High-risk B-cell Acute Lymphoblastic Leukemia Research Articles

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.

Abstract 3271: The casein kinase 2/IKZF1 axis attenuates ceramide accumulation through up-regulation of acid ceramidase: Implications for use of CK2 inhibitors in high-risk pediatric B-cell acute lymphoid leukemia

Abstract Casein Kinase II (CK2), a growth-promoting non-oncogene, is frequently over-expressed in pediatric high-risk B-cell acute lymphoblastic leukemia (B-ALL) leading to proliferation and survival. CK2 phosphorylates the tumor suppressor IKZF1 (IKAROS) resulting in a loss-of DNA-binding activity. Loss of IKZF1 function is associated with poor prognosis in high-risk B-ALL. As such, inhibition of CK2 using silmitasertib (CX-4945), to restore IKZF1 function, is being therapeutically investigated in high-risk B-ALL. CK2 also phosphorylates/activates the mammalian ceramide synthases to increase production of the pro-apoptotic sphingolipid, ceramide (Cer). Therefore, we hypothesized that inhibition of CK2 with CX-4945 would exert both pro-death (restoration of IKAROS function) and pro-survival (decreased Cer production) effects on B-ALL cells. Moreover, this suggests that targeting the sphingolipid metabolic pathway in tandem with CX-4945 could be a novel strategy for treatment of high-risk B-ALL. To this end, we examined the effects of CX-4945 on sphingolipid levels and the enzymes of the sphingolipid metabolic pathway. Unexpectedly, we determined that CX-4945 dose-dependently increased expression of ceramide synthase 1 (CERS1) and acid ceramidase (AC) proteins, in an IKZF1 dependent manner. Increased CERS1 expression/production of C18:0 Cer has been linked to enhanced mitophagy (i.e., lysosomal clearance of damaged mitochondria) in head and neck squamous cell carcinoma. Induction of mitophagy by CX-4945 was confirmed by western blot analysis of mitofusin-1 and Drp-1 levels. Up-regulation of AC, a lysosomal protein, metabolizes C18:0 Cer to sphingosine for recycling and prevents Cer-induced lysosomal membrane permeabilization. Thus, induction of mitophagy and metabolic breakdown of Cer could potentially reduce the apoptotic efficacy of CX-4945 in B-ALL cell lines. We, therefore, tested whether inhibition of AC would synergize with CX-4945 to enhance B-ALL cell death. Indeed, synergy was observed with the AC inhibitor, SACLAC, in multiple cell lines. Consistent with the observation of synergy between CX-4945 and SACLAC, the combination also enhanced cleavage of PARP indicating an enhancement of cell death. We are currently testing the efficacy of a combination of CX-4945 and AC inhibitors in cell-line derived xenograft models of human B-ALL. Together, these findings indicate that simultaneous targeting of CK2 and AC represents a rationally selected combinatorial therapeutic strategy that overcomes the ability of cancer cells to adapt to single agent targeted therapies by altering pro- and/or anti-apoptotic pathways. Citation Format: Jeremy A. Hengst, Diwakar Bastihalli Tukaramrao, Todd Fox, Arati Sharma, Dhimant Desai, Sinisa Dovat. The casein kinase 2/IKZF1 axis attenuates ceramide accumulation through up-regulation of acid ceramidase: Implications for use of CK2 inhibitors in high-risk pediatric B-cell acute lymphoid 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 3271.

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.

Fungal Otomastoiditis caused by Aspergillus fumigatus in an immunocompromised patient: case report and literature review

This case report describes a 10-year-old male diagnosed with high-risk B-cell Acute Lymphoblastic Leukemia at a tertiary care center undergoing consolidation with the Total XV protocol. The patient, with a history of Rhino-sinusal Aspergillosis and secondary prophylaxis, presented with recurrent middle ear infections, bilateral non-purulent serous discharge, otalgia, mastoid pain, persistent high-grade fever, and profound neutropenia. Fungal ostomastoiditis was diagnosed and treated with targeted antifungals, yielding a positive response.

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.

Pediatric Patients with High-Risk B-Cell ALL in First Complete Remission May Benefit from Less Toxic Immunotherapy with Blinatumomab - Results from Randomized Controlled Phase 3 Trial AIEOP-BFM ALL 2017

Background: One of the key questions in trial AIEOP-BFM ALL 2017 focused on the reduction of treatment-related complications by replacing parts of the highly intensive consolidation phase by two courses of Blinatumomab (Blina) in a prospective randomized trial. Herein, we report the toxicity profile of B-cell acute lymphoblastic leukemia (B-ALL) patients (pts) with high-risk (HR) characteristics pending final outcome data. Patients and Methods: 728 pts with HR B-ALL were enrolled from July 15, 2018 to October 31, 2022 in this multicenter trial run in 8 different countries. Patients were included in the HR group in view of the presence of at least one of the following criteria: induction failure; high levels of minimal residual disease (MRD) at day 15 of induction, or at the end of induction (EOI), or at the end of consolidation (EOC); presence of KMT2A::AFF1, of IKZF1+ and positive MRD at EOI (Stanulla et al, JCO 2018), TCF3::HLF, or hypodiploidy. B-ALL pts with one or several of these characteristics represented 20.8% of all pts aged 0-18 years of age with B-ALL. After a 4-drug induction phase, and two weeks of consolidation treatment, patients were randomized to receive Bortezomib in addition to standard consolidation (not part of this report). Before treatment continued with intensive consolidation block HR-1', MRD was analyzed in order to identify patients eligible for subsequent hematopoietic stem cell transplantation (HSCT) based on MRD results. After block HR-1', all B-ALL HR pts were randomized to receive either two courses of consolidation (blocks HR-2', and HR-3'), or two 28-day courses of Blina at 15µg/m 2/d administered by continuous IV infusion (with a 2-week treatment-free interval). Two intrathecal injections of methotrexate (MTX) for CNS prophylaxis were given on days 1 and 29 of each Blina course, respectively. Out of 728 HR B-ALL pts, 619 pts were eligible for randomization [reasons for non-eligibility were: Event (death or relapse) before randomization was due (26), Down syndrome (25; scheduled for a non-randomized intervention with Blina), presence of TCF3::HLF (3; could receive any alternative therapy including Blina), discontinuation/substantial change of preceding therapy (23) or other protocol exclusion criteria (32)]. 572 pts were randomized (92.4% of those eligible). One pt assigned to the experimental arm (EA) and 4 pts assigned to the control arm (CA) received the other arms, respectively. Results: Toxicity was evaluated in randomized pts according to treatment administered during the randomized phase, respectively, until next element started: 268 pts were treated in the control and 281 in the EA (see Table). 16 of them switched in/after the first Blina cycle to the HR blocks due to toxicity or poor response to Blina (due to increasing MRD, >=1x10 -4). Medically relevant adverse reactions of special interest (ARSI) according to MedDRA (specified in the protocol) were evaluated in the randomized treatment phases (CA: HR-2‘/HR-3‘ block, EA: 2 Blina cycles). ARSI were recorded in 61 of 268 pts in the CA (22.8%, 71 ARSI) and in 29 of 281 pts in the EA (10.3% [p<0.001], 33 ARSI); 3 of the 33 ARSI in the EA were related to HR blocks and were observed in 3 of the 16 pts that switched to HR blocks. Life-threatening SAR were seen in 14 pts of the control group (5.2%) and in no patient in the EA (p<0.001). Conclusions: Taken together, these results show for the first time in newly diagnosed pts with HR B ALL, the favorable toxicity profile previously reported with Blinatumomab in pediatric relapsed ALL (Locatelli F et al, JAMA 2021; Brown P et al, JAMA 2021). We have demonstrated that the toxicity profile of Blinatumomab is much more favorable as compared to the intensive chemotherapy approach using HR-blocks. If upcoming analyses of outcome data will show no inferiority of the EA, blinatumomab replacement of some of the intensive chemotherapy blocks will become the new standard of care for treatment if newly diagnosed patients with HR B-ALL.

Targeting Bone Marrow Microenvironment for Treatment of High-Risk B-Cell Acute Lymphoblastic Leukemia

Introduction B-cell acute lymphoblastic leukemia (B-ALL) is the most common form of cancer in children, accounting for approximately 20% of all pediatric cancers. Although treatment of B-ALL represents one of the success stories of modern medicine with 5-year survival rates approaching 90%, some children continue to have a dismal prognosis, particularly those with high-risk genetic alterations in their ALL cells or those who relapse. The leukemia microenvironment is an attractive novel therapeutic target, especially for children with high-risk leukemia as dose-limiting toxicities of conventional chemotherapeutic agents have prevented further improvements in survival. Aims In this study, we investigate whether therapeutically targeting the bone marrow (BM) osteoclasts can improve treatment outcome for B-ALL and the mechanisms of crosstalk between osteoclasts and leukemia cells. Methods We have established syngeneic and patient-derived xenograft (PDX) models for high-risk B- ALL that recapitulate the clinical symptoms of bone loss. For in vitro experiments, leukemia cells were cultured with osteoclast-derived conditioned media (CM) for 3 days. Results To evaluate the therapeutic potential of targeting osteoclasts during leukemia development, we administered zoledronic acid (2ug 5 days/week for 2 weeks), a bisphosphonate inhibitor of osteoclastic bone resorption, alone and in combination with imatinib (100mg/kg daily for 28 days) or dasatinib (10mg/kg daily for 28 days) in our BCR-ABL1 + B-ALL syngeneic mouse model. We showed that zoledronic acid treatment significantly reversed leukemia-induced bone loss by attenuating osteoclast activity. Zoledronic acid alone was found to enhance event-free survival in leukemia-bearing mice and further improvement was shown in combination with imatinib (p<0.05) or dasatinib (p<0.01). In addition, we administered zoledronic acid alone and in combination with vincristine, dexamethasone, and L-asparaginase (VXL) in a relapsed B-ALL PDX model. We further demonstrated that zoledronic acid alone or in combination with VXL improved survival compared to mice treated with vehicle (p<0.001) or VXL alone (p<0.01), respectively. In the clinical setting, we assessed the feasibility and safety of incorporating zoledronic acid early into leukemia therapy in three children with B-ALL. The patients were undergoing induction or consolidation chemotherapy and were administered zoledronic acid at the same time. Zoledronic acid was well tolerated without any significant adverse effects, indicating the feasibility of safely administering zoledronic acid in combination with chemotherapy in children with ALL. To gain mechanistic insight into the effect of osteoclasts on leukemia cells, we compared the molecular profile of the leukemia cells cultured with CM and control media using RNA sequencing. There were 30 differentially expressed genes identified at the 5% false discovery rate with a log fold-change value ≥1 or ≤-1. KEGG pathway analysis revealed a significant difference in cell cycle pathway in leukemia cells cultured with CM compared to control. Biological process analysis showed a positive regulation of B-cell proliferation and negative regulation of lymphocyte apoptotic process in leukemia cells cultured with CM compared to control. To functionally examine the effect of osteoclasts on leukemia cells, we showed that osteoclast-derived CM significantly increased B-ALL cell proliferation, as demonstrated by increased cell number (p<0.001), as well as reduced cell percentages in G0/G1 phases and increased S+G2/M phases (p<0.05) via cell cycle analyses. Using annexin V and DAPI staining, we further demonstrated that there were more live cells and less apoptotic and dead cells when the leukemia cells were cultured with CM compared to control (p<0.001). Together, our findings suggest that soluble factors produced by osteoclasts promote leukemia cell proliferation and survival. Conclusion Our study reveals osteoclasts play a role in leukemogenesis and leukemia-induced bone loss, and that targeting osteoclasts can provide dual clinical benefit in terms of bone health and improved survival for children with high-risk B-ALL.

Prophylactic or Preemptive Donor-Derived CD19 CAR-T Cell Infusion for Preventing Relapse in High-Risk B-ALL after Allogeneic Hematopoietic Stem Cell Transplantation

Introduction: Relapse remains a significant challenge in the management of high-risk B-cell acute lymphoblastic leukemia (B-ALL) patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). Existing post-transplant relapse prevention strategies for high-risk B-ALL patients after transplantation, particularly in cases of Philadelphia chromosome-negative B-ALL, have limitations and suboptimal efficacy. This study aims to evaluate the efficacy and safety profile of prophylactic or preemptive infusion of donor-derived CD19 chimeric antigen receptor T (CAR-T) cells in high-risk B-ALL patients after allo-HSCT. Methods: Between May 2017 and July 2022, high-risk B-ALL patients with minimal residual disease (MRD) positive or MRD negative status after allo-HSCT were enrolled in clinical trials of donor-derived CD19 CAR-T cell therapy (ChiCTR 2000041025 and ChiCTR-ONN-16009862). The primary outcome was the cumulative incidence of relapse (CIR). Secondary outcomes were progression-free survival (PFS), overall survival (OS) and CAR-T cell treatment-related toxicities. Results: A total of 25 high-risk B-ALL patients who received infusion of donor-derived CD19 CAR-T cells after allo-HSCT were enrolled in the CAR-T cell group, including 8 patients with MRD and 17 patients without MRD. A contemporaneous cohort of 43 high-risk B-ALL patients who did not receive CAR-T cell therapy in MRD-positive or MRD-negative status after transplantation was also included as a control group. The median age of patients enrolled in the CAR-T group was 29 years (range: 9-60 years). The median infused CAR-T cell dose was 2.5×10^6/kg (range: 1.0-5.0×10^6/kg), with a median time from transplantation to CAR-T cell treatment of 122 days (range: 45-315 days). The median follow-up duration was 23.6 months (range: 8.3-60.6 months). Of the 25 patients in CAR-T group, eight MRD-positive patients achieved MRD-negative remission after CAR-T cells treatment (Figure1A). The two-year cumulative incidence of relapse in the CAR-T cell group was significantly lower at 4.8% (95% CI: 0.0%-12.6%) compared to the control group's incidence of 26.6% (95% CI: 11.4%-41.8%, P = 0.03，Figure1B). Additionally, the CAR-T cell group exhibited a higher two-year PFS rate [86.3% (95% CI: 71.8%-100%)] compared to the control group [63.5% (95% CI: 48.0%-79.0%), P = 0.04]. However, the two-year OS rates were comparable between the CAR-T cell group [91.0% (95% CI: 79.0%-100%)] and the control group [79.1% (95% CI: 66.0%-92.2%), P = 0.20]. Adverse events were well tolerated, and no patients experienced grade 3-4 cytokine release syndrome or any grade of immune effector cell-associated neurotoxicity syndrome. Hematological cytopenia was the most severe CAR-T cell related toxicity, but the toxicity was manageable, and only three patients experienced acute graft-versus-host disease following CAR-T cell infusion. Conclusions: Prophylactic or preemptive infusion of CAR-T cells after allo-HSCT demonstrated a reduced incidence of relapse and acceptable adverse events in high-risk B-ALL patients. These findings highlight the potential of CAR-T cell therapy as a promising strategy for relapse prevention in high-risk B-ALL patients after allo-HSCT.

Probiotic-Derived Heptelidic Acid Demonstrates Therapeutic Efficacy Against Pediatric B-Cell Acute Lymphoblastic Leukemia

Introduction Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is known to be sensitive to chemotherapy. However, approximately 15-20% of pediatric B-ALL patients experience relapse, and survival rates after relapse can drop to 5-10%. Therefore, new drugs need to be developed. Probiotics are live microorganisms with potential health benefits. Heptelidic acid (HA) from the probiotic Aspergillus oryzae has been shown to exert antitumor effects against pancreatic cancer, lung cancer, thyroid cancer, breast cancer and melanoma in vivo as well as in vitro. In this study, we assessed the antitumor effects of HA in B-ALL, which is the most common type of pediatric cancer. Methods Two B-ALL cell lines (JM1 and Reh), four CD34 + hematopoietic stem cells (HSCs) and three high-risk patient-derived B-ALL cells (s90: age < 1 year old, s96: age > 10 years old, s98: relapse) collected from the spleen or bone marrow of a patient-derived xenograft (PDX) model were used in this study. Cytotoxicity of HA was assessed by MTS assay. GAPDH activity and intracellular ATP contents were measured, as HA binds to cysteine 152 of GAPDH, a crucial region for its enzymatic activity and ATP production in glycolysis. The synergistic effects of HA with therapeutics, vincristine (VCR), doxorubicin (DXR) and L-asparaginase (L-Asp), were evaluated. GAPDH is involved not only in glucose metabolism but also in amino acid and fatty acids for energy production. Therefore, we analyzed whether HA exerted cytotoxicity under glucose, amino acid or fatty acid-deprived conditions in Reh cells. To analyze the underlying mechanism for HA's cytotoxicity against B-ALL, cell cycle analysis by flowcytometry, western blotting of cleaved PARP, caspase assays, and inhibitory assays using specific inhibitors for PCD mechanisms, such as RIPK-1 inhibitor, MLKL inhibitor, and autophagy inhibitor, were conducted. In vivo studies were done using a B-ALL PDX model. Oral administration of 0.5mg/kg HA was carried out for 21 days, while intraperitoneal injection of 0.15mg/kg VCR was performed once per week for 3 cycles in the HA-VCR combinational therapeutic efficacy study. Results HA exhibited significant cytotoxicity in JM1 (IC50: 169 ng/ml), Reh (IC50: 126.5 ng/ml), and three samples obtained from PDX mice (s90 IC50: 66.6 ng/ml, s96 IC50: 89.9 ng/ml, and s98 IC50: 275.6 ng/ml), while sparing CD34 + HSCs. GAPDH activity of CD34+ HSCs was significantly lower than both B-ALL cell lines and patient-derived cells. The cytotoxic effect of HA was associated with the reduction of GAPDH activity and ATP contents, suggesting glycolysis inhibition. Glucose deprivation induced significant reduction of cell viability, and HA showed the cytotoxicity in amino acid and fatty acid deprived media in Reh cells. Oral daily administration of HA prolonged the survival of the B-ALL PDX mice (34.5 days, n=8) compared to control mice (28 days, n=7) without causing body weight loss (p<0.05) (Figure 1A). The effects of over 0.5mg/kg of HA was confirmed by the reduction in GAPDH activity observed in leukemia cells isolated from the bone marrow. HA demonstrated synergistic effects when combined with chemotherapeutic agents, especially VCR. The combination therapy of HA and VCR resulted in improved survival outcomes in the B-ALL PDX model (49 days, n=5) compared to single-agent treatments (HA: 28 days, n=5, VCR: 40 days, n=5) and control groups (26 days, n=5) (p<0.05) (Figure 1B). Mechanistic studies revealed that HA induced PCD in B-ALL cells. HA treatment caused G2/M arrest (Control: 18.8%, HA: 27.6% in JM1; Control: 13.3%, HA: 18.3% in Reh), and this was accompanied by increased cleavage of PARP, a hallmark of PCD, in both cell lines. Moreover, the cytotoxicity of HA was attenuated by RIPK1 inhibition in JM1 and Reh. Conclusion We have demonstrated that B-ALL cells utilize glucose for their survival and HA is cytotoxic in B-ALL cells by disrupting glycolysis through the inhibition of GAPDH. The therapeutic efficacy of HA is further enhanced when combined with chemotherapeutic agents. The underlying mechanisms of HA involve the induction of RIPK-1 mediated PCD. This is the first study to demonstrate HA as a novel therapeutic agent for B-ALL.

Blinatumomab Therapy Is Associated with Favorable Outcomes after Allogeneic Hematopoietic Cell Transplantation in Pediatric Patients with B Cell Acute Lymphoblastic Leukemia

Blinatumomab, a bispecific T cell engager that binds CD19 in leukemic cells and CD3 in cytotoxic T cells and leads to leukemic blast lysis, is often used in pediatric patients with relapsed/refractory (R/R) B cell acute lymphoblastic leukemia (B-ALL) prior to allogeneic hematopoietic cell transplantation (allo-HCT). Concerns about the potential risk of blinatumomab-related immune-mediated toxicities after allo-HCT have not been adequately addressed. These include graft-versus-host disease (GVHD), delayed engraftment, and graft failure or rejection. Pediatric-specific data reporting post-HCT outcomes of patients treated with blinatumomab are scarce and limited to small cohorts. We sought to investigate the clinical outcomes of pediatric patients with R/R B-ALL who received blinatumomab therapy pre-HCT, focusing on overall survival (OS), leukemia-free survival (LFS), cumulative incidence of relapse (CIR), and nonrelapse mortality (NRM), as well as the incidence of immune-mediated post-HCT complications including GVHD, delayed neutrophil or platelet engraftment, graft failure, and graft rejection. We also investigated blinatumomab's effects on B cell reconstitution based on achievement of i.v. immunoglobulin (IVIG) independence post-HCT. This single-center, retrospective study included patients with B-ALL receiving blinatumomab therapy before undergoing allo-HCT, with transplantation performed between 2016 and 2021 at our institution. Patients receiving blinatumomab for relapse after allo-HCT were excluded. Patients receiving chemotherapy alone before allo-HCT during the same period composed the control group. Seventy-two patients were included, 31 of whom received blinatumomab before allo-HCT. Survival estimates were obtained using the Kaplan-Meier method, and the log-rank test was used to analyze differences between groups. Categorical variables were compared between groups using the chi-square test or Fisher exact test, and continuous variables were compared using the Wilcoxon rank-sum test. Cumulative incidences were estimated using the competing risks method, and Gray's test was used to analyze differences between groups. A Cox proportional hazards regression model was used for univariate and multivariable analyses for OS. Landmark analysis was performed at the set time points of 30 days and 100 days post-allo-HCT. Most patients in the study cohort had high-risk relapsed B-ALL. Blinatumomab therapy induced minimal residual disease (MRD)-negative remissions in all patients, whereas 5 patients (12.2%) receiving chemotherapy alone had persistent MRD pre-allo-HCT. Time from the start of therapy to the date of allo-HCT was shorter for patients who received blinatumomab compared with those who received chemotherapy (P < .0001). Blinatumomab therapy was associated with greater LFS compared to chemotherapy alone (P = .049), but when limited to 1 year, LFS was not significantly different from control (P = .066). There appeared to be higher OS, lower CIR, and lower NRM in patients receiving blinatumomab compared to the control group; however, the differences were not significant. None of the variables assessed in multivariable analysis was associated with differences in OS. When compared to the controls, blinatumomab therapy did not result in a higher incidence of acute or chronic GVHD, delayed neutrophil or platelet engraftment, or graft failure or rejection. The time to IVIG infusion independence post-allo-HCT was similar in the 2 groups. This study supports the use of blinatumomab salvage therapy for R/R B-ALL before allo-HCT given its efficacy in inducing MRD-negative remissions and optimizing LFS, as well as its lack of association with an increased incidence of post-allo-HCT adverse immune-mediated toxicities. Larger, prospective studies are needed to confirm these findings and to investigate blinatumomab's effects in long-term post-allo-HCT events.

Targeting SF3B1 in High-Risk B-Cell Acute Lymphoblastic Leukemia

Introduction B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric cancer. The outcomes of young adults with B-ALL are poor, with an event-free survival (EFS) rate of &amp;lt;50%. The prognosis of children with certain types of B-ALL is also poor with an EFS rate of 70%. Therefore, there is a need for new treatments for these children with high-risk B-ALL. RNA splicing alternations have been suggested to contribute to the initiation and/or maintenance of cancer. 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, including myeloid malignancies and T-cell ALL. However, there have been no reports studying the efficacy and the function of spliceosome inhibitors including SF3B1 inhibitors in B-ALL. In this study, we determined the therapeutic potential of pladienolide B (Plad-B), an SF3B1 inhibitor, in B-ALL. Methods SF3B1 mRNA and protein expressions were determined in the cell lines Reh and JM1 and 14 patient samples (standard-risk: 7 samples, high-risk: 7 samples), by qRT-PCR and Western blotting, respectively. Efficacy of Plad-B was tested in two B-ALL cell lines, CD34 positive hematopoietic stem cells (HSCs), and three high-risk patient-derived xenograft (PDX) samples (sample#1: age &amp;lt; 1 year old, sample#2: age &amp;gt; 10 years old, sample#3: relapse), by an MTS assay. In vivo efficacy of Plad-B was tested using an Reh xenograft model and a PDX model. Function of Plad-B was assessed in cell lines by a cell cycle assay, Annexin V assay with flow cytometry, and Western blotting of cleaved PARP and cleaved caspase-3. To determine the changes in the splicing events and apoptosis-associated genes, we are performing RNA-seq at 15min, 30min, 60min, and 24 hours after the treatment. Results SF3B1 mRNA and protein expressions were significantly higher in Reh and JM1 than in hematopoietic monocular cells and CD34-positive HSCs (p &amp;lt; 0.05). SF3B1 protein, but not mRNA, expressions were higher in primary patient samples than in hematopoietic monocular cells and CD34-positive HSCs. There was no significant difference in the mRNA and protein expressions between standard-risk and high-risk groups. Plad-B treatments showed significant cytotoxicity in both Reh and JM1 cell lines with IC50 of 1.2nM and 0.6nM, respectively, at 48 hours after treatment. Plad-B did not show cytotoxicity at the same tested concentrations in CD34-positive HSCs. Plad-B treatments showed similarly significant cytotoxicity in three harvested PDXs with IC50 of 0.7nM, 2.5nM, and 1.1nM, respectively, at 48 hours after the treatment. Plad-B, at a dose of 10 mg/kg 2 times on 1 and 2 days, significantly prolonged survival in the Reh xenograft mouse model, with a median survival time of 33.5 days compared with 25.0 days in the control group (p &amp;lt; 0.05) (Figure 1). Plad-B, at a dose of 10 mg/kg 4 times on 1, 3, 5, and 7 days, prolonged survival in the PDX mouse model (sample#1), with a median survival time of 38.0 days compared with 32.0 days in the control group (p = 0.14). Cell cycle arrest was observed at 24 hours after Plad-B treatment in both Reh (Control: 12.6%, Plad-B 3nM: 23.8% in G2/M phase, p &amp;lt; 0.001) and JM1 (Control: 20.6%, Plad-B 3nM: 35.1% in G2/M phase, p &amp;lt; 0.01). Plad-B caused significant cell apoptosis in Reh (Control: 3.2%, Plad-B 3nM: 24.1% with Annexin V positive cells, p &amp;lt; 0.001) and JM1 (Control: 5.9%, Plad-B 3nM: 31.2% with Annexin V positive cells, p &amp;lt; 0.001) cells at 24 hours after treatment. Plad-B also caused significant cell apoptosis in harvested PDX sample #1 (Control: 29.8.%, Plad-B 3nM: 47.6% with Annexin V positive cells, p &amp;lt; 0.001) at 24 hours after treatment. Western blotting of anti-cleaved PARP and anti-cleaved caspase-3 showed that the expression of cleaved caspase-3 and cleaved PARP were significantly augmented in Reh and JM1 cells after Plad-B treatment. RNA seq data is currently being analyzed. Conclusions SF3B1 is highly expressed in B-ALL cell lines and in primary patient samples regardless of the risk group. Plad-B showed significant cytotoxicity in B-ALL leading leukemia cells to G2/M cycle arrest and apoptosis. Plad-B treatment demonstrated in vivo therapeutic efficacy in pre-clinical B-ALL animal models. These data suggest therapeutic potential of SF3B1 inhibition in B-ALL including high-risk patients.

Identification of USP9X as a leukemia susceptibility gene

AbstractWe recently reported that children with multiple birth defects have a significantly higher risk of childhood cancer. We performed whole-genome sequencing on a cohort of probands from this study with birth defects and cancer and their parents. Structural variant analysis identified a novel 5 kb de novo heterozygous inframe deletion overlapping the catalytic domain of USP9X in a female proband with multiple birth defects, developmental delay, and B-cell acute lymphoblastic leukemia (B-ALL). Her phenotype was consistent with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F). Genotype-phenotype analysis including previously reported female probands (n = 42) demonstrated that MRXS99F probands with B-ALL (n = 3) clustered with subjects with loss-of-function (LoF) USP9X variants and multiple anomalies. The cumulative incidence of B-ALL among these female probands (7.1%) was significantly higher than an age- and sex-matched cohort (0.003%) from the Surveillance, Epidemiology, and End Results database (P < .0001, log-rank test). There are no reports of LoF variants in males. Males with hypomorphic missense variants have neurodevelopmental disorders without birth defects or leukemia risk. In contrast, in sporadic B-ALL, somatic LoF USP9X mutations occur in both males and females, and expression levels are comparable in leukemia samples from both sexes (P = .54), with the highest expressors being female patients with extra copies of the X-chromosome. Overall, we describe USP9X as a novel female-specific leukemia predisposition gene associated with multiple congenital, neurodevelopmental anomalies, and B-ALL risk. In contrast, USP9X serves as a tumor suppressor in sporadic pediatric B-ALL in both sexes, with low expression associated with poorer survival in patients with high-risk B-ALL.

Prognostic analysis of children with Philadelphia chromosome-like acute lymphoblastic leukemia common genes

Objective: To summarize the clinical data and prognosis of children with Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) common genes. Methods: This was a retrospective cohort study.Clinical data of 56 children with Ph-like ALL common gene cases (Ph-like ALL positive group) treated from January 2017 to January 2022 in the First Affiliated Hospital of Zhengzhou University, Henan Children's Hospital, Henan Cancer's Hospital and Henan Provincial People's Hospital were collected, 69 children with other high-risk B cell acute lymphoblastic leukemia (B-ALL) at the same time and the same age were selected as the negative group. The clinical characteristics and prognosis of two groups were analyzed retrospectively. Comparisons between groups were performed using Mann-Whitney U test and χ2 test. Kaplan-Meier method was used for survival curve, Log-Rank test was used for univariate analysis, and the Cox regression model was used for multivariate prognosis analysis. Results: Among 56 Ph-like ALL positive patients, there were 30 males and 26 females, and 15 cases were over 10 years old. There were 69 patients in Ph-like ALL negative group. Compared with the negative group, the children in positive group were older (6.4 (4.2, 11.2) vs. 4.7 (2.8, 8.4) years), and hyperleukocytosis (≥50×109/L) was more common (25% (14/56) vs. 9% (6/69)), the differences were statistically significant (both P<0.05). In the Ph-like ALL positive group, 32 cases were positive for IK6 (1 case was co-expressed with IK6 and EBF1-PDGFRB), 24 cases were IK6-negative, of which 9 cases were CRLF2 positive (including 2 cases with P2RY8-CRLF2, 7 cases with CRLF2 high expression), 5 cases were PDGFRB rearrangement, 4 cases were ABL1 rearrangement, 4 cases were JAK2 rearrangement, 1 case was ABL2 rearrangement and 1 case was EPOR rearrangement. The follow-up time of Ph-like ALL positive group was 22 (12, 40) months, and 32 (20, 45) months for negative group. The 3-year overall survival (OS) rate of positive group was significantly lower than the negative group ((72±7) % vs. (86±5) %, χ2=4.59, P<0.05). Compared with the 24 IK6-negative patients, the 3-year event free survival (EFS) rate of 32 IK6 positive patients was higher, the difference was statistically significant ((88±9) % vs. (65±14) %, χ2=5.37, P<0.05). Multivariate Cox regression analysis showed that the bone marrow minimal residual disease (MRD) not turning negative at the end of first induction (HR=4.12, 95%CI 1.13-15.03) independent prognostic risk factor for patient with Ph-like ALL common genes. Conclusions: Children with Ph-like ALL common genes were older than other high-risk B-ALL patients at diagnosis, with high white blood cells and lower survival rate. The bone marrow MRD not turning negative at the end of first induction were independent prognostic risk factor for children with Ph-like ALL common gene.

Single-cell transcriptome analysis profiles the expression features of TMEM173 in BM cells of high-risk B-cell acute lymphoblastic leukemia

BackgroundAs an essential regulator of type I interferon (IFN) response, TMEM173 participates in immune regulation and cell death induction. In recent studies, activation of TMEM173 has been regarded as a promising strategy for cancer immunotherapy. However, transcriptomic features of TMEM173 in B-cell acute lymphoblastic leukemia (B-ALL) remain elusive.MethodsQuantitative real-time PCR (qRT-PCR) and western blotting (WB) were applied to determine the mRNA and protein levels of TMEM173 in peripheral blood mononuclear cells (PBMCs). TMEM173 mutation status was assessed by Sanger sequencing. Single-cell RNA sequencing (scRNA-seq) analysis was performed to explore the expression of TMEM173 in different types of bone marrow (BM) cells.ResultsThe mRNA and protein levels of TMEM173 were increased in PBMCs from B-ALL patients. Besides, frameshift mutation was presented in TMEM173 sequences of 2 B-ALL patients. ScRNA-seq analysis identified the specific transcriptome profiles of TMEM173 in the BM of high-risk B-ALL patients. Specifically, expression levels of TMEM173 in granulocytes, progenitor cells, mast cells, and plasmacytoid dendritic cells (pDCs) were higher than that in B cells, T cells, natural killer (NK) cells, and dendritic cells (DCs). Subset analysis further revealed that TMEM173 and pyroptosis effector gasdermin D (GSDMD) restrained in precursor-B (pre-B) cells with proliferative features, which expressed nuclear factor kappa-B (NF-κB), CD19, and Bruton’s tyrosine kinase (BTK) during the progression of B-ALL. In addition, TMEM173 was associated with the functional activation of NK cells and DCs in B-ALL.ConclusionsOur findings provide insights into the transcriptomic features of TMEM173 in the BM of high-risk B-ALL patients. Targeted activation of TMEM173 in specific cells might provide new therapeutic strategies for B-ALL patients.

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.

Pro-Active 4SCAR2.0 Therapy with NGS-MRD Disease Monitoring in High-Risk B Cell Leukemia Management

BACKGROUND: Allogeneic hematopoietic stem cell transplantation (HCT) is a standard treatment for high-risk relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL). However, about 30-40% of patients still relapse after HCT. Chimeric antigen receptor-modified T cell (CAR-T) therapy holds great promise as a salvage approach. Although CD19-targeted CAR-Ts have demonstrated a rapid and significant anti-tumor effect in patients with B-cell malignancies, many still suffer disease relapse due to the decrease or loss of CD19 antigen. Therefore, novel curative approaches are needed. PURPOSE: The aim of this study is to determine the best timing for applying CAR-T therapy in high-risk B-ALL patients based on high-sensitivity analysis of tumor cells by next-generation sequencing (NGS) detecting minimal residual disease (MRD). An innovative CAR-T therapy concept, CAR2.0, has been proposed, which uses multi-antigen-targeted CAR-Ts to prevent antigen escape and prolong remission. Based on NGS-MRD detection, patients with potential tumor relapse can be identified early and managed accordingly. On the other hand, if extended negative NGS-MRD is found, the patient is deemed at low risk and no further treatment is needed. The study proposes to treat high-risk B-ALL patients in the first remission period with CAR2.0 followed by continued disease monitoring by NGS-MRD to avoid HCT. METHODS: B-ALL patients who have high tumor burden and high-risk genetic indication is enrolled with the understanding that CAR-T therapy will be applied in the first remission and disease will be continuously monitored by NGS-MRD. The tumor cells from initial diagnosis will be analyzed for target antigens by immunostaining and to detect clonally rearranged immunoglobulin gene sequences by NGS-MRD with sensitivity ≤10-6. Patients will receive 4SCAR19 (CD19scFv-CD28/CD27/CD3ζ-iCasp9) therapy in the first remission and will be followed up for CAR-Ts, B cells and IgG/IgA/IgM in the blood, and bi-monthly NGS-MRD for residual tumor cells in the bone marrow (BM). A booster CAR-T treatment targeting additional tumor antigen such as CD22 will be applied 2 months later. A consolidation CAR-T treatment based on known target antigens will be applied 6 months after the first CAR-T infusion. The cyclophosphamide/fludarabine chemo-conditioning will be included prior to the first CAR-T treatment only. The CAR-T infusion dose is 1-5x106 CAR-Ts/kg. The quality of apheresis cells, efficiency of gene transfer, T cell proliferation, CAR-T infusion dose and blood CAR copies are quantitatively documented. The end point for this study is the establishment of NGS-MRD negativity for 1 year, with continued follow-up for 5 years. RESULTS: A 20 years old female was diagnosed with BCR/ABL1 P190 positive B-ALL, with 82.52% tumor blasts in the BM. NGS identified two high-frequency IgH clones at 66.29% and 30.41%. The patient received induction chemotherapy (VTCP, CAM, VP+MTX) combined with TKI therapy (Nilotinib) and achieved complete remission (CR) after the first round of treatment based on both flow cytometry and NGS MRD analyses. During the fourth round of chemotherapy (Methotrexate-Cytarabine-Dexamethasone), the patient suffered severe oral and intestinal mucositis, along with kidney and liver toxicity and required week-long dialysis. A decision was made to stop chemotherapy and start the first 4SCAR19 therapy of 3.53x106 CAR-Ts/kg, while maintaining the TKI therapy. The CAR-T cells in blood, the B cell count and Ig levels were monitored, and a booster CD22/CD19 dual CAR-Ts (4SCAR2219) was given at a dose of 3.35 x106 CAR-Ts/kg on day 96 (see figure). Consistent with 4SCART safety profile, the patient experienced no greater than grade 1 CRS. NGS-MRD detection of tumor cell clones remained negative on day 96 after the first CAR-T infusion and at 6 months into the remission. In summary, the 4SCAR2.0 therapy regimen appeared safe and effective in the innovative NGS-MRD/4SCAR2.0 B-ALL study regimen with in vivo persistency for more than three months. The simultaneous expansion of CD19 mono-specific and CD22/CD19 bi-specific CAR-Ts supports a stable maintenance treatment with good life quality as compared with conventional chemotherapy. CONCLUSIONS: The combination of 4SCAR2.0 with NGS-MRD detection of tumor clones in the management of high-risk B-ALL appears to be safe and may be a logical option for patients not elected for HCT therapy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Single-Cell Pan-Cancer Analysis Reveals Treatment Resistance Stem/Progenitor-like Subpopulation in the High-Risk Pediatric Leukemia

Leukemic stem cells have long been considered a therapy-resistant population in myeloid leukemia. Several recent publications have also described a population with stem/progenitor-like phenotype in pediatric B-cell acute lymphoblastic leukemia (B-ALL). However, the existence and cell-of-origin of stem/progenitor-like blasts in other subtypes of leukemias have not been studied extensively. Moreover, the relationship of this subpopulation with clinical outcomes and strategies to target them remain to be systematically explored in pediatric leukemia. To investigate these questions, we extensively characterized diagnostic samples of 84 patients with high-risk pediatric leukemias, including AML (10), B-ALL (23), ETP T-ALL (30), non-ETP T-ALL (10), and mixed phenotype acute leukemia (MPAL) (11). We performed scRNA-Seq and scATAC-Seq on all 84 patient samples, generating an atlas of more than one million cells (Figure 1A, UMAP colored by sample). By projecting leukemic cells onto a novel healthy reference atlas composed of pediatric and infant bone marrow and thymus, we identified and characterized a stem/progenitor-like subpopulation with a common immunophenotype CD34+CD44+CD133+ in all five leukemia subtypes (Figure 1B). More importantly, we found the frequency of this subpopulation is highly correlated with the level of minimal residual disease after induction chemotherapy, suggesting therapy resistance of stem/progenitor-like leukemic blasts. We identified several pathways commonly up-regulated in stem/progenitor-like subpopulations across different high-risk leukemias, including previously reported leukemia stem cell (LSC) signatures in AML, quiescent signature, and ribosome biogenesis. To better power analyses relating stem/progenitor-like subpopulations with clinical outcome, we deconvoluted and analyzed >3000 bulk RNA-Seq samples from the TARGET and Children's Oncology Group AALL0434 T-ALL databases using our single-cell molecular signatures and found a universal existence of stem/progenitor-like leukemic blasts that predict poor clinical outcome across different high-risk leukemias. Our single-cell analysis consistently associated chemoresistance with presence of stem/progenitor-like leukemic blasts across 5 subtypes of high-risk pediatric leukemia, leading us to seek novel therapeutic strategies targeting this subpopulation. Using single-cell derived cell signatures, we performed an in silico drug screen using multiple independent drug/target databases. This analysis revealed several pan-leukemia candidate drug targets for stem/progenitor-like leukemic blasts, including FLT3, CD44, CD133, BCL2, and PIK3R1. We also found leukemia-subtype-specific candidates such as BRAF for AML, TGFB1 for B-ALL, IL1B for ETP-ALL, and STAT3 for AML and B-ALL. Both pharmacological and genetic experiments using cell lines and PDX models are underway to validate the candidate drug targets. Finally, we employed ligand-receptor analysis to identify interactions that stem/progenitor-like blasts could have with their surrounding environment. This analysis revealed a set of immunosupressive ligand-receptor pairs between the stem/progenitor-like leukemic blasts and NK cells. Using our predicted ligand-receptor ineractions, we computed patient-specific NK cytotoxic scores and discovered an immunosuppressive role of stem/progenitor-like leukemic blasts towards NK cells in all leukemia subtypes, suggesting a mechanism for immune surveillance escape and potential resistance to immunotherapy in stem/progenitor-like blasts. Taken together, our data reveal the existence of a common stem/progenitor-like blast population in high-risk pediatric leukemias. These cells exhibit characteristics of leukemia stem cells, quiescence signatures, resistance to chemotherapy, and immunosuppressive effect towards NK cells. They are also highly predictive of poor clinical outcomes across different high-risk leukemias. We identified common and leukemia-subtype-specific candidate drug targets. Follow-up studies targeting these genes along with conventional chemotherapy are underway with promise to improve the clinical outcome for high-risk pediatric leukemias. CC & JX, as well as DTT & KT, contributed equally to the work. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Outcomes of allogeneic hematopoietic cell transplantation in adults with fusions associated with Ph-like ALL

AbstractAllogenic hematopoietic cell transplantation (alloHCT) is a well-established curative modality for acute lymphoblastic leukemia (ALL), yet large amounts of data describing alloHCT outcomes in Philadelphia (Ph)-like ALL are lacking. We retrospectively analyzed archived DNA samples from consecutive adults with B-cell Ph-negative ALL who underwent alloHCT in complete remission (CR) (n = 127) at our center between 2006 and 2020. Identification of fusions associated with Ph-like ALL was performed using cumulative results from RNA-seq, conventional cytogenetics, fluorescence in situ hybridization, and whole genome array studies. Fusions associated with Ph-like ALL were detected in 56 (44%) patients, of whom 38 were carrying CRLF2r. Compared with other non–Ph-like ALL (n = 71), patients with fusions associated with Ph-like ALL were more frequently Hispanic (P = .008), were less likely to carry high-risk cytogenetics (P < .001), and were more likely to receive blinatumomab prior to HCT (P = .019). With the median followup of 3.5 years, patients with Ph-like ALL fusions had comparable posttransplant outcomes compared with other B-cell ALL: 3-year relapse-free survival (RFS) (41% vs 44%; P = .36), overall survival (OS) (51% vs 50%; P = .59), and relapse (37% vs 31%; P = .47). In multivariable analysis, age (P = .023), disease status at the time of transplant (P < .001), and donor type (P = .015) influenced OS. RFS (primary endpoint) was significantly influenced by disease status (P < .001) and conditioning regimen intensity (P = .014). In conclusion, our data suggest that alloHCT consolidation results in similarly favorable survival outcomes in adult patients with Ph-like fusions and other high-risk B-cell ALL.

Abstract 6213: Chromatin accessibility landscape of pediatric high-risk B-cell acute lymphoblastic leukemia

Abstract B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy. Although overall cure rate has exceeded 90%, the prognosis of high-risk B-ALL remains poor. Genome sequencing studies have revealed key genetic aberrations in B-ALL. But driver remains unclear in 8% of B-ALL for leukemogenesis, and 40% of high-risk B-ALL for drug resistance. Epigenetic mechanisms contributing to leukemia have recently been recognized, including histone modification and methylation. To date, a comprehensive landscape of chromatin accessibility in B-ALL is still lacking. Here, we performed Assays for Transposase Accessible Chromatin using sequencing (ATAC-seq) on a total of 61 high-risk B-ALLs treated at Shanghai Children’s Medical Center, including major B-ALL subtypes. We generated 144 high quality chromatin accessibility profiles from 79 tumors, including 18 diagnosis-relapse paired tumors as well as 11 diagnosis and 32 relapsed tumors. We observed significantly higher chromatin accessibility in B-ALL as compared to normal B-cells. Functional chromatin state annotation showed a median of 27.1% open chromatin regions (OCRs) in B-ALL were constituted from quiescent regions that were absent for known histone modifications, indicating unveiled role of quiescent regions in B-ALL. We further investigated the allelic imbalanced chromatin accessibility in 32 B-ALL with matched ATAC-seq and whole genome sequencing data. Unexpectedly, we found a median of 10.8% of OCRs showed imbalanced accessibility between two heterozygous alleles. Moreover, the adjacent imbalanced OCRs tend to be in the same topologically associating domain, suggesting the transcription regulation from chromatin accessibility was constrained within 3-D genome architecture. We next looked into the OCRs among B-ALL subtypes. Consistent with the regulatory role of chromatin accessibility on gene transcription, we found subtype specific pattern of OCRs in B-ALL, with open regions from enhancer and bivalent chromatin states showed more power in subtype discrimination. A total of 15516 out of 765788 (2.03%) peaks were identified as subtype specific OCRs. Motif analysis associated these regions to 212 transcription factors (TFs). Consistently, genes regulated by these TFs also exhibited subtype specific expression. Finally, we analyzed differences in OCRs between diagnosis (D) and relapse (R) in each B-ALL subtype. Only 2.44% D-R differential peaks were shared between any two subtypes, suggesting subtype specific role of chromatin accessibility in relapse. Potential target genes were further identified with quantitative trait loci analysis. With data from DepMap project, we verified that the expression of the target genes identified was associated with drug response. These data unveiled potential role of chromatin accessibility in high-risk B-ALL and the treatment response of this malignancy. Citation Format: Han Wang, Huiying Sun, Bilin Liang, Fang Zhang, Fan Yang, Bowen Cui, Lixia Ding, Ronghua Wang, Yanjing Tang, Jianan Rao, Wenting Hu, Shuang Zhao, Wenyan Wu, Benshang Li, Jingyan Tang, Shuhong Shen, Yu Liu. Chromatin accessibility landscape of pediatric high-risk B-cell acute lymphoblastic leukemia [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 6213.

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.