-G, GNLY), co-stimulation and B-T cells crosstalk (CD40, CD27, TNFRSF18), immune recruitment (CXCL10, CCL4) and antigen-presentation (TNFSF14, ITGB2) pathways. Late synapses also expressed immunoregulatory molecules (TNFAIP8L2). This signature differed from classical anti CD3-CD28 induced activation and is independent of the donor and the target-cell identity. The malignant cells' response varied: RS4;11 cells manifested cellular senescence, while NALM-6 upregulated INFG-induced apoptotic pathways, suggesting indirect killing in the mechanism of action of BiTEs. Data on the introduction of primary B-ALL patients' cells will be presented at the ASH. Sustained effects We profiled >11,000 cells from three patients: Patient 1, 31-year-old (y/o) female, primary refractory B-ALL (50% BM blasts), attaining transient MRD negativity. Patient 2, 71-y/o male, primary refractory Ph+ B-ALL (74% BM blasts) achieving reduction in MRD following first cycle. Patient 3, 71 y/o, Ph+ B-ALL, treated as consolidation therapy, achieving MRD negativity. Blinatumomab induced a dramatic perturbation in the lymphocytic and myeloid compartments of the BM and was highly patient-specific ( Figure 2). The BM lymphocytic compartment prior to initiation of blinatumomab in molecular remission (patient 3) was characterized by active T and Natural Killer cell states, compared to an abundancy of naïve lymphocytes in active disease (patients 1 and 2). There were no signs of T-cell exhaustion pre or post treatment in all patients. Post-treatment, CD8 T-Central Memory cells proliferated in all patients. Patients treated for active disease (patients 2 and 3), had an expansion of the Tregs population post-treatment. In the myeloid compartment, patients with active disease had more non-classical monocytes, known to correlate with poor prognosis. These were replaced by classical monocytes following treatment, in addition to the emergence of a macrophage-precursor population. Data on the BM and peripheral blood dynamics of an additional six patients will be presented at the ASH. Conclusions We present an advanced single cell dissection of blinatumomab-induced target-effector interaction, providing novel insights into the mechanism of action and TME dynamics to guide patient selection and next generation BiTEs. A larger patients' cohort and introduction of patients' cells to the PIC-seq in vitro model will be presented at the ASH.

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia

BackgroundType I interferons (IFN-Is), secreted by hematopoietic cells, drive immune surveillance of solid tumors. However, the mechanisms of suppression of IFN-I-driven immune responses in hematopoietic malignancies including B-cell acute lymphoblastic...

Abstract A088: Targeting endoplasmic reticulum stress-induced apoptosis to reduce health disparity in high-risk B-cell acute lymphoblastic leukemia in Hispanic/Latino children

Abstract B-cell Acute Lymphoblastic Leukemia (ALL) is the most common childhood malignancy. The death rate from B-ALL in Hispanic/Latino (H/L) is 40% higher than in non-Hispanic whites (NHW) after correcting socioeconomic factors. Deletion of one IKZF1 allele is highly increased H/L children, which provides a biological rationale for the worse prognosis of B-ALL in this population. The very high incidence (31% in all children and 65% in children ≥10 yrs) makes the deletion of one IKZF1 allele the most frequent genetic alteration that confers adverse prognosis in B-ALL in H/L children. The IKZF1 gene encodes a DNA-binding protein, IKAROS, which functions as a transcriptional regulator. Identification of IKAROS target genes in B-ALL of H/L children is essential to understand the specificity of B-ALL pathogenesis in those children and develop the targeted treatment to reduce the health disparity in survival for H/L children with B-ALL. Global DNA-binding analysis of primary B-ALL cells from H/L children showed that IKAROS binds to the promoter of eukaryotic elongation factor 2 kinase (eEF2K). eEF2K regulates protein synthesis, cell cycle progression and malignant transformation. The activity of eEF2K is increased in human malignancies, including B-ALL, and eEF2K is a critical regulator of endoplasmic reticulum (ER) stress-induced autophagy and apoptosis in tumor cells. The role of IKAROS in the regulation of eEF2K expression in B-ALL of H/L children was established using gain-of-function and loss-of-function experiments. Overexpression of IKZF1 in H/L B-ALL cells results in reduced expression of eEF2K, while IKZF1 knock-down results in increased transcription of eEF2K in H/L B-ALL. Since IKAROS function in leukemia is regulated by pro-oncogenic Casein Kinase 2 (CK2), we tested whether CK2 can control the ability of IKAROS to regulate the expression of eEF2K in H/L B-ALL. Increased expression of CK2 in H/L B-ALL results in increased expression of the eEF2K gene due to the loss of IKAROS binding to the promoter of the eEF2K genes. Inhibition of CK2 with shRNA and/or a specific CK2 inhibitor, CX-4945, restores IKAROS binding to promoter of eEF2K in high-risk B-ALL with deletion of one IKZF1 allele in H/L children. Restoration of IKAROS binding to promoter of eEF2K in high-risk B-ALL in H/L children results in reduced expression of this gene. This was associated with increased sensitivity to Akt inhibition by MK-2206. Combination treatment with CK2 inhibitor and MK-2206 showed a synergistic effect on B-ALL cells from H/L children. In summary, presented data demonstrate that IKAROS and CK2 regulate ER stress-induced apoptosis via regulation of eEF2K expression in high-risk B-ALL in Hispanic/Latino children. Results suggest that targeting ER stress-induced apoptosis in combination with CK2 inhibitors can be an efficient treatment to reduce the health disparity in survival for Hispanic/Latino children with B-ALL. Citation Format: Sinisa Dovat, Yali Ding, Dhimant Desai, Arati Sharma. Targeting endoplasmic reticulum stress-induced apoptosis to reduce health disparity in high-risk B-cell acute lymphoblastic leukemia in Hispanic/Latino children [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A088.

Centrosome Amplification Is a Potential Molecular Target in Paediatric Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most common form of cancer in children, with most cases arising from fetal B cell precursor, termed B-ALL. Here, we use immunofluorescence analysis of B-ALL cells to identify centrosome amplification events that require the centrosome clustering pathway to successfully complete mitosis. Our data reveals that primary human B-ALL cells and immortal B-ALL cell lines from both human and mouse sources show defective bipolar spindle formation, abnormal mitotic progression, and cell death following treatment with centrosome clustering inhibitors (CCI). We demonstrate that CCI-refractory B-ALL cells exhibit markers for increased genomic instability, including DNA damage and micronuclei, as well as activation of the cyclic GMP-AMP synthase (cGAS)-nuclear factor kappa B (NF-κB) signalling pathway. Our analysis of cGAS knock-down B-ALL clones implicates cGAS in the sensitivity of B-ALL cells to CCI treatment. Due to its integral function and specificity to cancer cells, the centrosome clustering pathway presents a powerful molecular target for cancer treatment while mitigating the risk to healthy cells.

P618: SECOND-GENERATION CD19 TARGETING TRI-SPECIFIC KILLER ENGAGER DRIVES ROBUST NK CELL FUNCTION AGAINST B CELL MALIGNANCIES

Background: Chronic Lymphocytic Leukemia (CLL) involves uncontrollable clonal expansion of CD5+/CD19+ B lymphocytes. While patients can sometimes coexist with CLL for years, eventually there is progression to bulky adenopathy and pancytopenia from marrow suppression requiring therapy. In recent years, targeted therapies, including utilization of the inhibitors for B cell receptor (BCR) signaling and for B cell lymphoma 2 (Bcl-2) protein, have been effective treatment options. However, these treatments are associated with limitations such as development of drug resistance and the lower treatment efficacy ratio in high-risk patients. Meanwhile, CAR-T cell immunotherapy failed to produce effective treatment outcomes against CLL, mostly due to defects in the effector T cells leading to product failures, as well as being associated with high levels of off-target cytotoxicity. Aims: Thus, approaches to CLL treatment are necessary and NK cell immunotherapy presents a viable and non-toxic option to this problem. Methods: Our group previously demonstrated the immunotherapeutic potential of utilizing first-generation CD19-targeting 161519 Tri-Specific Killer Engager (TriKE®) to drive natural killer (NK) cell cytotoxicity against B-cell malignancies. We have now produced a novel second-generation CD19 TriKE, ‘CAM161519’, utilizing a humanized camelid anti-CD16 VHH single domain antibody (sdAb) ‘CAM16’, a wild-type IL-15 component, and anti-CD19 tumor antigen scFv all linked via short peptide linkers. The TriKE primarily works by generating a cytolytic bridge between NK cells and CD19 expressing B cell malignancies while also providing an expansion and survival signal to the NK cells. Using flow-based assays and imaging based cytolytic assays we explored the capability of CAM161519 to target a variety of B cell lines (Raji, Daudi, and Nalm6) and primary B cell malignancies from patients with CLL and B cell acute lymphoblastic leukemia (B-ALL). Expanded NK cells were incubated with primary CLL targets from 6 different patients and no treatment (NT), rhIL-15 (30 nM), Rituximab (10 ug/mL), or CAM16159 (30 nM). NK cell degranulation and IFNg production was evaluated after 5 hours of co-culture (Figure). CLL killing was evaluated in a similar co-culture, but with a staining mix containing CD5 and CD19, to identify CLL tumor cells in order to determine the percent CLL targets killed normalized to incubation of CLL cells with NK cells alone (Figure Image). Results: The CAM161519 robustly activated NK cell degranulation (CD107a) and inflammatory cytokine production (IFNg) against B cell lines. The activation was specific as it was strongly reduced against CD19 knockout Nalm6 cells. The TriKE also induced specific NK cell proliferation. IncuCyte imaging based cytolytic assays demonstrated strong killing activity against Raji targets. When evaluating activity against primary targets, CAM161519 induced enhanced NK cell degranulation, cytokine production, and cytotoxicity using flow cytometry-based assays against primary CLL (Figure Image) and B-ALL targets when compared to IL-15 treatment. CAM161519 also rescued functionality of NK cells from CLL patients against their autologous CLL cells. Image:Summary/Conclusion: Taken together, these data are indicative of the potential for clinical translation of the CAM161519 TriKE in the CLL and B-ALL settings alone or in combination with cellular products.

Abstract 846: Transcriptional regulation of Aurora-B kinase expression in B-cell acute lymphoblastic leukemia (B-ALL)

Abstract The Aurora kinases are serine/threonine kinases that are essential for mitosis. Aurora-B kinase is a component of the chromosomal passenger complex (CPC), chromosome condensation, the spindle-assembly checkpoint, and for cytokinesis. The activity of Aurora-B is essential for cellular division and proliferation. Inhibition of Aurora-B is cytotoxic, and inhibitor of Aurora-B - Barasertib (AZD1152) has been tested in clinical trials against different types of malignancies, including leukemia. However, regulation of Aurora-B expression is still largely unknown. Here, we present evidence that expression of Aurora-B in B-cell acute lymphoblastic leukemia (B-ALL) is regulated at the transcriptional level by Ikaros, a transcription factor and tumor suppressor protein. Analysis of global chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) in several B-ALL primary human B-ALL cells and cell lines, showed a strong enrichment of Ikaros at the promoter of the Aurora-B gene. Ikaros functions as a tumor suppressor protein and deletion of Ikaros is associated with development of high-risk B-ALL. Ikaros binding to Aurora-B promoter was confirmed by quantitative chromatin immunoprecipitation (qChIP) in primary B-ALL cells. The role of Ikaros in regulating Aurora-B transcription in B-ALL was tested using gain-of-function and loss-of-function experiments. Overexpression of Ikaros in human B-ALL was associated with strongly reduced transcription and overall expression of Aurora-B. Ikaros knock-down with shRNA results in increased expression of Aurora-B in B-ALL. Since Ikaros function in B-ALL is negatively regulated by pro-oncogenic Casein Kinase II (CK2), we tested whether CK2 can regulate expression of Aurora-B in B-ALL. Overexpression of CK2 via retroviral transduction resulted in increased expression of the Aurora-B gene. Increased expression of CK2 was associated with a loss of Ikaros binding to the Aurora-B gene promoter. Molecular inhibition of CK2 using shRNA resulted in reduced expression of Aurora-B in human B-ALL. Inhibition of CK2 was associated with increased Ikaros binding at the Aurora-B promoter. Ikaros knock-down abolished downregulation of Aurora-B expression in B-ALL cells following treatment with CK2 inhibitors. These data demonstrate that CK2 and Ikaros are critical regulators of Aurora-B expression in B-ALL. In conclusion, these results indicate that expression of the Aurora-B gene in B-ALL is regulated by the CK2-Ikaros signaling axis and provide a novel insight into mechanisms that regulate mitosis in leukemia. Citation Format: Yali Ding, Chunhua Song, Joseph Schramm, Soumya Maru, Daniel Bogus, Dhimant H. Desai, Arati K. Sharma, Chandrika Gowda, Sinisa Dovat. Transcriptional regulation of Aurora-B kinase expression in B-cell acute lymphoblastic leukemia (B-ALL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 846.

Prognostic Value of Average Daily Platelet Increase in Childhood B-cell Acute Lymphoblastic Leukemia Patients

To evaluate the prognosis value of average daily platelet amount increase in children with B-cell acute lymphoblastic leukemia(B-ALL) treated by CCCG-ALL-2015 regimen. 106 children with primary B-ALL were retrospective analyzed, standardized MRD test protocol was used to detect the MRD level (19 d and 46 d) after chemotherapy. The platelet count was measured by Sysmex XE-2100. Kaplan-Meier survival curve statistics was used to analyze the event free survival(EFS) rate of the children. The trend of negative correlation existed between PPC and TPR (rs=-0.519, P=0.021). The 3-year EFS rate of the patients in Ap>5.4×109/L group was 95.7%, which was significantly higher than those in Ap≤5.4×109/L group(79.5%) (χ2=5.236, P=0.035); multivariate analysis showed that Ap≤5.4×109/L was the independent prognostic factor affecting survival of the patients (RR=3.978; 95%CI: 1.336-11.523, P=0.041). With both MRD and Ap≤5.4×109/L as candidate variables, Ap≤5.4×109/L lost its independent prognostic value (RR=1.225; 95%CI: 0.892-13.696, P=0.089), the correlation between d 19/d 46 MRD levels and Ap>5.4×109/L (χ2=4.318, P=0.038) could explain the phenomenon. Ap can reflect the effect of B-ALL chemotherapy and can be used to monitor the curative effect and prognosis of B-ALL children.

High cystic fibrosis transmembrane conductance regulator expression in childhood B-cell acute lymphoblastic leukemia acts as a potential therapeutic target.

BackgroundThe role of cystic fibrosis transmembrane conductance regulator (CFTR) in hematopoiesis and adult leukemia has been demonstrated using a zebrafish model and leukemia cell lines in our previous works. Here, we continue to explore the association between CFTR and human childhood B-cell acute lymphoblastic leukemia (B-ALL).MethodsWe continued to collect the peripheral blood and bone marrows of human childhood patients diagnosed with primary B-ALL as well as non-leukemia controls and isolated lymphocytes for analysis using western blotting and quantitative real-time polymerase chain reaction (qPCR) assay. Then, we used immunofluorescence, co-immunoprecipitation, western blotting, luciferase, 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide (MTT) assays to identify the interaction of CFTR with Wnt signaling in B-ALL. Finally, we established B-ALL xenograft model in non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice using SUP-B15 cells, and examined whether the CFTR inhibitor CFTR-inh172 could active against SUP-B15-Dependent B-ALL in vivo.ResultsHighly expressed CFTR protein and mRNA are associated with primary childhood B-ALL patients. Aberrantly upregulated CFTR and Wnt signaling, our previously reported CFTR-Dvl2-β-catenin pathway, is found in human childhood B-ALL patients. Interference with CFTR in B-ALL cell lines induces the downregulation of DVL2/β-catenin and Wnt downstream target accompanied by a reduction of cell proliferation. Furthermore, B-ALL cell lines SUP-B15 cell-transplanted NOD/SCID mice treated with CFTR inhibitor CFTRinh-172 had significantly longer survival and slower leukemia progression compared with mice treated with vehicle dimethyl sulfoxide (DMSO).ConclusionsThese findings demonstrate that highly expressed CFTR is associated with human childhood B-ALL and the potential of CFTR inhibitor CFTR-inh172 for the treatment of human B-ALL.

Abstract PR-12: Novel targeted combination therapy to reduce health disparity in high-risk B-cell acute lymphoblastic leukemia in Hispanic/Latino children

Abstract Hispanic/Latino (H/L) children and adolescents have a 40% higher death rate than non-Hispanic whites (NHW) after correcting socioeconomic factors. Recently, we identified an increased incidence of deletion of one IKZF1 allele in H/L children, which provided a biological rationale for the worse prognosis of B-cell acute lymphoblastic leukemia (B-ALL) in this population. The very high incidence (29%) makes the deletion of one IKZF1 allele the most frequent genetic alteration that confers adverse prognosis in B-ALL in H/L children. The IKZF1 gene encodes a DNA-binding protein, Ikaros, which functions as a transcriptional regulator. Our goal is to determine the mechanism through which Ikaros regulates leukemia progression and to develop the novel therapy to treat B-ALL with deletion of one IKZF1 allele to reduce the health disparity in survival for H/L children with B-ALL. Global DNA-binding analysis of primary B-ALL cells from H/L children showed that Ikaros binds to the promoters of CDC20 and ANAPC7 genes. CDC20 and ANAPC7 genes have a critical role in mitosis progression and are essential for cellular proliferation. The role of Ikaros in the regulation of CDC20 and ANAPC7 expression in B-ALL of H/L children was established using gain-of-function and loss-of-function experiments. Overexpression of Ikaros in B-ALL cells results in reduced expression of CDC20 and ANAPC7, while Ikaros knock-down results in increased transcription of CDC20 and ANAPC7 in B-ALL. Since Ikaros function in hematopoietic malignancies is regulated by pro-oncogenic Casein Kinase 2 (CK2), we tested whether CK2 can control the ability of Ikaros to regulate the expression of CDC20 and ANAPC7 in B-ALL. Increased expression of CK2 in B-ALL results in increased expression of CDC20 and ANAPC7 genes due to the loss of Ikaros binding to the promoters of CDC20 and ANAPC7 genes. Inhibition of CK2 with shRNA and/or a specific CK2 inhibitor, CX-4945, restores Ikaros binding to promoters of CDC20 and ANAPC7 in high-risk B-ALL with deletion of one IKZF1 allele in H/L children. Restoration of Ikaros binding to promoters of CDC20 and ANAPC7 in high-risk B-ALL in H/L children results in reduced expression of these genes and cell cycle arrest. CK2 inhibition sensitizes B-ALL cells to treatment with an inhibitor of mitosis – vincristine. Combination treatment with CK2 inhibitor and vincristine showed a synergistic effect on B-ALL cells from H/L children. In summary, presented data demonstrate that IKAROS and CK2 regulate the progression of mitosis in high-risk B-ALL in Hispanic/Latino children. Results suggest that the combination treatment with CK2 inhibitors and vincristine can be an efficient novel treatment to reduce the health disparity in survival for Hispanic/Latino children with B-ALL. Citation Format: Sinisa Dovat, Dimant Desai, Arati Sharma, Chandrika Gowda. Novel targeted combination therapy to reduce health disparity in high-risk B-cell acute lymphoblastic leukemia in Hispanic/Latino children [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-12.

Preclinical Evaluation of a Novel Dual Targeting PI3Kδ/BRD4 Inhibitor, SF2535, in B-Cell Acute Lymphoblastic Leukemia.

The PI3K/Akt pathway—and in particular PI3Kδ—is known for its role in drug resistant B-cell acute lymphoblastic leukemia (B-ALL) and it is often upregulated in refractory or relapsed B-ALL. Myc proteins are transcription factors responsible for transcribing pro-proliferative genes and c-Myc is often overexpressed in cancers. The chromatin regulator BRD4 is required for expression of c-Myc in hematologic malignancies including B-ALL. Previously, combination of BRD4 and PI3K inhibition with SF2523 was shown to successfully decrease Myc expression. However, the underlying mechanism and effect of dual inhibition of PI3Kδ/BRD4 in B-ALL remains unknown. To study this, we utilized SF2535, a novel small molecule dual inhibitor which can specifically target the PI3Kδ isoform and BRD4. We treated primary B-ALL cells with various concentrations of SF2535 and studied its effect on specific pharmacological on-target mechanisms such as apoptosis, cell cycle, cell proliferation, and adhesion molecules expression usingin vitro and in vivo models. SF2535 significantly downregulates both c-Myc mRNA and protein expression through inhibition of BRD4 at the c-Myc promoter site and decreases p-AKT expression through inhibition of the PI3Kδ/AKT pathway. SF2535 induced apoptosis in B-ALL by downregulation of BCL-2 and increased cleavage of caspase-3, caspase-7, and PARP. Moreover, SF2535 induced cell cycle arrest and decreased cell counts in B-ALL. Interestingly, SF2535 decreased the mean fluorescence intensity (MFI) of integrin α4, α5, α6, and β1 while increasing MFI of CXCR4, indicating that SF2535 may work through inside-out signaling of integrins. Taken together, our data provide a rationale for the clinical evaluation of targeting PI3Kδ/BRD4 in refractory or relapsed B-ALL using SF2535.

In vitro and in vivo effects of AVA4746, a novel competitive antagonist of the ligand binding of VLA-4, in B-cell acute lymphoblastic leukemia.

Treatment of resistant or recurrent acute lymphoblastic leukemia (ALL) remains a challenge. It was previously demonstrated that the adhesion molecule integrin α4, referred to hereafter as α4, mediates the cell adhesion-mediated drug resistance (CAM-DR) of B-cell ALL by binding to vascular cell adhesion molecule-1 (VCAM-1) on bone marrow stroma. In addition, it was previously observed that the blockade of α4 with natalizumab or inhibition using the small molecule antagonist TBC3486 sensitized relapsed ALL cells to chemotherapy. However, α4-targeted therapy is not clinically available for the treatment of leukemia to date. In the present study, the use of a novel non-peptidic small molecule integrin α4 antagonist, AVA4746, as a potential new approach to combat drug-resistant B-ALL was explored. An in vitro co-culture = model of primary B-ALL cells and an in vivo xenograft model of patient-derived B-ALL cells were utilized for evaluation of AVA4746. VLA-4 conformation activation, cell adhesion/de-adhesion, endothelial tube formation, in vivo leukemia cell mobilization and survival assays were performed. AVA4746 exhibited high affinity for binding to B-ALL cells, where it also efficiently blocked ligand-binding to VCAM-1. In addition, AVA4746 caused the functional de-adhesion of primary B-ALL cells from VCAM-1. Inhibition of α4 using AVA4746 also prevented angiogenesis in vitro and when applied in combination with chemotherapy consisting of Vincristine, Dexamethasone and L-asparaginase, it prolonged the survival of ~33% of the mice in an in vivo xenograft model of B-ALL. These data implicate the potential of targeting the α4-VCAM-1 interaction using AVA4746 for the treatment of drug-resistant B-lineage ALL.

Novel in Vitro and In Vivo Drug Screening Platform for ALL.

Acute Lymphoblastic leukemia (ALL) is a malignancy of bone marrow. Accumulation of mutations in lymphoid progenitor cells give rise to either B-ALL or T-ALL. Treatment for ALL has improved in recent years, yet relapse of the disease and development of resistance are observed in patients. Lack of suitable and robust in vitro and in vivo drug testing platforms for primary ALL cells along with the lack of rapid development of novel therapeutics drugs encompassing the heterogeneity of the disease contribute to the delay in approved patient treatments.We have developed a short-term culture system that supports the survival of primary B-ALL and T-ALL cells. Our ALL bank includes patient-derived specimens with complete cytogenetics and surface marker expression information. Different culture conditions were evaluated to select conditions that support the survival and maintenance of primary B-ALL and T-ALL specimens. Cell growth/viability was assessed using the Cell Titer-Glo ® assay. Primary B-ALL cells survived in the optimized media for 3 days and a heterogenous dose dependent response was observed across the models to chemotherapeutic drugs doxorubicin, vincristine, imatinib and cytarabine. BCR-ABl - B-ALL patient samples were found to be resistant to imatinib in contrast to BCR-ABL + samples which were sensitive to imatinib. Similarly, culture conditions optimized for T-ALL primary cells supported the survival until day 6 and displayed a diverse response to standard of care drugs like venetoclax, imatinib, vincristine, cytarabine and methotrexate, reflecting the heterogeneity of the patient derived specimens. Immunophenotypic characterization of ALL cells grown in culture displayed retention of the B and T cells surface marker expression.Further, a patient derived pre-clinical xenograft model was developed in NCG mice to study in vivo ALL drug efficacy. 100% engraftment was observed for B-ALL primary cells, with latency of engraftment (>3%) in peripheral blood varying from 15 days to 3.5 months. 30-90% of the bone marrow cells were occupied by human CD45 cells. Infiltration of human B-ALL cells were observed in the spleen causing splenomegaly. 8 out of the 14 models having high penetrance were passaged until P3. Flow analysis at each passage demonstrated surface marker expression displaying low divergence from the primary samples. Additionally, evaluation of ex vivo drug response from B-ALL PDX splenocytes was largely concordant with the primary specimen ex vivo data in three of the models evaluated. In an in vivo drug efficacy study administration of venetoclax, CHOP and R-CHOP inhibited the proliferation of B-ALL cells. Significant reduction of B-ALL cells was observed while on treatment with Venetoclax. At termination of the study, up to 80% reduction of human B-ALL cells was observed in whole blood, bone marrow, and spleen after treatment with CHOP and R-CHOP in comparison to the vehicle cohort.Similarly, patient derived T-ALL pre-clinical xenograft model development is in progress. Thus, we have developed a robust in vitro drug testing platform for B-ALL and T-ALL to evaluate drug efficacy. We also demonstrate that NCG mice support the growth and proliferation of primary B-ALL cells and have successfully developed an in vivo platform that will facilitate the testing of clinically relevant chemotherapeutic drugs for ALL. DisclosuresNo relevant conflicts of interest to declare.

Single-Cell Decoding of Minimal Residual Disease in Pediatric B Cell Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, of which B cell ALL (B-ALL) accounts for up to 85% of all cases. Although risk-stratified chemotherapy significantly improves the clinical outcome of affected pediatric patients with B-ALL, relapse still occurs in approximately 10% of children, representing the main cause of pediatric cancer deaths. Minimal residual disease (MRD) that persists after chemotherapy was the most valuable prognostic marker for hematological malignancies and solid cancers. Unfortunately, our understanding of the resistance mechanisms elicited in MRD is limited due to the rarity and heterogeneity of these residual cells. In our study, we employed paired scRNA-seq and single-cell BCR sequencing (scBCR-seq) to study the distinct features of leukemic cells from longitudinal samples obtained at the diagnosis, residual and relapsed stages at the single-cell level.By performing unsupervised clustering of the scRNA-seq data from 16,543 bone marrow CD19 -CD34 +cells and 20,392 CD19 +cells of healthy donors, we successfully defined the cell clusters of different B cell development stages sequentially, from hematopoietic stem cell / lymphoid-primed multipotential progenitors (HSC/LMPP) to common lymphoid progenitor (CLP), proB, preBI, preBII, immature/mature B cells and finally, activated B cells.By referring to the landmarks of normal cells, we then employed scRNA-seq and scBCR-seq to further dissect the phenotypic complexities within and across 4 pediatric B-ALL diagnostic-relapsed pairs at the single cell level. Our study found that BCR states can be used to distinguish leukemic cells and normal cells. From the four relapsed pediatric B-ALL patients, we obtained a total of 104,055 CD19 +cells with paired scRNA-seq and scBCR-seq data encompassing the three stages of B cell differentiation that passed the quality control. By examining the scBCR-seq data at the diagnosis stage to distinguish leukemic and normal (or non-leukemic) B cells based on genome-wide expression patterns rather than a few marker genes, we employed a machine learning approach. To train the classifier, CD19 +cells with non-clonal BCRs in D19 samples were selected as “non-leukemic”, and CD19 +cells with clonal BCRs (B265) and without detected BCRs (B590, B069 and B887) in D19 samples were selected as “leukemic”.Using this strategy, we compared the gene expression profiles of the leukemic cells at the diagnosis and relapse for each patient, with the aim to identify specific features of relapse stage leukemia cells at the single-cell level. We found that the cell composition profile tended to shift to early differentiation stages in the relapsed samples in all four patients. By analyzing the differentiation stage, cell cycle and gene expression characteristics of relapsed cell samples at the single-cell level, we obtained some unique findings, such as significantly increased expression of CDKN1A in relapsed cells.To understand the basis of such specific differentiation stage and cell cycle transition during chemotherapy, we performed differential expression analysis to identify genes specifically altered at D19 compared to diagnosis and relapse. Then, pathway enrichment analysis applied to the differentially expressed genes revealed that the hypoxia pathway was one of the top hits, being significantly upregulated during intensified chemotherapy. We obtained experimental support by validating the efficacy of the HIF-1a inhibitor PX478 combined with chemotherapy drugs in two B-ALL cell lines and two primary B-ALL cells.In summary, our study leveraged single-cell transcriptomic analysis with paired BCR repertoire profiling to decode the molecular aberrations across the phenotypically heterogeneous disease, B-ALL. We also applied a powerful B cell development classifier and an innovative machine learning model for B-ALL cell identification at single-cell resolution to determine the clonal signatures, and to track residual cell evolution in a longitudinal manner from diagnosis, to post-treatment, and finally relapse. We propose that hypoxia signaling pathway activation might serve as valuable MRD therapeutic target. While this study provided great insights into the transcriptomic characteristics of MRD cells, practically, our analytical approach could readily be applied to other hematological malignancies and solid cancers. DisclosuresNo relevant conflicts of interest to declare.