Acute Lymphoblastic Leukemia Cases Research Articles

Experience in improving treatment outcomes for childhood acute lymphoblastic leukemia: real-world results for a province in China, 2011-2020.

The present study aimed to investigate the real-world results of childhood acute lymphoblastic leukemia (cALL) cases in Fujian, China. The clinical data of 1414 patients with newly diagnosed cALL in Fujian were retrospectively analyzed. Patients were treated according to the Chinese Children Leukemia Group 2008 protocol (CCLG-ALL 2008 group) or Chinese Children's Cancer Group 2015 protocol (CCCG-ALL 2015 group). Cumulative incidence of treatment abandonment (TA) at 5 years was 4.2% ± 0.6% and significantly associated with treatment period and risk stratification. The 5-OS and EFS were significantly higher in the CCCG-ALL 2015 group than in the CCLG-ALL 2008 group. Patients treated with CCCG-ALL 2015 from Fujian Medical Union Hospital had a significantly higher 4-year OS and EFS than did those from the other four hospitals. Real-world TA of cALL greatly decreased, and its long-term survival significantly increased in Fujian, which may be related to optimizing programs, multi-center collaboration, and improving treatment compliance.

A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID.

Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter. The insertion is detected years before T-ALL in multiple lineages, suggesting that further hits occurred in a thymic progenitor. Blast cells contain known and novel somatic mutations as well as germline mutations which may have contributed to transformation. Before T-ALL onset, the insertion profile is similar to those of other ADA-deficient patients. The limited incidence of vector-related adverse events in ADA-deficiency compared to other γ-RV GT trials could be explained by differences in transgenes, background disease and patient's specific factors.

A Case of Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia with Coexistence of JAK2 V617F Clone.

A Case of Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia with Coexistence of JAK2 V617F Clone.

Abstract 1763: Long-read sequencing of pediatric leukemia identifies clinically relevant genomic rearrangements

Abstract Clinical detection of genomic rearrangements currently depends on a range of complementary and overlapping methods including fluorescence in situ hybridization (FISH), karyotyping, and DNA and/or RNA sequencing. This requirement for multiple tests results in higher total costs, extended analysis time, and increased usage of sometimes limited tumor material. In our laboratory, we apply long high-fidelity reads to human samples using PacBio circular consensus sequencing (HiFi-GS) of 12-18kb DNA fragments, which offers better structural variant detection relative to short-read sequencing. Here, we assess the ability of HiFi-GS to detect clinically relevant genomic rearrangements (CRGRs) in pediatric leukemia. We selected 11 pediatric leukemia cases with corresponding normal (remission) samples, including 7 cases of B-cell acute lymphoblastic leukemia (B-ALL) and 4 cases of acute myeloid leukemia (AML); 5 of these 11 leukemia cases had known CRGRs as below. The remaining 6 leukemia cases had also undergone clinical genetic profiling via karyotyping, FISH, microarray, and sequencing yet a clinical grade genomic driver was not identified. DNA from each sample was sequenced on a Revio instrument (PacBio, Menlo Park, CA) to a target depth of 30x. The PacBio Human Whole Genome Sequencing (WGS) workflow was used to process HiFi reads for haplotagged alignment and phasing, followed by somatic structural variant calling using Severus. Subsequent analysis focused on the presence of break ends in known cancer-relevant genes. We found that HiFi-GS detected the known CRGRs in all 5 cases with prior findings, providing precise break ends and clarifying sometimes unclear cytogenetic observations (such as exact partner genes), in these cases. These included detection of an ETV6-RUNX1 fusion, NUP98-NSD1 fusion, KMT2A-AFF1 fusion, KMT2A-AFDN fusion, and RUNX1-RUNX1T1 fusion. HiFi sequencing also detected CRGRs in 2 of the 6 “undiagnosed cases”; namely, one case of ZNF384-TCF3 fusion and one case of KMT2A-MLLT10 fusion. The former can be cytogenetically cryptic, while the latter can often be missed due to its potentially complex nature. Our results demonstrate that HiFi-GS can reliably detect CRGRs, bringing us closer to the promise of a single comprehensive genetic test for cancer characterization. Additional work examining other somatic structural and copy number variants (i.e., inversions, deletions, and duplications) in these cases, as well as oncogenic sequence variants, is ongoing. Citation Format: Byunggil Yoo, Ayse Keskus, Chengpeng Bi, Lisa Lansdon, Tanveer Ahmad, Irina Pushel, Adam Walter, Margaret Gibson, Erin Guest, Tomi Pastinen, Mikhail Kolmogorov, Midhat S. Farooqi. Long-read sequencing of pediatric leukemia identifies clinically relevant genomic rearrangements [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 1763.

Abstract 3057: The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL

Abstract TAL1 is overexpressed in 40-60% of T-cell acute lymphoblastic leukaemia (T-ALL) cases and forms an oncogenic core regulatory circuit (CRC) with other transcription factors such as LMO1, LMO2 and GATA3. In 5% of T-ALL cases an insertion of a consensus GT dinucleotide is observed upstream of the TAL1 gene, termed the “Mutation of TAL1 enhancer” (MuTE), driving TAL1 overexpression. Using an in vitro reconstitution DNA pull-down assay combined with quantitative mass spectrometry, we identified nine candidate proteins that preferentially bound to the MuTE sequence compared to the WT sequence. Among the candidates, we demonstrate by reciprocal immunoprecipitation experiments coupled to quantitative mass spectrometry that the RNA methyltransferase TARBP1 and the zinc finger proteins ZBTB2, ZBTB25 and ZNF639 formed a complex that we term TARZN. Interestingly, the TARZN complex also bound to de novo super enhancer sites upstream of the LMO1 and LMO2 genes in T-ALL cells, indicating a putative common mechanism between these different non-coding driver mutations. Furthermore, knock-down of all TARZN members resulted in lower TAL1 protein expression in MuTE-positive but not in MuTE-negative T-ALL cells. Overall, these data suggest that the TARZN complex cooperatively promotes oncogenic expression in T-ALL. Citation Format: Nurkaiyisah Zaal Anuar, Chai Yeen Goh, Boon Haow Chua, Shi Hao Tan, Joana R. Costa, Marc R. Mansour, Takaomi Sanda, Dennis Kappei. The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL [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 3057.

Williams-Beuren syndrome in pediatric T-cell acute lymphoblastic leukemia: A rare case report and review of literature.

Williams-Beuren syndrome (WBS) is a rare genetic disorder caused by hemizygous microdeletion of contiguous genes on chromosome 7q11.23. Although the phenotype features extensive heterogeneity in severity and performance, WBS is not considered to be a predisposing factor for cancer development. Currently, hematologic cancers, mainly Burkitt lymphoma, are rarely reported in patients with WBS. Here in, we report a unique case of T-cell acute lymphoblastic leukemia in a male child with WBS. This retrospective study analyzed the clinical data of this case receiving chemotherapy were analyzed. This is a retrospective study. The patient, who exhibited a typical WBS phenotype and presented with hemorrhagic spots. Chromosomal genome-wide chip analysis (CMA) revealed abnormalities on chromosomes 7 and 9. The fusion gene STIL-TAL1 and mutations in BCL11B, NOTCH1, and USP7 have also been found and all been associated with the occurrence of T-cell leukemia. The patient responded well to the chemotherapy. To the best of our knowledge, this is the first reported case of WBS in T-cell acute lymphoblastic leukemia. We want to emphasize that the occurrence of leukemia in this patient might be related to the loss of 7q11.23 and microdeletion of 9p21.3 (including 3 TSGs), but the relationship between WBS and malignancy remains unclear. Further studies are required to clarify the relationship between WBS and malignancy.

Evidence of spatial clustering of childhood acute lymphoblastic leukemia cases in Greater Mexico City: report from the Mexican Inter-Institutional Group for the identification of the causes of childhood leukemia.

A heterogeneous geographic distribution of childhood acute lymphoblastic leukemia (ALL) cases has been described, possibly, related to the presence of different environmental factors. The aim of the present study was to explore the geographical distribution of childhood ALL cases in Greater Mexico City (GMC). A population-based case-control study was conducted. Children <18 years old, newly diagnosed with ALL and residents of GMC were included. Controls were patients without leukemia recruited from second-level public hospitals, frequency-matched by sex, age, and health institution with the cases. The residence address where the patients lived during the last year before diagnosis (cases) or the interview (controls) was used for geolocation. Kulldorff's spatial scan statistic was used to detect spatial clusters (SCs). Relative risks (RR), associated p-value and number of cases included for each cluster were obtained. A total of 1054 cases with ALL were analyzed. Of these, 408 (38.7%) were distributed across eight SCs detected. A relative risk of 1.61 (p<0.0001) was observed for the main cluster. Similar results were noted for the remaining seven ones. Additionally, a proximity between SCs, electrical installations and petrochemical facilities was observed. The identification of SCs in certain regions of GMC suggest the possible role of environmental factors in the etiology of childhood ALL.

A Case of Acute Lymphoblastic Leukemia Complicated with Sinonasal Mucormycosis Infection

Acute lymphoblastic leukemia (ALL) is an aggressive hematologic malignancy of lymphoid progenitor cells. During treatment of ALL, the patients may be complicated by fatal infections such as sinonasal mucormycosis. In patients with immunocompromised conditions like haematologic malignancies, mucormycosis can be deadly. Once mucormycosis has been detected, it is critical to act quickly to begin treatment. Amphotericin B, posaconazole, or isavuconazole are the medications of choice. Effective treatment requires a long-term course of therapy. Switching to other effective medications should be considered when the preferred treatment is not working. The factors contributing to mucormycosis must also be treated, such as the underlying conditions (haematologic malignancies). Herein, we aimed to discuss a clinically stable ALL patient complicated with extensive sinonasal mucormycosis. She improved with amphotericin B (5 mg/kg/day) and oral posaconazol (300 mg/day) treatment.

Deciphering stage 0 hematogones by flow cytometry in follow-up bone marrow samples of pediatric B-Acute lymphoblastic leukemia cases: A potential mimicker of residual disease after anti CD19 therapy.

CD19 is frequently targeted for immunotherapy in B cell malignancies, which may result in loss of CD19 expression in leukemic cells as an escape mechanism. Stage 0 hematogones (Hgs) are normal CD19-negative very early B cell precursors that can be potentially mistaken for CD19 negative residual leukemic cells by flow cytometry (FCM) in B cell acute lymphoblastic leukemia (BCP-ALL) cases treated with anti CD19 therapy. Our main objective was to characterize and study the incidence of stage 0 hematogones in follow-up bone marrow samples of pediatric BCP-ALL cases. We analyzed the flow cytometry standard files of 61 pediatric BCP-ALL cases treated with conventional chemotherapy and targeted anti-CD19 therapy, for identifying the residual disease and normal B cell precursors including stage 0 Hgs. A non-CD19 alternate gating strategy was used to isolate the B cells for detecting the residual disease and stage 0 Hgs. The stage 0 Hgs were seen in 95% of marrow samples containing CD19+ Hgs. When compared with controls and posttransplant marrow samples, the fraction of stage 0 Hgs was higher in patients receiving anti CD19 therapy (p = 0.0048), but it was not significant when compared with patients receiving chemotherapy (p = 0.1788). Isolated stage 0 Hgs are found in samples treated with anti-CD19 therapy simulating CD19 negative residual illness. Our findings aid in understanding the stage 0 Hgs and its association with CD19+ Hgs in anti CD19 therapy and conventional chemotherapy. This is crucial as it can be potentially mistaken for residual disease in patients treated with anti CD19 therapy.

Molecular biology techniques for assessing the loss of HLA heterozygosity after allogeneic hematopoietic stem cell transplantation in children with acute leukemia

According to several observations, up to a third of post-transplant relapses in childhood acute leukemia are associated with the loss of heterozygosity of the major histocompatibility complex (HLA). Furthermore, the inefficacy of the graft-versus-leukemia reaction, as evidenced by the lack of therapeutic effect from the infusion of donor lymphocytes, indicates the need for timely detection of this marker to change the treatment strategy in the post-transplant period. To detect the loss of HLA heterozygosity, the method using the commercial KMR-HLA system and analysis using next-generation sequencing (NGS), as well as the method based on the analysis of highly polymorphic STR and VNTR markers located in the HLA loci region on the short arm of chromosome 6, are widely used. The primary objective of our study was to compare the informativeness of these approaches in diagnosing HLA heterozygosity loss in children during the post-transplant period. The obtained data on the frequency of detecting HLA heterozygosity loss were comparable to the literature data and constituted 23 % of cases of post-transplant relapse of B-cell acute lymphoblastic leukemia, 33 % of cases of T-cell acute lymphoblastic leukemia, and 23% of cases of acute myeloid leukemia. We also demonstrated that the method based on STR marker analysis has sensitivity comparable to allele-specific PCR and NGS sequencing methods. Meanwhile, preliminary sorting of the blast population increases the sensitivity of STR analysis and can be recommended in routine practice.

Clinical characteristics and prognosis of 28 cases of infant acute lymphoblastic leukemia

Objective: To analyze the clinical characteristics and prognosis of patients with infant acute lymphoblastic leukemia (IALL). Methods: A retrospective cohort study.Clinical data, treatment and prognosis of 28 cases of IALL who have been treated at Beijing Children's Hospital, Capital Medical University and Baoding Children's Hospital from October 2013 to May 2023 were analyzed retrospectively. Based on the results of fluorescence in situ hybridization (FISH), all patients were divided into KMT2A gene rearrangement (KMT2A-R) positive group and KMT2A-R negative group. The prognosis of two groups were compared. Kaplan-Meier method and Log-Rank test were used to analyze the survival of the patients. Results: Among 28 cases of IALL, there were 10 males and 18 females, with the onset age of 10.9 (9.4,11.8) months. In terms of immune classification, 25 cases were B-ALL (89%), while the remaining 3 cases were T-ALL (11%). Most infant B-ALL showed pro-B lymphocyte phenotype (16/25,64%). A total of 22 cases (79%) obtained chromosome karyotype results, of which 7 were normal karyotypes, no complex karyotypes and 15 were abnormal karyotypes were found. Among abnormal karyotypes, there were 4 cases of t (9; 11), 2 cases of t (4; 11), 2 cases of t (11; 19), 1 case of t (1; 11) and 6 cases of other abnormal karyotypes. A total of 19 cases (68%) were positive for KMT2A-R detected by FISH. The KMT2A fusion gene was detected by real-time PCR in 16 cases (57%). A total of 24 patients completed standardized induction chemotherapy and were able to undergo efficacy evaluation, 23 cases (96%) achieved complete remission through induction chemotherapy, 4 cases (17%) died of relapse. The 5-year event free survival rate (EFS) was (46±13)%, and the 5-year overall survival rate (OS) was (73±10)%.The survival time was 31.3 (3.3, 62.5) months. There was no significant statistical difference in 5-year EFS ((46±14)% vs. (61±18)%) and 5-year OS ((64±13)% vs. (86±13)%) between the KMT2A-R positive group (15 cases) and the KMT2A-R negative group (9 cases) (χ2=1.88, 1.47, P=0.170, 0.224). Conclusions: Most IALL patients were accompanied by KMT2A-R. They had poor tolerance to traditional chemotherapy, the relapse rate during treatment was high and the prognosis was poor.

Клиническое наблюдение развития острого миелоидного лейкоза у женщины на фоне ремиссии острого лимфобластного лейкоза

The article presents a case of T-cell acute lymphoblastic leukemia (T-ALL) in a patient aged 54 years, against which acute myeloid leukemia developed. The main methods of laboratory examination are given. Intensive polychemo-therapy of T-ALL in 50% of cases causes long-term remission in adults. Treatment of acute T-cell lymphoblastic leukemia consists in long-term intensive systemic chemotherapy and intrathecal administration of chemopreparations. However, despite significant achievements in treatment of patients with this pathology, relapse of the disease occurs in 40% of patients and the risk of secondary leukemia development increases.

Warburg effect mimicking inborn errors of metabolism in childhood hematologic malignancies: A case-based systematic review.

Type B lactic acidosis and hypoglycemia can occur in various pediatric conditions. In young children with a history of fasting preceding these metabolic derangements, inborn errors of metabolism should be primarily considered. However, the Warburg effect, a rare metabolic complication, can also manifest in children with hematologic malignancies. Only a few reports of this condition in children have been published in the literature. To identify the clinical course, treatment strategies, and outcomes of childhood hematologic malignancies with type B lactic acidosis. We performed a comprehensive search of the PubMed, Scopus, and Cochrane databases without any time restriction but limited to English language articles. The databases were last accessed on July 1st, 2023. A total of 20 publications were included in the analysis, all of which were case reports or case series. No higher quality evidence was available. Among children with hematologic malignancies and Warburg effect, there were 14 cases of acute lymphoblastic leukemia and 6 cases of non-Hodgkin's lymphoma including our illustrative case. Lactic acidosis occurred in 55% of newly diagnosed cases and 45% of relapsed cases. The mean age was 10.3 ± 4.5 years, and 80% of cases were male. The mean serum lactate was 16.9 ± 12.6 mmol/L, and 43.8% of the cases had concomitant hypoglycemia. Lactic acidosis initially subsided in 80% of patients receiving chemotherapy compared to 60% in the contrast group. The mortality rate of newly diagnosed cases was 45.5%, while the relapsed cases represented a 100% mortality rate. All 8 patients reported before 2001 died from disease-related complications. However, patients described in reports published between 2003 and 2023 had a 54.5% rate of complete remission. This complication has historically led to fatal outcome; however, patients who received chemotherapy showed a more favorable response. Therefore, it is crucial to promptly initiate specific treatment in this context.

Scylla and Charybdis: Unpalatable choices in managing hypodiploid acute lymphoblastic leukemia

Acquired TP53 alterations are present in > 90% of cases of paediatric low-hypodiploid acute lymphoblastic leukaemia (ALL), and ≈ 50% of patients with this subtype harbor germline pathogenic / likely pathogenic (P/LP) TP53 alterations. Despite dose intensified, conventional chemotherapy, survival in low-hypodiploid ALL remains dismal compared to other paediatric ALL. Individuals with underlying Li-Fraumeni Syndrome (LFS) are known to have increased sensitivity to genotoxic effect of chemotherapy and radiotherapy. Recent evidence shows a 25.1% 5-year cumulative incidence of SMNs post ALL therapy in an LFS population as compared to 0.7% in patients with either a wild type or VUS TP53. The parallel high risks of both relapse and SMN present unpalatable choices facing clinicians.

A profile of hematological malignancies diagnosed in a tertiary care center of Assam: Highlighting the experience from a resource constraint perspective

Background: Hematological disorders require a systematic approach, from clinical examination to a complete blood count, followed by a bone marrow study for diagnosis. To effectively plan, treat, and prognosticate, immunophenotyping and molecular studies are essential to incorporate. Aims and Objectives: The aim of our study is to understand the pattern of neoplastic hematological conditions encountered in Assam and share our experience during the diagnosis. Materials and Methods: This was a single-centered, observational study carried out for 18 months (January 2022–June 2023). A thorough hematological workout was done, including cytochemical staining and conventional polymerase chain reaction for the BCR-ABL transcript, after satisfying inclusion and exclusion criteria. The data were analyzed and correlated before arriving at the final diagnosis. Results: The total of 38 neoplastic cases confirmed by bone marrow study. Out of 38 cases, 14 were chronic myeloid leukemia, 10 were chronic, 4 were in the blastic phase, and BCR-ABL was positive in 13 cases. Two cases were pediatric, of which 1 was in the blastic phase. All 8 cases of plasma cell dyscrasia presented with anemia, bone lesions, and hypercalcemia. The acute leukemia category consisted of 4 acute myeloid leukemia cases, of which 1 was acute promyelocytic leukemia. A total of 10 acute lymphoblastic leukemia (ALL) cases, where 1 case was T-ALL and the rest was B-ALL. Two cases showed a subleukemic presentation in peripheral blood. Conclusion: The experience of pathologists and their meticulous approach can greatly aid in accurate diagnosis, but the immunophenotyping facility and molecular hematology setup can provide most of the relevant information for the best decision-making.

Unilateral Orbital mass in a 3-Year-Old Boy of Acute Lymphoblastic Leukemia : A Rare Presentation

Background &amp; objective: We report a case of a 3-year-old boy who presented with left eye swelling, low-grade fever, pallor, and generalized lymphadenopathy. He was diagnosed with a case of B-cell acute lymphoblastic leukemia (ALL) on the basis of morphology and immunophenotyping of bone marrow. Orbital manifestation is rarely seen in ALL; rather it is more common in acute myeloid leukemia (AML). Knowledge regarding the unusual presentation of ALL will help timely diagnosis and treatment which is crucial for preserving the eye as well as the vision. Ibrahim Card Med J 2022; 12 (2): 64-66

Long-Term Outcomes of T-Cell Acute Lymphoblastic Leukemia and Risk Factors for Survival in a Multicenter Registry Study from Brazil

Introduction T-cell acute lymphoblastic leukemia (T-ALL) constitutes around 25% of all newly diagnosed cases of acute lymphoblastic leukemia (ALL) in adults. While most pediatric treatment protocols categorize patients (pts) based on their phenotype, this approach is seldom applied to adults. Nevertheless, there is a scarcity of reported cohorts specifically focusing on adult T-ALL. Often, these cases are studied alongside B-cell cases, despite their notable biological differences, or grouped with T-cell lymphoblastic lymphoma, which exhibits a more favorable prognosis compared to T-ALL. The objective of this study is to present outcomes and identify prognostic factors for survival of adults newly diagnosed with T-ALL, utilizing data from a real-world multicenter registry study conducted in Latin America. Methods This registry encompassed four different academic centers in Brazil. The study included pts aged 15 years and above newly diagnosed with T-ALL between January 2009 and June 2022. Clinical data were collected from medical records after ethical approval. Overall (OS) and event-free (EFS) survivals were calculated by Kaplan-Meier method, with Cox regression multivariate analysis (MVA) for finding risk factors and competing risk analysis for relapse. Results A total of 97 pts were included, with a median age of 27 years (range, 15 - 82). Thymic T-ALL accounted for 51% of the cases. Mediastinal bulky was found in 48% and positivity of initial cerebrospinal fluid (CSF) evaluation was 12.5% (by morphology or flow cytometry). Baseline features of this cohort are summarized in table 1. Most pts (88%) were treated with pediatric-inspired regimens (asparaginase [ASP]-based), mostly adapted GMALL (43%) and adapted BFM (22%). Native E. coli ASP was used in 76% and pegylated ASP (PEG-ASP) was used in remaining cases. During presentation or treatment, 15% of the subjects experienced thrombosis of any site, with most cases being associated with the use of ASP (64%) and diagnosed during induction (64%). Following the frontline regimen, 77.3% of pts achieved complete response (CR). Overall, 11.3% of pts died during the induction phase, while 8% were primary refractory. Univariate analysis for CR showed correlation with age (p=0.002), bulky size (p=0.016), and use of ASP (p=0.009). Median follow-up period was 6 years. Overall, allogeneic stem cell transplant (alloHSCT) was performed in 18 pts, being 11/18 in first CR. Five-year OS and 5y EFS were 43.7% (95% confidence interval [CI]: 34.4-55.5) and 36.4% (95% CI 27.9-47.5), respectively. Over the follow-up, 5-year relapse rate and non-relapse mortality (NRM) were 35.6% and 27.9%, respectively. Among pts who underwent alloHSCT, 5y OS was 64%. In the univariate analysis, older age (HR 1.02 [1.01-1.04], p&amp;lt;0.01) was associated with lower OS. Conversely, thymic T-ALL (HR 0.54 [0.3-0.96], p=0.03) and use of ASP (HR 0.35 [0.17-0.716], p&amp;lt;0.01) were associated with higher OS. Initial white blood cell count was not statistically associated with OS. Subsequently, we performed a subgroup analysis focusing on the adult and young adult population (AYA, age between 15-45 years). In this subgroup (n=85), 89% were treated with pediatric-inspired regimens and 5y OS was 46.5%. In the univariate analysis, thrombosis (HR 2.21 [1.09-4.48], p=0.02) was associated with lower OS, while thymic T-ALL (HR 0.48 [0.24-0.93], p=0.03) and the use of ASP (HR 0.317 [0.13-0.75], p&amp;lt;0.01) were associated with higher OS. In the MVA for AYA, thymic T-ALL (HR 0.50 [0.25-0.98], p=0.04) and thrombosis (HR 2.23 [0.97-5.13], p=0.054) remained associated with OS, while older age was not (HR 1.004 [0.96 - 1.04], p=0.81) (Figure 1). Conclusions Reported outcomes of T-ALL in this registry from Latin America are comparable to older reports from large groups worldwide. Currently, European groups have reported OS rates surpassing 70% for adults with T-ALL.However, in our setting, even in the AYA population, OS was disappointing. This could be attributed to increased NRM due to treatment toxicity and limited access to HSCT, which may have contributed to these findings. As previously reported, thymic T-ALL remains a lower-risk subtype. Additionally, thrombosis has emerged as an independent risk factor for OS in the AYA population, which is a novel finding that warrants further research. To the best of our knowledge, this is the first study specifically focusing on adult T-ALL from Latin America.

Optical Genome Mapping for Genome-Wide Structural Variation Analysis in Hematologic Malignancies: A Prospective Study Demonstrates Additional Findings Compared to Standard-of-Care (SOC) Cytogenomic Methods

Genomic structural variants (SVs) are key in understanding the pathogenesis of hematologic malignancies. The current standard-of-care (SOC) cytogenomic methods, including chromosome karyotyping (KT) and fluorescence in situ hybridization (FISH), have inherent limitations in identifying SVs, while next-generation sequencing technologies have limited ability to detect most SVs. Optical Genome Mapping (OGM) is a high-resolution cytogenomic technique that overcomes the limitations of SOC cytogenomic methods and detects all classes of SVs. Recent studies, mostly retrospective, have demonstrated OGM's analytic validity and clinical utility for detecting SVs in both hematologic malignancies and constitutional genetic disorders. This prospective study, using OGM as a validated laboratory developed test (LDT) for detection of SVs, included 112 patients with a wide variety of hematologic malignancies undergoing clinical evaluation and management and demonstrates OGM as superior to SOC cytogenomic methods. Patient blood or bone marrow samples were subject to the Bionano OGM-Dx™ HemeOne assay. OGM analysis was successful for 105/112 (94%) samples with 7/112 (6%) samples failing analysis. Of the 105 analyzed samples, 74 (70%) had abnormal and 31 (30%) had normal findings by OGM analysis, with 49% of abnormal OGM findings classified as complex. At initial diagnosis, 49 cases had guideline and SOC result-based disease risk stratification with 18/49 (37%) graded as high risk, 15/49 (31%) as intermediate risk, and 16/49 (32%) as low risk. Additionally, 60 cases had SOC cytogenomic analysis (KT or FISH) results available; 37% with KT and FISH, 27% with only KT, and 35% with only FISH. OGM cases with normal findings were concordant with KT in 9/10 (90%) of cases and FISH in 8/12 (67%) of cases. For those cases that had abnormal findings by KT and/or FISH, OGM detected additional cytogenomic findings in 79% of cases. A change of risk stratification was made in 12/42 (29%) of cases with additional findings by OGM analysis compared to KT and/or FISH; 9/12 (75%) with upgraded risk and 3/12 (25%) with downgraded risk stratification. In 10/42 (24%) of cases, OGM findings resulted in a change in therapeutic management recommendations. This is exemplified by an acute lymphoblastic leukemia case: KT detected a sole t(9;22) abnormality however, OGM detected t(9;22) and additional findings of gains at chromosomes 1q, 17q, and 19p and losses at chromosomes 5q, 7p, and 11q (see figure 1), changing the risk stratification from intermediate to adverse and directly leading to a change in therapeutic management. The impact of OGM on disease risk stratification and case management is in alignment with previously published studies with OGM analysis demonstrating its power to detect additional findings not seen by SOC cytogenomic analysis. The prospective study outcomes suggest a significant role for OGM in delivering comprehensive results for improved diagnostic assessment and significant prognostic information for better case management and care compared to SOC cytogenomic methods.

Uncovering the Cis-Regulatory Program of Early Human B-Cell Commitment and Its Implications in the Pathogenesis of B-Cell Acute Lymphoblastic Leukemia

The early stages of the B-cell system are key for cellular immunity development. The development of functional B cells requires appropriate regulation of dynamic transcription-factor networks. These regulatory networks are responsible for lineage-specific gene expression activation and lineage commitment. Thus, understanding the gene regulatory network (GRN) of this system is essential for studying healthy development and malignant transformations. To this end, in the present study, we aim to uncover the complete chart of the cis-regulatory elements and their dynamic activity over early B-cell commitment in healthy humans. We generated matched human data for chromatin accessibility (ATAC-Seq) and transcriptome (RNA-Seq) in eight sorted B-cell subpopulations (HSCs, CLPs, pro-B cells, pre-B cells, Immature B cells, and Transitional B cells as well as CD5+ and CD5- Naive B cells) isolated from bone marrow and peripheral blood from the same healthy donors (n=13). These comprehensive profiles of the stepwise progression of B-cell precursors and the combined analysis of both omics allowed us to infer the regulatory elements of B-cell differentiation and the resulting GRNs. Our data identified 169 TFs, 7,310 genes, and 16,074 OCRs governing the early B-cell differentiation, resulting in a GRN with 377,268 TF-OCR-gene interactions. The inferred GRN included genes and OCRs able to draw the entire regulatory dynamics over differentiation behaving in accordance with established knowledge. As example, we identified genes and TFs related to homeostasis and stemness, such as MEIS1, CD34, and CDH2, and antiapoptotic genes such as BCL2, highly expressed in HSC, CLP, and pro-B cells. We identified surface marker genes and TFs involved in the commitment and differentiation of B cell lineage, including CD79A/B, PAX5, TCF3, EBF1, and FOXO1, to become upregulated in pro-B cells, as well as down-regulation in pre-B cells of genes linked to T cell development such as NOTCH1. To identify the key regulatory elements along B cell differentiation, we generated a snapshot of the GRN for each cell subpopulation. As a result, the networks' node hub architectures revealed those TFs with relevant transcriptional activity per subpopulation (Figure 1). In the analysis we recovered the primary TFs involved in B cell commitment, differentiation, maintenance, and class-switch recombination: TCF3, BCL11A, IRF8, PAX5, REL, IRF4, EBF1, POU2F2, FOXO1, and LEF1; but also identified ELK3 as a novel TF critical in pro-B cells. Interestingly, this ETS-factor, recently defined as a novel oncogene, has been reported to increase in ETV6-RUNX1+ acute lymphoblastic leukemia cases and other carcinogenic processes. Moreover, it has been associated with pro-B cell expansion. In a deeper approach, our GRNs allowed the exploration of upstream regulators of specific genes. In the case of ELK3, the TFs ERG, STAT5A/B, E2F3, ETS2, ETV6, SPIB, and POU2F2 were uncovered as putative regulators. As a positive control, we explored the upstream regulation of EBF1 gene, a well-known and key TF of B cell fate. Besides the already described regulators (PAX5, TCF3, FOXO1, RUNX1, etc.), we identified new candidates such as MLXIP. Finally, we translated our findings into a disease context using public data. Our resource facilitated the identification of triggers for specific B-cell acute lymphoblastic leukemia (B-ALL) subtypes, pinpointing the inflection point of malignant transformation. We found ETV6-RUNX1 fusions significantly enriched in pro-B cells, MEF2D fusions and TCF3-PBX1 mutations in pre-B cells, DUX4 fusions in HSCs, and KMT2A fusions in CLPs. Moreover, our data shed light on the functional implications of B-ALL susceptibility loci. The susceptibility locus rs17481869, associated with ETV6-RUNX1 patients, was identified within a small OCR specific to pro-B cells. The ALL-associated rs4762284 locus was observed in a closed chromatin region, but we could identify two proxies (rs2268508 and rs17736737) in open regions. Furthermore, from the list of SNPs associated with BCP ALL-related traits from the GWAS catalog (NHGRI-EBI), we identified 11 SNPs overlapping some of our OCRs. In summary, we are presenting the most comprehensive publicly available atlas of early B cell regulation (B-rex; https://brex.shinyapps.io/brex/), and therefore a powerful resource for understanding early B cell differentiation in health and disease.

CD38 Is a Functional Partner of CD9 in B-Cell Precursor Acute Lymphoblastic Leukemia

Background: We previously showed that CD9 was expressed in ~80% of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cases and its positivity was associated with an inferior relapse-free survival (Leung et al, Leukemia, 2020), suggesting its oncogenic role in this disease entity. Yet, the mechanisms underlying how CD9 affects leukemia progression remain completely unknown. As a prototypic member of the tetraspanin superfamily proteins, CD9 is able to organize with transmembrane or intracellular proteins to form the “tetraspanin web” to exert its modulatory functions. In BCP-ALL, though there has been a standalone study reporting 28 CD9-binding proteins in NALM-6 cells, the results are unlikely representative of the entire disease spectrum due to tumor heterogeneity. Here, we perform an in-depth proteomic study to dissect the CD9 web composition and downstream protein partners to drive disease progression in BCP-ALL. Methods: Immunoprecipitation coupled mass spectrometry (IP-MS) was performed to map the overall composition of CD9 web in five CD9 + BCP-ALL cell lines with distinct cytogenetic backgrounds, including 697 ( TCF3-PBX1+), BV-173 ( BCR-ABL1+), HAL-01 ( TCF3-HLF+), KASUMI-2 ( TCF3-PBX1+) and RS4;11 ( KMT2A-AFF1+). Overlapping protein partners were then validated by IP-Western blot (IP-WB) in 13 patient samples spanning major BCP-ALL subtypes. Shortlisted CD9 partners were further characterized by antibody blockade and CRISPR/Cas9 loss-of-function experiments to evaluate their impact on leukemia proliferation in vitro and leukemia progression in vivo, coupled with enzymatic and phenotypic assays to evaluate the direct impact of CD9 on partner functions. Results: A total of 278 CD9-binding proteins comprising 24 known and 254 novel partners were identified by IP-MS. Venn analysis revealed a marked heterogeneity of CD9-binding proteins across leukemia subtypes, with only 10 being intersected representing the “universal CD9 partners” in BCP-ALL. These proteins consisted of 5 established CD9 partners: ADAM10, CD19, CD38, CD81 and IGSF8 as well as 5 novel partners: ANXA11, HBG2, TMEM109, SLC44A1 and STXBP3. Two universal CD9 partners, namely CD38 and CD81, were consistently detected in all pediatric BCP-ALL samples. Neutralizing antibodies against CD9, CD38 or CD81 unanimously inhibited proliferation of 697 cells in vitro ( P&amp;lt;0.05). However, in the background of CD9 neutralization, CD81, but not CD38, offered an additional impact on leukemia suppression ( P&amp;lt;0.05). Likewise, CD38 knockout cells treated with CD9 antibody did not appear to inhibit cell proliferation in an additive manner. Concordantly, in the 697 xenografts, CD9 or CD38 antibodies alone prolonged animal survival by 2.1- and 1.6-fold, but combinational treatment did not produce the projected additive effect (2.5-fold only). In addition, CD9 neutralization significantly reduced the enzymatic activity of CD38 by 52.5% ( P&amp;lt;0.05) without altering its expression. Conclusions: This work presents the composition of the CD9 protein web in BCP-ALL, revealing homogenous and heterogeneous partners across the leukemia subtypes. We also provide definitive evidence showing that CD9 binds to and regulates CD38 activity to mediate leukemia progression, representing the first universal protein partner being identified to have a functional consequence in BCP-ALL, thereby providing a mechanistic basis to support the development of CD9-targeted therapies for this life-threatening malignancy.