T-lineage Acute Lymphoblastic Leukemia Research Articles

Myb overexpression synergizes with the loss of Pten and is a dependency factor and therapeutic target in T-cell lymphoblastic leukemia.

T-lineage acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that accounts for 10%-15% of pediatric and 25% of adult ALL cases. Although the prognosis of T-ALL has improved over time, the outcome of T-ALL patients with primary resistant or relapsed leukemia remains poor. Therefore, further progress in the treatment of T-ALL requires a better understanding of its biology and the development of more effective precision oncologic therapies. The proto-oncogene MYB is highly expressed in diverse hematologic malignancies, including T-ALLs with genomic aberrations that further potentiate its expression and activity. Previous studies have associated MYB with a malignant role in the pathogenesis of several cancers. However, its role in the induction and maintenance of T-ALL remains relatively poorly understood. In this study, we found that an increased copy number of MYB is associated with higher MYB expression levels, and might be associated with inferior event-free survival of pediatric T-ALL patients. Using our previously described conditional Myb overexpression mice, we generated two distinct MYB-driven T-ALL mouse models. We demonstrated that the overexpression of Myb synergizes with Pten deletion but not with the overexpression of Lmo2to accelerate the development of T-cell lymphoblastic leukemias. We also showed that MYB is a dependency factor in T-ALL since RNA interference of Myb blocked cell cycle progression and induced apoptosis in both human and murine T-ALL cell lines. Finally, we provide preclinical evidence that targeting the transcriptional activity of MYB can be a useful therapeutic strategy for the treatment of T-ALL.

Genomic analysis of venous thrombosis in children with acute lymphoblastic leukemia from diverse ancestries.

Venous thrombosis is a common adverse effect of modern therapy for acute lymphoblastic leukemia (ALL). Prior studies to identify risks of thrombosis in pediatric ALL have been limited by genetic screens of pre-identified genetic variants or genome- wide association studies (GWAS) in ancestrally uniform populations. To address this, we performed a retrospective cohort evaluation of thrombosis risk in 1,005 children treated for newly diagnosed ALL. Genetic risk factors were comprehensively evaluated from genome-wide single nucleotide polymorphism (SNP) arrays and were evaluated using Cox regression adjusting for identified clinical risk factors and genetic ancestry. The cumulative incidence of thrombosis was 7.8%. In multivariate analysis, older age, T-lineage ALL, and non-O blood group were associated with increased thrombosis while non-low-risk treatment and higher presenting white blood cell count trended toward increased thrombosis. No SNP reached genome-wide significance. The SNP most strongly associated with thrombosis was rs2874964 near RFXAP (G risk allele; P=4x10-7; hazard ratio [HR] =2.8). In patients of non-European ancestry, rs55689276 near the α globin cluster (P=1.28x10-6; HR=27) was most strongly associated with thrombosis. Among GWAS catalogue SNP reported to be associated with thrombosis, rs2519093 (T risk allele, P=4.8x10-4; HR=2.1), an intronic variant in ABO, was most strongly associated with risk in this cohort. Classic thrombophilia risks were not associated with thrombosis. Our study confirms known clinical risk features associated with thrombosis risk in children with ALL. In this ancestrally diverse cohort, genetic risks linked to thrombosis risk aggregated in erythrocyte-related SNP, suggesting the critical role of this tissue in thrombosis risk.

Inflammatory Signatures Define a New High-Risk T-Lineage ALL Subtype

T-lineage acute lymphoblastic leukemia (ALL) is an aggressive cancer comprising of diverse subtypes that are challenging to stratify using conventional immunophenotyping and have historically exhibited poor treatment outcomes in response to cytotoxic chemotherapy ( Nguyen, K et al. Leukemia 2008). Early T-cell Precursor ALL (ETP-ALL) represent a distinct subtype that displays a developmental block at the earliest stages of T-cell commitment, accompanied by the aberrant expression of myeloid and stem cell markers ( Coustan-Smith, E. et al. Lancet Oncol. 2009). The classification can be further complicated by T/Myeloid Mixed phenotype acute leukemia (T/My-MPAL), a rare and aggressive malignancy characterized by blasts with both T-cell lymphoid and myeloid markers ( George, B. S. et al. Biomedicines 2022). Accurate clinical diagnosis of T-lineage ALL is hindered by phenotypic variations among its subsets. Nevertheless, the precise diagnosis holds critical importance as drug sensitivity in preclinical models of T-lineage ALL is closely linked to the differentiation state, such as the sensitivity of ETP-ALL to the BCL-2 inhibitor venetoclax ( Chonghaile, T. N. et al. Nat Cancer 2021). This highlights the critical need to identify consistent phenotypic traits associated with unique therapeutic vulnerabilities to effectively tailor therapy to individual patients. To gain insights into subset-specific therapeutic vulnerabilities, we performed an integrative multiomic analysis of bone marrow (BM) samples (n=21) from newly diagnosed T-lineage ALL patients, including T-cell ALL (T-ALL), ETP-ALL, and T/My-MPAL. Leveraging cellular indexing of transcriptomes and epitopes in conjunction with T-cell receptor sequencing, we identified a distinct subset of patients spanning all three subtypes characterized by the high frequency of leukemic cells that most closely resemble healthy hematopoietic stem and progenitor cells (HSPC) by Symphony ( Kang, J. B. et al. Nat Commun 2021) query mapping, indicative of an earlier stage of differentiation arrest ( Figure 1A bottom). Pathway analysis revealed an inflammatory signature in patients with high frequencies of stem-like cells suggestive of an inflammatory microenvironment akin to high-risk AML ( Lasry, A. et al. Nat Cancer 2023), which we refer to as inflammatory T-lineage ALL. Next, we mined our multiomic data to generate a comprehensive geneset for inflammatory T-lineage ALL scoring in single cells and bulk samples ( Figure 1A top). Interestingly, Olink cytokine array analysis uncovered upregulation of production of cytokines IL-1β, IL-18, and/or OSM in inflammatory T-lineage ALL samples. Thus, this comprehensive multiomic analysis identified a subset of T-lineage ALL patients characterized by early differentiation arrest and inflammatory signatures. To explore the relationship between inflammatory T-lineage status and clinical response, we utilized the ssGSEA algorithm to score activity of our inflammatory signature in bulk RNA-sequencing data from the TARGET T-lineage ALL dataset (n=265, 74/265 inflammatory) ( Liu, Y. et al. Nat Genet 2017) and the Tran et al. study (n=27, 17/27 inflammatory) ( Tran, T. H. et al. Blood Adv 2022). We found a significant association between high inflammatory ssGSEA score and elevated MRD. To uncover the inflammatory T-lineage ALL mutational landscape, we performed whole exome sequencing on our study cohort, and compiled the reported mutations in the TARGET dataset. Interestingly, inflammatory T-lineage ALL patients, as predicted by inflammatory signature activity, had a significantly higher prevalence of mutations affecting cytokine signaling ( NRAS, JAK3), chromatin remodeling genes ( EZH2), and the WT1 oncogene. These analyses demonstrate a significant relationship between inflammatory status, genomic lesions, and MRD. Finally, we demonstrate that inflammatory, but not non-inflammatory, T-lineage ALL cells are significantly more sensitive to BCL-2 inhibitor venetoclax ex vivo (Figure 1B).Overall, our study has identified a new subtype of T-lineage ALL defined by an early arrest in T-cell development, inflammatory signaling, a unique mutational landscape, sensitivity to venetoclax, and an association with adverse clinical parameters.

Outcomes after Hematopoietic Cell Transplantation for T-Lineage Acute Lymphoblastic Leukemia and Lymphoma: A Cooperative Study from the Adult Acute Lymphoblastic Leukemia Working Group and the Adult Malignant Lymphoma Working Group of the Japanese Society for Transplantation and Cellular Therapy

Background: T-lineage acute lymphoblastic leukemia (T-ALL) and lymphoblastic lymphoma (T-LBL) arise from immature precursor T cells and are currently considered a single disease entity according to the World Health Organization Classification. Patients with T-ALL or T-LBL typically receive ALL-type intensive chemotherapy if applicable, and those with high-risk features or relapsed disease undergo hematopoietic cell transplantation (HCT). Although autologous HCT for T-ALL is uncommon, it remains a choice in the general practice of T-LBL, resulting in different donor selection strategies for these diseases. However, there is limited data on outcomes for these patients. Methods: We analyzed nationwide registry data (Transplant Registry of Unified Management Program Japan, TRUMP) from 2000 to 2017 to evaluate outcomes after the first HCT and identify prognostic factors among p with T-ALL/T-LBL. Five patients who underwent autologous HCT for T-ALL were excluded from the analysis. Overall and disease-free survival (OS and DFS) were assessed using the Kaplan-Meier method with the log-rank test. Univariate and multivariate analyses were performed to identify the potential prognostic factors. The Cox proportional hazards method was used for the multivariate analysis to assess OS, whereas Gray's test and the Fine-Gray model were used to determine the cumulative incidence of relapse (CIR) considering competing risks such as relapse and non-relapse mortality (NRM). Results: A total of 1345 patients (T-ALL, n=808; T-LBL, n=537) were included in the database. The median follow-up period of survivors was 4.5 (interquartile range, 2.0-7.7) years. The median age at HCT was 32 (range, 16-70) years. The OS and DFS at 4 years after HCT were comparable between T-ALL and T-LBL (OS 51.7% vs. 52.0%, p = 0.494; DFS 48.3% vs. 45.4%, p = 0.066). However, higher NRM and lower CIR were observed in T-ALL compared with T-LBL (4-year NRM 21.8% vs. 14.5%, p = 0.002; 4-year CIR 29.9% vs. 40.1%, p < 0.001). In T-LBL, patients who received allogeneic HCT (allogeneic LBL, n = 402) had significantly worse survival than those who received autologous HCT (autologous LBL, n = 135) (4-year OS 47.4% vs. 66.2%, p < 0.001; 4-year DFS 47.4% vs. 66.2%, p < 0.001), with significantly worse NRM and comparable CIR (4-year NRM 18.0 vs 3.8%, p < 0.001; 4-year CIR 39.6% vs. 41.6%, p = 0.875). Compared with the allogeneic ALL or allogeneic LBL groups, the autologous LBL group had a significantly older age at HCT (the respective median age was 31 years [range, 16-70], 33 [16-86], and 49 [16-76]; p < 0.001). The allogeneic LBL group had a lower rate of first complete remission (CR1) and a higher rate of non-CR at SCT (CR1/non-CR: allogeneic ALL, 57.1%/30.4%; allogeneic LBL, 37.6%/47.0%; autologous LBL, 57.8%/31.1%; p < 0.001). Among patients in CR1 at HCT, OS and DFS were comparable among the allogeneic ALL (n = 461), allogeneic LBL (n = 151), and autologous LBL (n = 78) groups (Fig. 1, 4-year OS 69.3% vs. 72.6% vs. 76.7%, respectively, p = 0.389; 4-year DFS 64.9% vs. 65.5% vs. 67.1%, respectively, p = 0.830). However, the NRM was lower in the autologous LBL group (4-year NRM 16.6% vs. 8.3% vs. 0.0%, respectively, p < 0.001), and the CIR was lower in the allogeneic ALL group (4-year CIR 18.9% vs. 26.3% vs. 32.9%, respectively, p = 0.004). Among patients without CR at SCT, outcomes were comparable between allogeneic ALL (n = 246), allogeneic LBL (n = 189), and autologous LBL groups (n = 42) (4-year OS 18.4%, 24.6%, vs 36.9%, respectively, p = 0.347; 4-year DFS 17.4%, 21.9%, vs 23.6%, respectively, p = 0.818; 4-year NRM 29.8%, 28.0%, vs 12.7%, respectively, p = 0.107; 4-year CIR 52.8%, 50.2%, vs 63.7%, respectively, p = 0.347). In T-ALL, multivariate analysis identified age ≥ 41 years, male sex, PS ≥ 2, disease status other than CR1, HLA disparity ≥ 2 loci, myeloablative conditioning (MAC) without total body irradiation (TBI), and HCT before 2010 as factors associated with poor OS (Table 1, Upper). In T-LBL, PS ≥ 2, non-CR at HCT, MAC without TBI, use of anti-thymocyte globulin, and multiple treatment regimens before HCT were significant factors for poor OS (Table 1, Lower). Donor type did not affect OS. Conclusion: This largest-ever retrospective study shows comparable OS after HCT for T-ALL or T-LBL. Active disease, PS ≥ 2, and non-TBI MAC were potent poor prognostic factors. In T-LBL, autologous HCT can be a suitable option, which should be confirmed in further prospective studies.

Venetoclax Combined with Hag Regimen in Newly Diagnosed ETP-ALL: Interim Analysis of a Prospective, Multicenter, Phase 2 Trial

Background: Early T-cell precursor (ETP) acute lymphoblastic leukemia (ALL) is identified as a subset of T-lineage ALL with a unique immunophenotype and genome profile in 2009. Patients with ETP-ALL have a relatively poor outcome with standard chemotherapy and studies showed that therapies utilized for myeloid neoplasms may be effective in ETP-ALL given the relatively high frequency of molecular myeloid features. In recent years, targeting of the antiapoptotic protein BCL-2 has emerged as an effective approach in acute myeloid leukemia (AML). Preclinical studies reported that ETP-ALL cells also express high level of BCL-2 and are sensitive to the BCL-2 inhibitor venetoclax (VEN). However, the clinical efficacy of venetoclax combination therapies in ETP-ALL patients is still limited. Our data showed that homoharringtonine (HHT) showed strong synergistic effect with VEN in ETP-ALL (2022 ASH abstract #170604). We therefore conducted a study of combination of VEN and HHT-based HAG regimen (V-HAG regimen) in newly diagnosed ETP-ALL patients. The aim of this study was to investigate the activity and tolerability of V-HAG regimen for newly diagnosed ETP-ALL. Methods: In this prospective, multicenter, phase 2 clinical trial conducted in 7 different hematological centers in China, eligible patients were newly diagnosed ETP-ALL(aged≥16 years old) based on the 2016 WHO classification with an Eastern Cooperative Oncology Group performance status of 0-2. Patients received venetoclax (100mg on day1, 200mg on day 2 and 400mg on day 3-14, if the blast cells in bone marrow was more than 5% on day 14, the patient continued to receive venetoclax 400mg until day 28), homoharringtonine (1.4 mg/m 2,2mg maximum daily, intravenously daily from on d1-10), Low-dose cytarabine (10 mg/m2 subcutaneously every 12h on d1-14), and G-CSF (100ug/m 2 daily on d1-14). Venetoclax dose was reduced by at least 50% in the patients receiving concomitant moderate or strong CYP3A4 inhibitors (such as azole antifungals et al). The primary endpoint was the rate of composite complete remission (CRc) after one cycle of induction treatment, including CR and CR with incomplete count recovery (CRi). Secondary endpoints included bone marrow (BM) minimal residual disease (MRD) by flow cytometry after one cycle of induction treatment, overall survival (OS), event-free survival (EFS), and adverse events (AEs). Here, we report results of the interim analysis. Results: Between July 2022 and July 2023, we enrolled 18 patients with newly diagnosed ETP-ALL in 7 different hematological centers. 14 of 18 patients (77.8%) were male and 22.2% were female, with a median age of 51 years (range, 29 to 73 years). As of July 31, 2023, 15 patients were available for the assessment of treatment results. Among the 15 patients, 14 patients were given standard V-HAG regimen as showed above and one 73-year-old patient, who had interstitial pneumonia at the onset of ETP-ALL, was given dose-reduced V-HAG regimen. To our surprise, after the first cycle of treatment with V-HAG, all the 15 patients achieved CRc (100% CRc rate), including the 73-year-old patient with dose-reduced regimen. Then, after one to three cycles of consolidation treatment with V-HAG regimen, 7 of 15 patients have proceeded to allo-HSCT so far. With a median follow-up of 7.7 months, both the median OS and EFS were not achieved. In fact, to date, except for the 73-year-old patient who eventually relapsed (6% blasts in BM after receiving a second cycle of dose-reduced V-HAG regimen as consolidation) and died of respiratory failure, all the other 14 patients are remaining alive and event-free. For the adverse events, the most common toxicities were grade 4 neutropenia (93.33%), grade 4 thrombocytopenia (73.33%) and grade 3 febrile neutropenia (26.67%). No early death occurred. Conclusions: Venetoclax Combined with HAG regimen achieved an 100% CRc rate in newly diagnosed ETP-ALL to date. Enrollment is ongoing to assess its efficacy and safety in treating newly diagnosed ETP-ALL. This therapy is a promising and well-tolerated regimen in newly diagnosed ETP-ALL patients. Trial registration: The trial was registered in the Chinese Clinical Trial Register with the registration number ChiCTR2200061708.

FCM marker importance for MRD assessment in T-cell acute lymphoblastic leukemia: An AIEOP-BFM-ALL-FLOW study group report.

T-lineage acute lymphoblastic leukemia (T-ALL) accounts for about 15% of pediatric and about 25% of adult ALL cases. Minimal/measurable residual disease (MRD) assessed by flow cytometry (FCM) is an important prognostic indicator for risk stratification. In order to assess the MRD a limited number of antibodies directed against the most discriminative antigens must be selected. We propose a pipeline for evaluating the influence of different markers for cell population classification in FCM data. We use linear support vector machine, fitted to each sample individually to avoid issues with patient and laboratory variations. The best separating hyperplane direction as well as the influence of omitting specific markers is considered. Ninety-one bone marrow samples of 43 pediatric T-ALL patients from five reference laboratories were analyzed by FCM regarding marker importance for blast cell identification using combinations of eight different markers. For all laboratories, CD48 and CD99 were among the top three markers with strongest contribution to the optimal hyperplane, measured by median separating hyperplane coefficient size for all samples per center and time point (diagnosis, Day 15, Day 33). Based on the available limited set tested (CD3, CD4, CD5, CD7, CD8, CD45, CD48, CD99), our findings prove that CD48 and CD99 are useful markers for MRD monitoring in T-ALL. The proposed pipeline can be applied for evaluation of other marker combinations in the future.

Frequent, high density expression of surface CD38 as a potential therapeutic target in adult T-lineage acute lymphoblastic leukemia.

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PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility

PTEN loss in fetal liver hematopoietic stem cells (HSCs) leads to alterations in myeloid, T-, and B-lineage potentials and T-lineage acute lymphoblastic leukemia (T-ALL) development. To explore the mechanism underlying PTEN-regulated hematopoietic lineage choices, we carry out integrated assay for transposase-accessible chromatin using sequencing (ATAC-seq), single-cell RNA-seq, and invitro culture analyses using invivo-isolated mouse pre-leukemic HSCs and progenitors. We find that PTEN loss alters chromatin accessibility of key lineage transcription factor (TF) binding sites at the prepro-B stage, corresponding to increased myeloid and T-lineage potentials and reduced B-lineage potential. Importantly, we find that PU.1 is an essential TF downstream of PTEN and that altering PU.1 levels can reprogram the chromatin accessibility landscape and myeloid, T-, and B-lineage potentials in Ptennull prepro-B cells. Our study discovers prepro-B as the key developmental stage underlying PTEN-regulated hematopoietic lineage choices and suggests a critical role of PU.1 in modulating the epigenetic state and lineage plasticity of prepro-B progenitors.

Dual Targeting of Apoptotic and Signaling Pathways in T-Lineage Acute Lymphoblastic Leukemia.

Relapsed T-acute lymphoblastic leukemia (T-ALL) has limited treatment options. We investigated mechanisms of resistance to BH3 mimetics in T-ALL to develop rational combination strategies. We also looked at the preclinical efficacy of NWP-0476, a novel BCL-2/BCL-xL inhibitor, as single agent and combination therapy in T-ALL. We used BH3 profiling as a predictive tool for BH3 mimetic response in T-ALL. Using isogenic control, venetoclax-resistant (ven-R) and NWP-0476-resistant (NWP-R) cells, phosphokinase array was performed to identify differentially regulated signaling pathways. Typical T-ALL cells had increased dependence on BCL-xL, whereas early T-precursor (ETP)-ALL cells had higher BCL-2 dependence for survival. BCL-2/BCL-xL dual inhibitors were effective against both subtypes of T-lineage ALL. A 71-protein human phosphokinase array showed increased LCK activity in ven-R cells, and increased ACK1 activity in ven-R and NWP-R cells. We hypothesized that pre-TCR and ACK1 signaling pathways are drivers of resistance to BCL-2 and BCL-xL inhibition, respectively. First, we silenced LCK gene in T-ALL cell lines, which resulted in increased sensitivity to BCL-2 inhibition. Mechanistically, LCK activated NF-κB pathway and the expression of BCL-xL. Silencing ACK1 gene resulted in increased sensitivity to both BCL-2 and BCL-xL inhibitors. ACK1 signaling upregulated AKT pathway, which inhibited the pro-apoptotic function of BAD. In a T-ALL patient-derived xenograft model, combination of NWP-0476 and dasatinib demonstrated synergy without major organ toxicity. LCK and ACK1 signaling pathways are critical regulators of BH3 mimetic resistance in T-ALL. Combination of BH3 mimetics with tyrosine kinase inhibitors might be effective against relapsed T-ALL.

In vivo activity of the dual PI3Kδ and PI3Kγ inhibitor duvelisib against pediatric acute lymphoblastic leukemia xenografts.

Acute lymphoblastic leukemia (ALL) remains one of the most common causes of cancer-related mortality in children. Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases, and aberrations in the PI3K pathway are associated with several hematological malignancies, including ALL. Duvelisib (Copiktra) is an orally available, small molecule dual inhibitor of PI3Kδ and PI3Kγ, that is Food and Drug Administration (FDA) approved for the treatment of relapsed/refractory chronic lymphocytic leukemia and small lymphocytic lymphoma. Here, we report the efficacy of duvelisib against a panel of pediatric ALL patient-derived xenografts (PDXs). Thirty PDXs were selected for a single mouse trial based on PI3Kδ (PIK3CD) and PI3Kγ (PIK3CG) expression and mutational status. PDXs were grown orthotopically in NSG (NOD.Cg-Prkdcscid IL2rgtm1Wjl /SzJAusb) mice, and engraftment was evaluated by enumerating the proportion of human versus mouse CD45+ cells (%huCD45+ ) in the peripheral blood. Treatment commenced when the %huCD45+ reached greater than or equal to 1%, and events were predefined as %huCD45+ greater than or equal to 25% or leukemia-related morbidity. Duvelisib was administered per oral (50mg/kg, twice daily for 28days). Drug efficacy was assessed by event-free survival and stringent objective response measures. PI3Kδ and PI3Kγ mRNA expression was significantly higher in B-lineage than T-lineage ALL PDXs (p-values <.0001). Duvelisib was well-tolerated and reduced leukemia cells in the peripheral blood in four PDXs, but with only one objective response. There was no obvious relationship between duvelisib efficacy and PI3Kδ or PI3Kγ expression or mutation status, nor was the in vivo response to duvelisib subtype dependent. Duvelisib demonstrated limited in vivo activity against ALL PDXs.

Opposing effects of KDM6A and JDP2 on glucocorticoid sensitivity in T-ALL.

Glucocorticoids (GCs) are the cornerstone of acute lymphoblastic leukemia (ALL) therapy. Although mutations in NR3C1, which encodes the GC receptor (GR), and other genes involved in GC signaling occur at relapse, additional mechanisms of adaptive GC resistance are uncertain. We transplanted and treated 10 primary mouse T-lineage acute lymphoblastic leukemias (T-ALLs) initiated by retroviral insertional mutagenesis with GC dexamethasone (DEX). Multiple distinct relapsed clones from 1 such leukemia (T-ALL 8633) exhibited discrete retroviral integrations that upregulated Jdp2 expression. This leukemia harbored a Kdm6a mutation. In the human T-ALL cell line CCRF-CEM, enforced JDP2 overexpression conferred GC resistance, whereas KDM6A inactivation unexpectedly enhanced GC sensitivity. In the context of KDM6A knockout, JDP2 overexpression induced profound GC resistance, counteracting the sensitization conferred by KDM6A loss. These resistant "double mutant" cells with combined KDM6A loss and JDP2 overexpression exhibited decreased NR3C1 mRNA and GR protein upregulation upon DEX exposure. Analysis of paired samples from 2 patients with KDM6A-mutant T-ALL in a relapsed pediatric ALL cohort revealed a somatic NR3C1 mutation at relapse in 1 patient and a markedly elevated JDP2 expression in the other. Together, these data implicate JDP2 overexpression as a mechanism of adaptive GC resistance in T-ALL, which functionally interacts with KDM6A inactivation.

How should childhood acute lymphoblastic leukemia relapses in low-income and middle-income countries be managed: The AHOPCA-ALL study group experience.

Children with relapsed acute lymphoblastic leukemia (ALL) in low-income and middle-income countries rarely survive. The Pediatric Hematology-Oncology Association of Central America (AHOPCA) developed the AHOPCA-ALL REC 2014 protocol to improve outcomes in resource-constrained settings without access to stem cell transplantation. The AHOPCA-ALL REC 2014 protocol was based on a modified frontline induction phase 1A, a consolidation therapy with six modified R-blocks derived from the ALL-Berlin-Frankfurt-Munster REZ 2002 protocol and intermittent maintenance therapy. Children with B-lineage ALL were eligible after a late medullary relapse, an early or late combined relapse, or any extramedullary relapses. Those with T-lineage ALL were eligible after early and late extramedullary relapses, as were those with both B-lineage and T-lineage relapses occurring at least 3months after therapy abandonment. The study population included 190 patients with T-lineage (n=3) and B-lineage (n=187) ALL. Of those with B-lineage ALL, 25 patients had a very early extramedullary relapse, 40 had an early relapse (32 extramedullary and 8 combined), and 125 had a late relapse (34 extramedullary, 19 combined, and 72 medullary). The main cause of treatment failure was second relapse (52.1%). The 3-year event-free survival rate (± standard error) was 25.9%±3.5%, and the 3-year overall survival rate was 36.7%±3.8%. The 3-year event-free survival rate was 47.2%±4.7% for late relapses. The most frequently reported toxicity was grade 3 or 4 infection. Mortality during treatment occurred in 17 patients (8.9%), in most cases because of infectious complications. Selected children with relapsed ALL in Central America can be cured with second-line regimens even without access to consolidation with stem cell transplantation. Children in low-income and middle-income countries who have lower risk relapses of ALL should be treated with curative intent.

Targeting Apoptosis with Novel BH3 Mimetics in T-Lineage Acute Lymphoblastic Leukemia

Targeting Apoptosis with Novel BH3 Mimetics in T-Lineage Acute Lymphoblastic Leukemia

Parental occupational exposure to combustion products, metals, silica and asbestos and risk of childhood leukaemia: Findings from the Childhood Cancer and Leukaemia International Consortium (CLIC).

Parental occupational exposures around conception (father) or during pregnancy (mother) have been hypothesized as potential predisposing factors for childhood leukaemia. We investigated parental exposure to several known occupational carcinogens and childhood leukaemia risk. We conducted a pooled analysis using case-control data from four European countries (3362 childhood leukemia cases and 6268 controls). Parental occupational exposures to polycyclic aromatic hydrocarbons (PAH), diesel engine exhaust (DEE), chromium, nickel, crystalline silica, and asbestos were assessed by a general population job-exposure matrix. We estimated odd ratios (ORs) and 95% confidence intervals (CIs) using unconditional logistic regression models for all childhood leukaemia combined, by leukaemia type (ALL and AML) and by ALL subtype (B-lineage and T-lineage). We found an association between high paternal occupational exposure to crystalline silica and childhood ALL (OR 2.20, CI 1.60–3.01) with increasing trend from no exposure to high exposure (P = <0.001), and also for AML (OR 2.03, CI 1.04–3.97; P for trend = 0.008). ORs were similar for B- and T-lineage ALL. For ALL, ORs were also slightly elevated with wide confidence intervals for high paternal occupational exposure to chromium (OR 1.23, CI 0.77–1.96), and DEE (OR 1.21, CI 0.82–1.77). No associations were observed for paternal exposures to nickel, PAH and asbestos. For maternal occupational exposure we found several slightly elevated odds ratios but mostly with very wide confidence intervals due to low numbers of exposed mothers. This is a first study suggesting an association between fathers’ occupational exposure to crystalline silica and an increased risk of childhood leukaemia in their offspring. As this association was driven by certain occupations (field crop farmers and miners) where other potentially relevant exposures like pesticides and radon may also occur, more research is needed to confirm our findings of an association with crystalline silica, and if so, mechanistic studies to understand the pathways.

P349: CLONAL ARCHITECTURE DISSECTING AT SINGLE-CELL RESOLUTION REVEALS MECHANISMS OF CHEMOTHERAPY RESISTANCE AND RELAPSE IN T CELL ACUTE LYMPHOBLASTIC LEUKEMIA

Background: T-lineage acute lymphoblastic leukemia (T-ALL) comprises approximately 10-15% of pediatric ALL cases with distinct feature in biology and largely inferior outcome compared to B-ALL. Growing evidence has reflected pivotal roles of clonal evolution in T-ALL recurrence, but bulk sequencing may not serve as the perfect model to reliably infer clonal heterogeneities and their immunomodulatory milieu during leukemia development. In this study, single-cell sequencing was applied to uncover leukemic clonal relationships with relapse throughout chemotherapy in T-ALL at a more accurate resolution. Aims: We performed bulk and single cell multi omics analysis for diagnostic and relapse T-ALL, with the aim to dissect mechanisms of chemotherapy resistance and relapse in T cell acute lymphoblastic leukemia. Methods: We performed bulk whole-exome sequencing for sorted CD7+ BMMCs from 5 pairs of diagnosis-relapse (Dx_Rel) samples, revealing a series of well-reported hotspot mutations in T-ALL. To dissect clonal diversities within and across the 5 Dx_Rel T-ALL pairs, we carried out high-throughput droplet-based 5’-single-cell RNA-seq (scRNA-seq) and paired T cell receptor sequencing (scTCR-seq). Results: By performing unsupervised clustering of scRNA- seq profiles encompassing 10 samples, we identified 23 distinct T-lineage clusters (Cluster 0-22) based on the two-dimensional UMAP visualization. In 2 out of 5 patients, diffusion map of T-lineage sub-clusters between diagnostic and relapsed samples appeared to be almost identical, while distinct shifts from diagnosis to relapse in the compositions have been observed in the other 3 out of 5 patients. We sought to further deconvolute the clonal architecture trajectory for T-ALL Dx_Rel pairs. We observed that dominant diagnostic clones of 4 patients diminished or vanished at relapse, sparing newly emerged subclones predominantly substituted at relapse. We clearly depicted two distinct patterns of evolutionary trajectories in these 4 Dx_Rel pairs by comprehensively mapping hierarchical TCR clonotypes onto leukemic clonotypes at single cell levels. Specifically, in T956 and T723, we observed significant outgrowth of incidental diagnostic sub-clones at relapse, whereby surrogate TCR repertoires correspondingly enumerated, suggestive of dynamic shifts in dominant clone over continuous chemo-exposure. Whereas in T593 and T856, expanding clones at relapse were showed up with completely different gene signatures from the diagnostic ones, but dominant clones at diagnosis and relapse were surprisingly presented with identical TCR repertoires. This was undoubtedly informative of leukemic “clonal drift” within which hypothetical intrinsic transformation happened to the same subclones over persistent chemotherapy. Image:Summary/Conclusion: Collectively, our presented study accurately distinguished leukemic cells from normal T cells in T-ALL at a single-cell resolution. By tracking transcriptomic profiles within and across Dx_Rel T-ALL pairs, we further identified distinct clonal evolutionary patterns, which may determine diversified fates of leukemic clones in response to therapeutic pressures, extending significant implications for future precise chemotherapies.

Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing.

Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.

Protocol for ICiCLe-ALL-14 (InPOG-ALL-15-01): a prospective, risk stratified, randomised, multicentre, open label, controlled therapeutic trial for newly diagnosed childhood acute lymphoblastic leukaemia in India

BackgroundIn the west, survival following treatment of childhood acute lymphoblastic leukaemia (ALL) approaches 90%. Outcomes in India do not exceed 70%. To address this disparity, the Indian Collaborative Childhood Leukaemia group (ICiCLe) developed in 2013 a contemporary treatment protocol for uniform risk-stratified management of first presentation ALL based on cytogenetics and minimal residual disease levels (MRD). A multicentre randomised clinical trial opened in 2016 (ICiCLe-ALL-14) and examines the benefit of randomised interventions to decrease toxicity and improve outcomes.MethodsPatients 1–18 years with newly diagnosed ALL are categorised into four risk groups based on presentation features, tumour genetics and treatment response. Standard risk includes young (< 10 years) B cell precursor ALL (BCP-ALL) patients with low presentation leucocyte count (< 50 × 109/L) and no high-risk features. Intermediate risk includes BCP-ALL patients with no high-risk features but are older and have high presentation leucocyte counts and/or bulky disease. High risk includes BCP-ALL patients with any high-risk feature, including high-risk genetics, central nervous system leukaemia, poor prednisolone response at treatment day 8 and high MRD (≥ 0·01%) at the end of induction. Patients with T-lineage ALL constitute the fourth risk group. All patients receive four intensive treatment blocks (induction, consolidation, interim maintenance, delayed intensification) followed by 96 weeks of maintenance. Treatment intensity varies by risk group. Clinical data management is based on a web-based remote data capture system. The first randomisation examines the toxicity impact of a shorter induction schedule of prednisolone (3 vs 5 weeks) in young non-high-risk BCP-ALL. The second randomisation examines the survival benefit of substituting doxorubicin with mitoxantrone in delayed intensification for all patients. Primary outcome measures include event-free survival (overall, by risk groups), sepsis rates in induction (first randomisation) and event-free survival rates following second randomisation.DiscussionICiCLe-ALL-14 is the first multicentre randomised childhood cancer clinical trial in India. The pre-trial phase allowed standardisation of risk-stratification diagnostics and established the feasibility of collaborative practice, uniform treatment, patient enrolment and data capture. Pre-trial observations confirm the impact of risk-stratified therapy in reducing treatment-related deaths and costs. Uniform practice across centres allows patients to access care locally, potentially decreasing financial hardship and dislocation.Trial registrationClinical Trials Registry-India (CTRI) CTRI/2015/12/006434. Registered on 11 December 2015

Isolated Myeloid Sarcoma and Intracardiac Thrombus Resulting in Superior Mediastinal Syndrome.

Superior mediastinal syndrome (SMS) is a relatively common emergency in the practice of Pediatric Oncology. It typically results from the compression of large airways and superior vena cava by a swiftly growing mass. T-lineage acute lymphoblastic leukemia or lymphoma, neuroblastoma, and germ cell tumor are the common etiologies of SMS in children. Occasionally, SMS can be an unexpected presentation of less common childhood cancers and a surprise for the diagnostic and treating teams. The present paper reports the diagnostic and therapeutic challenge of managing a 9-y-old boy with SMS resulting from mediastinal myeloid sarcoma. The presence of a sizeable intracardiac thrombus, in addition, contributed to the SMS. The initial pleural fluid cytology and image-guided fine-needle aspiration cytology of the mediastinal mass were nondiagnostic. A thoracotomy was subsequently performed to debulk the tumor for symptomatic relief and obtain tissue for diagnosis.

Decoding Clonal Evolution in Relapsed T Cell Acute Lymphoblastic Leukemia at Single Cell Resolution

T-lineage acute lymphoblastic leukemia (T-ALL) comprises approximately 10-15% of pediatric ALL cases with distinct feature in biology and largely inferior outcome compared to B-ALL. Growing evidence has reflected pivotal roles of clonal evolution in T-ALL recurrence, but bulk sequencing may not serve as the perfect model to reliably infer clonal heterogeneities and their immunomodulatory milieu during leukemia development. In this study, single-cell sequencing was applied to uncover leukemic clonal relationships with relapse throughout chemotherapy in T-ALL at a more accurate resolution.We performed bulk whole-exome sequencing for sorted CD7 + BMMCs from 5 pairs of diagnosis-relapse (Dx_Rel) samples, revealing a series of well-reported hotspot mutations in T-ALL. Among those, we observed diagnosis-specific variations and relapse-emerged variations, suggesting the putative correlations with chemo-resistance. Transcriptomic sequencing highlighted additional stemness and metabolic abnormalities underlying leukemic re-occurrence. Incorporated Dx_Rel paired ATAC-seq depicted relapse-specific activated chromatin regions, such as ELK1, ELK4, RUNX1.To dissect clonal diversities within and across the 5 Dx_Rel T-ALL pairs, we carried out high-throughput droplet-based 5'-single-cell RNA-seq (scRNA-seq) and paired T cell receptor sequencing (scTCR-seq). By performing unsupervised clustering of scRNA-seq profiles encompassing 10 samples, we identified 23 distinct T-lineage clusters (Cluster 0-22) based on the two-dimensional UMAP visualization. In 2 out of 5 patients (T593 and T788), diffusion map of T-lineage sub-clusters between diagnostic and relapsed samples appeared to be almost identical, while distinct shifts from diagnosis to relapse in the compositions have been observed in the other 3 out of 5 patients (T956, T723 and T856). Besides, it was noteworthy that two T-cell sub-clusters were concluded as “normal” T cells (Cluster 9 and 12) uniformly presented in both diagnostic and relapsed diffusion of T-cell sub-clusters across 5 Dx_Rel, from which TCR repertoires and expression profiles could well discriminate leukemic cells.Next, we sought to further deconvolute the clonal evolution patterns for T-ALL Dx_Rel pairs. We observed that except in T788 lacking of clonal TCRs, dominant diagnostic clones of the other 4 patients diminished (T593) or vanished (T956, T723, T856) at relapse, sparing newly emerged subclones predominantly substituted at relapse. We clearly depicted two distinct patterns of evolutionary trajectories in these 4 Dx_Rel pairs by comprehensively mapping hierarchical TCR clonotypes onto leukemic clonotypes at single cell levels. Specifically, in T956 and T723, we observed significant outgrowth of incidental diagnostic sub-clones at relapse, whereby surrogate TCR repertoires correspondingly enumerated, suggestive of dynamic shifts in dominant clone over continuous chemo-exposure. Whereas in T593 and T856, expanding clones at relapse were showed up with completely different gene signatures from the diagnostic ones, but dominant clones at diagnosis and relapse were surprisingly presented with identical TCR repertoires. This was undoubtedly informative of leukemic “clonal drift” within which hypothetical intrinsic transformation happened to the same subclones over persistent chemotherapy.Besides, we took advantage of our well-discriminated model to fully delineated the involvement of “normal” T subclusters in leukemic latency and chemo-responsiveness. By analyzing TCR repertoires in combined with expression profiles, we noted that “normal” T cells infiltrated by T-ALL were majorly distributed in CD8-effector sub-clusters compared to those from healthy donor, suggesting a robust leukemic stimulation on effector CD8 signaling in T-ALL microenvironment.Collectively, our presented study accurately distinguished leukemic cells from normal T cells in T-ALL at a single-cell resolution. By tracking transcriptomic profiles within and across Dx_Rel T-ALL pairs, we further identified distinct clonal evolutionary patterns, which may determine diversified fates of leukemic clones in response to therapeutic pressures. In the meantime, we provided a comprehensive phenotypic view on “normal” T cells under leukemic prevalence and re-occurrence, extending significant implications for future precise immunotherapies. DisclosuresNo relevant conflicts of interest to declare.

SOX11 Functions As an Oncogene in Lmo2-Driven T-Cell Lymphoblastic Leukemia (T-ALL)

Background: T-lineage acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy that accounts for 10%-15% of pediatric and 25% of adult ALL cases. Although the prognosis of T-ALL has been improving over time, the outcome of T- ALL patients with primary resistant or relapsed leukemia remains poor. Thus, further advances in the treatment of T-ALL require the identification of new targets for the development of highly specific molecularly targeted drugs. SRY-related HMG-box 11 (SOX11) is a member of the SOXC family, which also includes SOX4 and SOX12. SOX11 is single-exon gene that encodes a transcription factor, but its molecular properties and functions remain incompletely understood. Expression of SOX11 is strongly associated with neurogenic activity, and it is confined to the central nervous system. Aberrant SOX11 upregulation has been observed in several cancer types, such as medulloblastoma, glioma, and B- and T-cell lymphomas. Under physiological conditions, SOX11 is absent in the T-cell lineage. However, SOX11 expression is consistently found in a subset of TAL/LMO T-ALL cases characterized by an abundancy of PTEN mutations and an underrepresentation of NOTCH mutations. Since the expression of SOX11 is restricted to a malignant context, we postulate that SOX11 might act as an oncogene in T-ALL.Aims: We want to assess SOX11's potential to promote a (pre)leukemic state, and to identify the role of SOX11 during oncogenic transformation in vivo.Methods: We generated a R26-SOX11 knock-in mouse model that allows conditional SOX11 expression in thymocytes, by using Lck-Cre (SL). Using this model, we analyzed the (immuno)phenotype and transcriptome of T-cell populations in 8- to 12-weeks old mice. In the future, we will also perform a syngeneic transplantation of SL thymocytes into sublethally irradiated mice to assess their colonizing potential. Additionally, we have set up an aging cohort of SL mice to investigate whether expression of SOX11 suffices to induce malignant transformation. Since the expression of SOX11 is associated with the TAL/LMO subgroup, we also crossed SL mice with a well-established murine T-ALL model, CD2-Lmo2, to give rise to mice that express both transgenes in their thymocytes (SCL). An aging cohort of this T-ALL model was followed, and we generated a survival curve and collected biological samples. These tumor samples are being analyzed, and their transcriptomic profile will be compared with that of mice overexpressing Lmo2 only. Lastly, we will lentivirally transduce human T-ALL cell lines from the TAL/LMO subgroup using a vector for SOX11 expression. These cell-lines will be used to study the consequences of expressing this transcription factor in a pre-established malignant setting.Results: In order to determine the effects of SOX11 expression in T-cells, we collected and analyzed blood, spleen, and thymus of 12-weeks old SL mice and their Cre-negative littermates (WT). To validate this model, we performed real-time PCR and immunoblotting to confirm the overexpression of SOX11 in T-cells. Interestingly, we observed a significant reduction in the number of lymphocytes in the peripheral blood and in the spleen of SL mice. Furthermore, significant changes were found in the proportions of all thymic populations, featuring an increase in double negative (DN) T-cells (Fig. 1A), particularly the DN3 subpopulation (Fig. 1B), and a decreased double positive CD4/CD8 fraction (DP). Based on that finding, we decided to sort out DN3 and DP cells from WT and SL thymi, and performed RNA-sequencing to further characterize the effect of SOX11 in these cells. In addition, we are following a cohort of SL mice, but so far no tumor formation was observed (average age of the cohort=300-days old). On the other hand, simultaneous overexpression of SOX11 and Lmo2 greatly accelerated the development of T-cell malignancies in SCL mice when compared with CD2-Lmo2 mice (Fig. 1C; median survival of 177 days versus 307; p<0.0001), revealing a synergistic effect upon combination of both genetic events. Not surprisingly, most tumors were composed of immature T-cells, mainly DN cells, and no noteworthy differences were found between the composition and location of SCL and CD2-Lmo2 tumors.Conclusion: We showed that SOX11 skews the normal development of thymocytes in vivo. Additionally, we developed a murine SOX11 T-ALL model, thus confirming an oncogenic role for SOX11. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.