Pediatric AML Patients Research Articles

NUP98::NSD1 and FLT3/ITD co-expression is an independent predictor of poor prognosis in pediatric AML patients

ObjectivePatients who carry NUP98::NSD1 or FLT3/ITD mutations are reported to have poor prognosis. Previous studies have confidently reported that the poor outcome in younger AML patients is owning to dual NUP98::NSD1 and FLT3/ITD positivity, with a high overlap for those two genetic lesions. In this study, we assessed the prognostic value of the presence of both NUP98::NSD1 and FLT3/ITD in pediatric AML patients.MethodsWe screened a large cohort of 885 pediatric cases from the COG-National Cancer Institute (NCI) TARGET AML cohort and found 57 AML patients with NUP98 rearrangements.ResultsThe frequency of NUP98 gene fusion was 10.8% in 529 patients. NUP98::NSD1 fusion was the most common NUP98 rearrangement, with a frequency of 59.6%(34 of 57). NUP98::NSD1 -positive patients who carried FLT3/ITD mutations had a decreased CR1 or CR2 rate than those patients carried FLT3/ITD mutation alone (P = 0.0001). Moreover, patients harboring both NUP98::NSD1 fusion and FLT3/ITD mutation exhibited inferior event-free survival (EFS, P < 0.001) and overall survival (OS, P = 0.004) than patients who were dual negative for these two genetic lesions. The presence of only NUP98::NSD1 fusion had no significant impact on EFS or OS. We also found that cases with high FLT3/ITD AR levels ( > = 0.5) with or without NUP98::NSD1 had inferior prognosis. Multivariate analysis demonstrated that the presence of both NUP98::NSD1 and FLT3/ITD was an independent prognostic factors for EFS (hazard ratio: 3.2, P = 0.001) in patients with pediatric AML. However, there was no obvious correlation with OS (hazard ratio: 1.3, P = 0.618). Stem cell transplantation did not improve the survival rate of cases with NUP98 fusion or NUP98::NSD1 AML in terms of EFS or OS.ConclusionPresence of both NUP98::NSD1 and FLT3/ITD was found to be an independent factor for dismal prognosis in pediatric AML patients. Notably, lack of FLT3/ITD mutations in NUP98::NSD1 -positive patients did not retain its prognostic value.

Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials

In this study, we leveraged machine-learning tools by evaluating expression of genes of pharmacological relevance to standard-AML chemotherapy (ara-C/daunorubicin/etoposide) in a discovery-cohort of pediatric AML patients (N = 163; NCT00136084) and defined a 5-gene-drug resistance score (ADE-RS5) that was predictive of outcome (high MRD1 positivity p = 0.013; lower EFS p < 0.0001 and OS p < 0.0001). ADE-RS5 was integrated with a previously defined leukemic-stemness signature (pLSC6) to classify patients into four groups. ADE-RS5, pLSC6 and integrated-score was evaluated for association with outcome in one of the largest assembly of ~3600 AML patients from 10 independent cohorts (1861 pediatric and 1773 adult AML). Patients with high ADE-RS5 had poor outcome in validation cohorts and the previously reported pLSC6 maintained strong significant association in all validation cohorts. For pLSC6/ADE-RS5-integrated-score analysis, using Group-1 (low-scores for ADE-RS5 and pLSC6) as reference, Group-4 (high-scores for ADE-RS5 and pLSC6) showed worst outcome (EFS: p < 0.0001 and OS: p < 0.0001). Groups-2/3 (one high and one low-score) showed intermediate outcome (p < 0.001). Integrated score groups remained an independent predictor of outcome in multivariable-analysis after adjusting for established prognostic factors (EFS: Group 2 vs. 1, HR = 4.68, p < 0.001, Group 3 vs. 1, HR = 3.22, p = 0.01, and Group 4 vs. 1, HR = 7.26, p < 0.001). These results highlight the significant prognostic value of transcriptomics-based scores capturing disease aggressiveness through pLSC6 and drug resistance via ADE-RS5. The pLSC6 stemness score is a significant predictor of outcome and associates with high-risk group features, the ADE-RS5 drug resistance score adds further value, reflecting the clinical utility of simultaneous testing of both for optimizing treatment strategies.

CD74 is expressed in a subset of pediatric acute myeloid leukemia patients and is a promising target for therapy: a report from the Children's Oncology Group.

As curative therapies for pediatric acute myleoid leukemia (AML) remain elusive, identifying potential new treatment targets is vital. We assessed the cell surface expression of CD74, also known as the major histocompatibility complex-II invariant chain, by multidimensional flow cytometry in 973 patients enrolled in the Children's Oncology Group AAML1031 clinical trial (clinicaltrials gov. Identifier: NCT01371981). Thirty-eight percent of pediatric AML patients expressed CD74 at any level and a comparison to normal hematopoietic cells revealed a subset with increased expression relative to normal myeloid progenitor cells. Pediatric AML patients expressing high intensity CD74 typically had an immature immunophenotype and an increased frequency of lymphoid antigen expression. Increased CD74 expression was associated with older patients with lower white blood cells and peripheral blood blast counts, and was enriched for t(8;21), trisomy 8, and CEBPA mutations. Overall, high CD74 expression was associated with low-risk status, however 26% of patients were allocated to high-risk protocol status and 5-year event-free survival was 53%, indicating that a significant number of high expressing patients had poor outcomes. In vitro preclinical studies indicate that anti-CD74 therapy demonstrates efficacy against AML cells but has little impact on normal CD34+ cells. Together, we demonstrate that CD74 is expressed on a subset of pediatric AML at increased levels compared to normal hematopoietic cells and is a promising target for therapy in expressing patients. Given that nearly half of patients expressing CD74 at high levels experience an adverse event within 5 years, and the availability of CD74 targeting drugs, this represents a promising line of therapy worthy of additional investigation.

Development and validation of a promising 5-gene prognostic model for pediatric acute myeloid leukemia

Risk classification in pediatric acute myeloid leukemia (P-AML) is crucial for personalizing treatments. Thus, we aimed to establish a risk-stratification tool for P-AML patients and eventually guide individual treatment. A total of 256 P-AML patients with accredited mRNA-seq data from the TARGET database were divided into training and internal validation datasets. A gene-expression-based prognostic score was constructed for overall survival (OS), by using univariate Cox analysis, LASSO regression analysis, Kaplan–Meier (K-M) survival, and multivariate Cox analysis. A P-AML-5G prognostic score bioinformatically derived from expression levels of 5 genes (ZNF775, RNFT1, CRNDE, COL23A1, and TTC38), clustered P-AML patients in training dataset into high-risk group (above optimal cut-off) with shorter OS, and low-risk group (below optimal cut-off) with longer OS (p < 0.0001). Meanwhile, similar results were obtained in internal validation dataset (p = 0.005), combination dataset (p < 0.001), two treatment sub-groups (p < 0.05), intermediate-risk group defined with the Children's Oncology Group (COG) (p < 0.05) and an external Japanese P-AML dataset (p = 0.005). The model was further validated in the COG study AAML1031(p = 0.001), and based on transcriptomic analysis of 943 pediatric patients and 70 normal bone marrow samples from this dataset, two genes in the model demonstrated significant differential expression between the groups [all log2(foldchange) > 3, p < 0.001]. Independent of other prognostic factors, the P-AML-5G groups presented the highest concordance-index values in training dataset, chemo-therapy only treatment subgroups of the training and internal validation datasets, and whole genome-sequencing subgroup of the combined dataset, outperforming two Children's Oncology Group (COG) risk stratification systems, 2022 European LeukemiaNet (ELN) risk classification tool and two leukemic stem cell expression-based models. The 5-gene prognostic model generated by a single assay can further refine the current COG risk stratification system that relies on numerous tests and may have the potential for the risk judgment and identification of the high-risk pediatric AML patients receiving chemo-therapy only treatment.

Single Cell Transcriptome Comparisons of Diagnosis-Relapse Pairs Uncover Programs Associated with Chemoresistance in Pediatric AML

Background: Relapse rates for pediatric AML remain unacceptably high at nearly 50% after frontline therapy. Once relapse occurs, the disease is often refractory to further chemotherapy. Prior studies have shown that acquired mutations conferring chemoresistance are uncommon, and most relapses are thought to arise from the selection of clones already present at diagnosis. Therefore, characterizing chemoresistant disease at the gene expression level could lead to new insights and novel therapy targets. Profiling cases by bulk RNA sequencing has revealed important disease features such as novel gene fusions. However, identifying resistant subpopulations by bulk sequencing is challenging, particularly if they constitute small fractions of the leukemia cells at diagnosis. We hypothesize that by applying single-cell transcriptome profiling (scRNA-seq) to diagnosis-relapse pairs we can identify and characterize the subclones selected by treatment. Additionally, we will discover pathways and gene-expression programs that are associated with chemoresistance. Methods: We profiled thirteen diagnosis-relapse pairs from pediatric AML patients who were treated on or similarly to the Children's Oncology Group (COG) study AAML1031 and consented to banking of cells for future research. Six pairs were banked at Texas Children's Cancer Center and 7 were obtained from the COG biobank. The COG cases were flow-sorted to enrich for blasts before undergoing scRNA-seq with 10X-Chromium and Illumina NovaSeq systems. In addition, two local normal bone marrow cases were profiled, one with prior sorting and one with and without prior sorting. We included scRNA-seq profiles of 8 pediatric AML patients and 4 non-cancer bone marrow samples from Bailur et al. (JCI insight, 2020) as additional controls. Sequencing data were analyzed using CellRanger and Seurat. Four of the COG cases were profiled at the protein level by mass cytometry (CyTOF) and analyzed in Cytobank. Results: In total, for the 13 diagnosis-relapse pairs, 17,233 to 34,246 cells were profiled per patient, and 22,800 transcripts were detected. Unsupervised clustering of our samples and controls yielded 43 clusters (Figure 1) that could be confidently identified as either malignant or non-malignant (normal). We further classified all clusters into inferred hematopoietic developmental stages based on comparisons to publicly available expression reference data (Figure 2). We distinguished between patients with cell types at relapse that were also identified at diagnosis (Group 1), albeit often at a lower proportion, and patients whose cell types at relapse were not detected at diagnosis (Group 2). We also characterized 4 of the diagnosis-relapse pairs by CyTOF with an antibody panel that quantified surface lineage markers and intracellular signaling proteins. The protein expression data validated the RNA data in both the degree of differentiation of AML cells and the degree of similarity between diagnosis and relapse. We identified a Relapse-Up signature composed of 139 differentially expressed genes that were upregulated in AML clusters that expanded between diagnosis and relapse, compared to clusters that diminished between diagnosis and relapse. The Relapse-Up gene signature is enriched in genes that are co-expressed with FLT3, CDK6, and ILK kinase genes. With publicly available TARGET gene expression data, we confirmed that this gene signature is upregulated in relapsed AML samples when compared to diagnosis samples. We further used the profiles of the cell types that expanded between diagnosis and relapse to construct a risk-predictive function that predicted patient outcomes based on bulk RNA-Seq profiles of their diagnostic samples with significant accuracy. Conclusion: Single-cell RNA-seq of diagnosis-relapse pairs from pediatric patients with AML revealed distinct patterns of relapse that were also apparent at the protein level. The Relapse-Up signature was enriched in pediatric AML relapse samples in a large bulk RNA-seq data set, confirming its broader applicability. The kinase co-expression programs present in the signature are likely to be functionally associated with chemotherapy resistance and represent targets for future preclinical therapeutic studies.

Measurable Residual Disease As Assessed By Flow Cytometry As Predictor of Survival in Pediatric AML Patients

Introduction Pediatric acute myeloid leukemia (pedAML) is a heterogeneous group of hematological malignancies classified according to morphology, immunophenotyping, and genomics. The optimal adjustment of therapy based on level of response is not well defined. Aim: Herein, we present the results of a retrospective study aiming to analyze the prognostic value of measurable residual disease (MRD) as determined by flow cytometry (FC-MRD) in pediatric AML. Patients and Methods All pediatric and adolescent patients (aged 0-18 years old) with AML treated in our unit between 1/2013-6/2023 were included in this study. French American British (FAB) morphological classification, immune-phenotype analysis, and molecular characterization were performed on diagnosis, and all patients were treated according to AML-BFM protocols. Final risk classification was based on evaluation of response and on genetic abnormalities at diagnosis. MRD was assessed by FC-MRD after Induction 1 and 2, and, either after course 5 or before hematopoietic stem cell transplantation (HSCT). Complete Remission (CR) was defined as regenerative or normocellular bone marrow with &amp;lt;5% blasts; in peripheral blood ≥1.0x10 9/L neutrophil granulocytes and ≥80x10 9/L thrombocytes or Remission with partial regeneration ( CRp: regenerative or normocellular bone marrow with &amp;lt;5% blasts; in the blood: ≥1.0x10 9/L leukocytes, ≥0.5x10 9/L, neutrophil granulocytes and ≥50x10 9/L, self-sustained platelets), lasting at least 4weeks; no extramedullary disease. Overall survival (OS) was defined as the time interval from the treatment initiation date to the date of death due to any cause. Progressive free survival (PFS) was defined as the time interval from the response date to the date of disease relapse or death due to any cause. The probabilities of OS and PFS were estimated with the Kaplan-Meier method. Results Overall, there were 52 patients (median age at diagnosis:7 years, 37males/15 females) diagnosed with AML, of whom: 40 patients with de novo AML, 5 patients with therapy- or myelodysplasia-related AML and 7 patients with mixed-lineage leukemia. Cytogenetics were considered favorable for 16 (31.0%), intermediate for 4 (7.6%), and adverse for 32 (61.4%) patients. Standard-risk patients (n=16) received only chemotherapy, whereas all high-risk patients, and intermediate-risk patients with available matched donors, underwent HSCT should they have reached remission. Forty-four patients (84.6%) achieved complete response (CR). Among these patients, 43 patients (97.7%) achieved CR after 1 course of induction, and 1 patient (2.3%) required at least 2 courses. Twenty-four patients (46.1%) underwent HSCT during either their first (20/24) or second (4/24) CR. Overall, 12 patients (23.07%) died, 4 patients due to resistant disease, 3 patients due to relapse, 2 patients due to serious complications upon diagnosis, 1 patient due to infection and 2 patients due to transplant-related complications. With a median follow-up time of 3.7 years (range 0.1-11.1years), the five-year OS and PFS of the entire cohort was 74.0% and 70.0%, respectively. The level of FC-MRD was a significant prognostic factor for OS and PFS. More specifically, achievement of FC-MRD &amp;lt; 0.1% at all time points was associated with a significant improvement in PFS and OS. (figure 1). FC-MRD ≥ 0.1% after course 5 or before HSCT was the only independent adverse prognostic factor that was statistically significant for both progression-free (P=0.001) and overall survival (P&amp;lt;0.001) (figure1). Conclusions We investigated the association between FC-MRD and survival in Greek pediatric patients with AML. In our cohort, achieving an MRD status &amp;lt;0.1% according to FC is associated with significant improvement in the outcome of pediatric patients with AML.

XPO2 Is Essential for a Subset of AML Cells and Is a Biomarker for Poor Response and Survival in Pediatric and AYA AML

Importins &amp; exportins regulate protein transport across the nuclear membrane. Twenty nuclear transport receptors (NTRs) have been identified; six are involved in nuclear export. NTRs contribute to cancer development, through abnormal localization of protein cargos. The exportin, XPO1, is associated with high risk AML &amp; shorter survival times. However, little is known regarding the functional importance of the related exportin, XPO2 (alias CSE1L). We analyzed a public database of CRISPR/Cas9 depletion screens in 26 AML cell lines. XPO2 ranked in the top 1.4% of essential genes, along with XPO1 (top 1.3%) (DepMap 22Q2 Public+Score, Chronos). An RNAi depletion screen confirmed this, with XPO2 ranked in the top 0.2% of AML genes. Leukemia cells were more dependent on XPO2 vs solid tumors (P = 0.0394) &amp; gene dependency scores indicated a greater reliance on XPO2 vs XPO1 (P &amp;lt;0.0001). Increased expression of XPO2 mRNA was associated with decreased event free survival (EFS) (P = 0.0014) &amp; overall survival (OS) (P = 0.00091) in pediatric &amp; adolescent/young adult (AYA) AML patients (TARGET dataset). In the BeatAML dataset, increased XPO2 mRNA expression was associated with decreased OS in patients &amp;lt;40 years, but not in patients &amp;gt;40 years (P &amp;lt;0.0001). We analyzed protein expression databases &amp; identified XPO2 as the highest expressed exportin in AML cells lines &amp; patient samples. Increased XPO2 expression was detected in 7/7 primary AML samples &amp; 9 AML cell lines by immunoblot (HL60, MV4-11, MOML13, NB4, OCI-AML2, OCI-M2, TEX, U937 &amp; 1254 cells), compared to normal hematopoietic cells. Expression of XPO2 was increased in younger (&amp;lt;40 years) vs older patients (&amp;gt;70 years) (P = 0.0454). Genetic silencing of XPO2 decreased growth &amp; viability of OCI-AML2, TEX, NB4 &amp; 1254 cells. Gambogic acid is an inhibitor of XPO2-mediated nuclear transport. In OCI-AML2, TEX &amp; NB4 cell lines, gambogic acid decreased viability of AML cells (TEX IC50 = 369nM, OCI-AML2 IC50 = 433nM, NB4 IC50 = 161nM). Next, we interrogated a BioID database (PXD007976) &amp; performed gene set enrichment analysis on XPO2 targets. Processes related to ribosome biogenesis were enriched in XPO2 cargo, whereas XPO1 cargo were enriched for snRNA transcription processes (P &amp;lt;0.05). A gene expression signature encompassing XPO2 &amp; its associated cargo genes was enriched in functionally defined LSCs (P = 0.001, in patients with more primitive AML subtypes (P &amp;lt; 2.22 x 10 -16), in more primitive AML blasts as defined by FAB subtype and in high risk subsets, including WT1 mutated pediatric AML. Additionally, the XPO2 gene signature was associated with minimal-residual-disease (MRD) positive disease after induction cycle I (P &amp;lt; 5.1x 10 -6) and II (P = 0.0013), decreased complete remission (CR) rates after cycle I (P = 0.00025) and II (P = 0.02), worse EFS (P = 0.019) and worse OS (P = 0.02) in pediatric and AYA AML patients. In summary, we identified XPO2 as an essential gene for AML . XPO2 is increased in AML cells &amp; primary samples from younger patients. Increased XPO2 expression &amp; increased expression of XPO2 mediated processesare associated with worse outcomes in pediatric AML &amp; correlate with LSC enrichment &amp; primitive AML subtypes. XPO2 may function to enhance ribosomal biogenesis, demonstrating a critical role in leukemogenesis. Thus, this work demonstrates a new dependency of pediatric AML on XPO2 highlighting a new target and biomarker for this disease.

Transcriptional Heterogeneity and Clonal Evolution between Diagnosis and Relapse in Pediatric Acute Myeloid Leukemia

Clonal evolution of leukemia is driven by different selection pressures operating on a heterogeneous population of cells. These pressures may include therapy-induced and immune-mediated effects which eradicate the majority of cells, but which simultaneously provide a selective advantage to a minor population of cells that is genetically or transcriptionally distinct and which grow out towards relapse. We integrated single-cell RNA-seq, DNA-seq, ATAC-seq and long-read Oxford Nanopore sequencing of matched diagnosis and relapse samples of 20 pediatric AML patients with various genetic driver mutations representative of the mutational spectrum to map the genetic and transcriptional evolution of these cancers (Figure 1). We investigated whether and how differences in AML-initiating mutations impact on transcriptional programs in AML blasts and their surrounding microenvironmental cells and how the mutational and transcriptional features of these cells are impacted by cancer therapy. Specifically, we traced the progression of these traits from the point of diagnosis to the occurrence of relapse. Our single cell RNA and ATAC data showed high patient-to-patient heterogeneity, with gene expression patterns that were largely conserved between diagnosis and relapse. Analyses of the differentially expressed genes and factorization into “metaprograms” revealed gene sets that were shared between relapse samples but could not be tied to interpretable common “biological signatures”. Exome-seq revealed highly significant changes in somatic variants, most notably in members of the RAS-signaling pathway (i.e., KRAS, NRAS, PTPN11, NF1 and CBL). Interestingly, pathogenic RAS mutations were often gained, but also lost, or switched between different RAS-pathway members, indicating that RAS-mutations are associated with extensive clonal evolution/rewiring. To unveil the effect of accumulation or loss of (sub)clones with RAS mutations on the transcriptional phenotype and epigenetic landscape of leukemic blasts, we performed targeted screening of somatic variants at single-cell resolution. To this aim, we combined long-read nanopore sequencing with 10x Genomics single-cell technologies, enabling us to directly link genetic, transcriptomics and epigenetic changes in distinct (sub)clones. Taken together, we successfully reconstructed patient-specific genetic and transcriptional evolutionary trajectories in pediatric AML. This knowledge will be essential for our understanding of AML relapse and therapy resistance.

A Longitudinal Single-Cell Atlas of Treatment Response in Pediatric AML

Introduction: Pediatric acute myeloid leukemia (pAML) is a heterogeneous disease in terms of driver alterations, treatment response and patient outcomes. Although approximately 90% of pAML patients respond to initial treatment, tumours relapse frequently. Despite large-scale genomic sequencing efforts, it remains elusive why tumors relapse. Previously, mutations have been identified that affect transcriptional regulation, indicating that epigenetic processes may contribute to treatment resistance in pAML. We therefore studied how tumor epigenetic patterns, transcriptional regulation and cell populations change over the course of treatment using single-cell ATAC sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) in pediatric populations. Methods: We profiled 330,047 cells using scRNA-seq and 353,984 cells using scATAC-seq derived from 28 uniformly treated pAML patients, driven by either MLL fusions, CBFB fusions, RUNX1 fusions, FLT3-ITD or other aberrations (i.e. CEBPA mutations). All patients were enrolled in the AAML1031 trial (https://childrensoncologygroup.org/aaml1031), a randomized phase 3 clinical trial that investigated the addition of Bortezomib (BTZ) and Sorafenib to standard treatment modalities. Samples were obtained serially at diagnosis, at remission and at relapse and single-cell profiles were compared between these stages. Results: We identified malignant and non-malignant populations in the scATAC-seq and scRNA-seq data, showing that in all cases, malignant cells from patients at diagnosis were distinct from those taken at relapse. Major differences between diagnosis and relapse were associated with differentiation, and by inferring distinct cell populations we identified that relapsed cell populations appeared to shift towards a more primitive state. The extent of this shift was dependent on the genetic subtype and the effects were more pronounced in MLL-rearranged tumors. To identify the candidate mechanisms and transcription factors involved in this shift we studied the monocytic, lymphocytic and erythrocytic lineages in non-malignant cells and compared these to the tumor at diagnosis and relapse. Based on motif enrichment we found that across all different subgroups, transcription factors (TFs) that drive monocytic differentiation (i.e. CEBPA) have a lower activity while TFs driving erythrocytic and lymphocytic differentiation (i.e. TCF3) have a higher activity. Analysis of hematopoietic stem-like and progenitor-like cells (HSPC-like) confirmed this change, indicating that the “priming” towards other lineages is not only a result of shifts in cell populations but also a result of rewiring of early progenitors. To investigate this rewiring, we analysed regions of open chromatin that were enriched in malignant HSPCs compared to normal HSPCs across different subgroups. We found that those regions were highly specific to the driving alteration and were enriched for MEF2C binding sites in MLL-driven tumors and AP-1 binding sites in other tumors. Overall, upon relapse MEF2C expression and inferred TF activity appeared to increase, coinciding with an apparent increase in lymphoid priming and early lymphoid factors including LMO2, LYL1 and TCF3, among others. Two cases in the cohort appeared to switch lineage from a monocytic to lymphocytic phenotype and were enriched in CD19 and CD79A positive malignant cells upon relapse. Both cases shared the characteristic that MEF2C was upregulated upon relapse and showed upregulation of typical B-lymphoid transcription factors such as PAX5. Discussion: By generating a large dataset of pediatric AML patient samples collected at diagnosis, remission and relapse, we have identified changes in cellular hierarchies and transcriptional networks that occur upon relapse. Our study shows that shifts in cell populations readily occur upon treatment and are dependent on subgroup-defining alterations. Particularly MLL-rearranged tumors show a high level of plasticity that could explain the poor outcome of this group. Furthermore, we show that tumors appear to adapt their transcriptional programs towards a more “stem-like” state, with a likely higher propensity to differentiate towards other lineages such as the lymphoid lineage. We have identified MEF2C as a possible regulator of these processes, opening a new perspective to target the plasticity of these tumors.

Combination of Liposomal Mitoxantrone, Venetoclax, Homoharringtonine, and Olverembatinib (HQP1351) (MVHO) in Pediatric Patients with Refractory or Relapsed Acute Myeloid Leukemia (AML): Case Series

Introduction: AML accounts for up to 25% of all pediatric acute leukemias. Although overall survival (OS) in pediatric AML has increased to 70% in recent years because of enhanced risk stratified intensive chemotherapy and hematopoietic stem cell transplantation. Unfortunately, more than 30% of patients experience relapse. Further increase intensity of chemotherapy was proven unfeasible for the toxicity and treatment related mortality. Hence, specific targeted therapy has been being explored to treat pediatric AML in recent decade. Because of the heterogeneity of AML and multiple pathways involved in leukemogenesis, single agent targeting one pathway was effective in limited cases. In this study, we designed a regimen to block multiple pathways with combination of Liposomal Mitoxantrone, Venetoclax, Homoharringtonine, and Olverembatinib (MVHO) to investigate its efficacy and safety in treatment of refractory or relapsed AML. Methods: We enrolled patients with relapsed or newly diagnosed AML with poor prognosis with adverse molecular abnormalities, such as NUP98 rearrangements, FUS::ERG, CBFA2T3::GLIS2, and del7/7q, who did not achieve complete remission (CR) after first-line chemotherapy. Patients were administered the MVHO regimen, which included 1 dose of liposome mitoxantrone 8mg/m 2; venetoclax, 300 to 350mg/m 2 once daily, from day1 to day 7, (dose escalation for up to 3days from 50mg/m 2 if high tumor burden occur); homoharringtonine 2mg/m 2 once daily, from day1 to day 7; and Olverembatinib (HQP1351) 20-30mg/m 2 every other day, for 4 doses from day 1 to day 7. Prophylactic oral levofloxacin and posaconazole were administered from day 8 through whole myelosuppression period of every cycles. One cycle (28-35 days, depending on hematopoietic recovery) response, total response, cumulative incidence of relapse (CIR), event-free survival (EFS), hematologic toxicity, and infection during this study were evaluated. Results: A total of 18 patients were enrolled (9 boys and 9 girls), with a median (range) age of 7.3 (4 months-13 years) years, and underwent a total of 27 cycles of MVHO therapy. Half of the patients underwent 1 cycle and the other half, 2 cycles. Per French-American-British (FAB) classification criteria: patients had myelodysplastic syndrome (n = 2); mixed-phenotype acute leukemia (n = 2); and AML subtypes M7 (n = 4), M2 (n = 4), M5 (n = 4), M4 (n = 1), and M0 (n = 1). The median (range) follow-up time was 131 (26-256) days. After cycle one, the objective response rate (ORR, CR plus CR with incomplete hematological recovery [Cri] and partial response [PR]) was 94.4% (17/18), and the remission rate (CR + Cri) was 72.2% (13/18). The total ORR and remission rate before transplantation were 83.3% (15/18) and 66.7% (12/18), respectively. 8 patients among them reached minimum residual disease (MRD) negative remission. For 6 patients with relapsed AML, the ORR and one cycle remission rate was 100% and 66.7%, respectively. A total of 3 patients discontinued because of no response or disease progression, and 12 patients underwent hematopoietic stem cell transplantation (HSCT), after which 1 patient experienced relapse. Remaining 2 patients are being underwent further MVHO cycles. The CIR was 6.7% (1/15). The 8-month mean (± SD) EFS was 60.1% (±19%) and the OS, 100%. Among 26 cycles of MVHO treatment, there were no associated fatal infections or bleeding events. There were 21 episodes of breakthrough infection occurred in 26 cycles of MVHO. There was 1 case of septic shock, and the incidence of ≥grade 3 infection was 80.7%, which included pneumonia, bloodstream infection. Common grade 4 treatment-related adverse events were neutropenia, which was experienced by 100% of patients, and grade 4 thrombocytopenia, which was experienced by 46.1%. Most notably, platelets were stably normal in nearly 20% (5/26) MVHO cycles. Conclusions: MVHO therapy was effective and reasonably well tolerated in pediatric patients with refractory or relapsed AML, suggesting that it may comprise a suitable first-line treatment option for pediatric AML patients.

FLT3ITD drives context-specific changes in cell identity and variable interferon dependence during AML initiation

AbstractAcute myeloid leukemia (AML) initiation requires multiple rate-limiting mutations to cooperatively reprogram progenitor cell identity. For example, FLT3 internal tandem duplication (FLT3ITD) mutations cooperate with a variety of different initiating mutations to reprogram myeloid progenitor fate. These initiating mutations often skew toward either pediatric or adult AML patient populations, though FLT3ITD itself occurs at similar frequencies in both age groups. This raises the question of whether FLT3ITD might induce distinct transcriptional programs and unmask distinct therapeutic vulnerabilities when paired with pediatric, as opposed to adult AML-initiating mutations. To explore this possibility, we compared AML evolution in mice that carried Flt3ITD/NUP98-HOXD13 (NHD13) or Flt3ITD/Runx1DEL mutation pairs, which are respectively most common in pediatric and adult AML. Single-cell analyses and epigenome profiling revealed distinct interactions between Flt3ITD and its cooperating mutations. Whereas Flt3ITD and Flt3ITD/Runx1DEL caused aberrant expansion of myeloid progenitors, Flt3ITD/NHD13 drove the emergence of a pre-AML population that did not resemble normal hematopoietic progenitors. Differences between Flt3ITD/Runx1DEL and Flt3ITD/NHD13 cooperative target gene expression extended to fully transformed AML as well. Flt3ITD/NHD13 cooperative target genes were enriched in human NUP98-translocated AML. Flt3ITD/NHD13 selectively hijacked type I interferon signaling to drive expansion of the pre-AML population. Blocking interferon signaling delayed AML initiation and extended survival. Thus, common AML driver mutations, such as FLT3ITD, can coopt different mechanisms of transformation in different genetic contexts. Furthermore, pediatric-biased NUP98 fusions convey actionable interferon dependence.

RAS Pathway Alterations in Pediatric AML Patients

RAS pathway alterations are highly prevalent in hematologic malignancies1,2, often involving gain of function KRAS, NRAS or HRAS mutations and have been linked to tumorigenesis and associated with poorer prognosis in different cancer entities3-5. In adult myeloid leukemia, RAS mutations are one of the most common mutations, yet show no clear prognostic value6. In a study of the Japanese pediatric AML cohort, NRAS mutations were associated with a favorable outcome, the effect of KRAS mutations could not be analyzed due to the limited patient size7. Here we report the outcome of 372 pediatric AML patients of the German AML-BFM study between 2016 and 2021 that were characterized by morphology, multicolor flow cytometry, classical cytogenetics and mutation analysis via panel sequencing. In total, 27% (n=102) of the patients showed a RAS pathway alteration, involving n=32 patients (9%) with a KRAS mutation and n=75 (20%) with a NRAS mutation. Notably, no HRAS mutation was detected in our cohort. Age distribution did not differ between the groups (Fig. A). Interestingly, the KRAS cohort consisted mostly of male patients (72%, p=0,0087), while the overall cohort was balanced (48,7% male patients). NRAS and KRAS mutations were strong predictors of therapy response and early death. Only 1/75 (1,3%) of all patients harboring a NRAS mutations showed poor response to induction therapy compared to patients without a NRAS mutation (10,10%, p=0,01). KRAS mutations on the opposite were strongly associated with non-response (21,9%; p<0,01) and subsequent early deaths (n=6/32; p=0,001) compared to patients without KRAS mutations (3,2%). Of note, only 1/75 (1,3%) of patients with NRAS mutation and 17/372 (4,6%) of all AML patients suffered early deaths. Risk stratification taking into account re-stratification after poor therapy response showed a significant higher proportion of high-risk patients in the KRAS-mutated cohort (43,8 %) compared to 20% in the patients with NRAS mutations (p=0,0022). KRAS mutations correlated with KMT2A-MLLT1 (15,6%; p=0,01) translocations, which were significantly rarer in patients without KRAS mutations (3,5%). NRAS mutations occurred frequently with CBFA2T3-RUNX1 (14,7%; p=0,0002) and CBFB-MYH11 translocations (12%; p=0,0068%) as well as KIT mutations (12%; p=0,026). Existence of RAS mutations showed overall no significant impact on event-free survival (EFS=69,6% ±4,8%) and overall survival (OS=82,8% ±4,2%) compared to RAS wildtype (EFS=66,4% ±3,1% ; OS=76,5% ±2,9%) (Fig. B). Multivariate analysis comparing outcome for several subgroups also showed no significant differences. In summary, we show worse therapy response and increased early death rates in patients with KRAS mutations, while NRAS mutations are associated with better therapy response. These findings warrant further analyses and longer follow-up on the cohort to determine long-term significances of RAS pathway alterations in pediatric AML patients. 1.de Luca, A., Maiello, M. R., D'Alessio, A., Pergameno, M. & Normanno, N. The RAS/RAF/MEK/ERK and the PI3K/AKT signalling pathways: role in cancer pathogenesis and implications for therapeutic approaches. Expert Opin Ther Targets16 Suppl 2, (2012). 2.Hobbs, G. A., Der, C. J. & Rossman, K. L. RAS isoforms and mutations in cancer at a glance. Journal of Cell Science129, 1287-1292 (2016). 3.Hsu, H. C. et al. Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients. Oncotarget7, 22257 (2016). 4.Vauthey, J., Zimmitti, G., Kopetz, S., ... J. S.-A. of & 2013, undefined. RAS mutation status predicts survival and patterns of recurrence in patients undergoing hepatectomy for colorectal liver metastases. ncbi.nlm.nih.gov. 5.Dinu, D. et al. Prognostic significance of KRAS gene mutations in colorectal cancer - preliminary study. Journal of Medicine and Life7, 581 (2014). 6.Neubauer, A. et al. Patients With Acute Myeloid Leukemia and RAS Mutations Benefit Most From Postremission High-Dose Cytarabine: A Cancer and Leukemia Group B Study. Journal of Clinical Oncology26, 4603 (2008). 7.Kaburagi, T. et al. Clinical significance of RAS pathway alterations in pediatric acute myeloid leukemia. Haematologica107, 583-592 (2022). Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Revision of Complete Remission Criteria in Pediatric AML

In AML, complete remission (CR) is traditionally defined by < 5 % blasts, absolute neutrophil count (ANC) < 1000/µL and platelets (plt) > 100000/µL in adult and > 80000/µL in pediatric AML (Cheson et al. 2003). This largely morphologically based definition has remained unchanged for more than two decades. Though proven as a valuable predictor of outcome and survival in clinical practice and trials, awaiting complete hematopoietic recovery still displays a hurdle of unknown prognostic significance in clinical practice. In addition, a great variety of diverse criteria, considering hematopoietic recovery, were established in clinical trials to counter this problem. Thus, the actual relevance of the inclusion of ANC and plt in the current CR definition needs to be reassessed and newly defined in pediatric AML. Data of 1051 pediatric AML patients diagnosed between 2004 and 2020 have been analyzed. Acute promyelocytic leukemia, secondary-, treatment-related and Down syndrome-related AML were excluded. Patients were treated according the German pediatric AML-BFM studies and registries between 2004 and 2019 (Essen, Germany). Diagnostic bone marrow and peripheral blood samples from defined timepoints were collected and reviewed centrally. Patients were allocated to alternative response groups, using combinations of 5 % bone marrow blasts with different thresholds for ANC (250, 500 and 1000 / ul) and plt (20000, 50000 and 80,000 / µl). Survival and outcome of these stratified response groups were compared with the current, established CR criteria (blasts < 5%, ANC < 1000, 80000/ul; -CRtrad). Overall survival (OS) and event-free survival (EFS) were estimated by the Kaplan-Meier method and significance was determined using the log-rank statistic. A total of 1051 patients with a median age at diagnosis of 8.4±6 year (y) were analyzed. OS and EFS were 79.4±1% and 61.2±2%, respectively. CR with hematological regeneration (ANC>1000/µl; Plt >80.000/µl) showed a similar outcome compared with CRp (ANC> 500/µl)/Plts >50000/µl) or CRp (ANC>200/µl; Plts >20000/µl) or "no blasts; Plts > 20000/µl). Only patients with >5% blasts after 1st induction have an inferior EFS (51±3%; p<0.01). According to the centrally reviewed response data provided by the AML-BFM study group, the former CR definition in pediatric AML needs to be revised. Only the presence of leukemic blasts (>5%) after the 1st induction predicts a significantly inferior outcome (in IR and HR). Thus, postponement of the 2nd induction does not seem justified. Our results suggest that the Cheson criteria in AML should be omitted and replaced by a definition CR with ≥ 5% blasts. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Genome-Wide Association Study Identifies Variants Associated with Clinical Outcomes in Pediatric Patients with Newly Diagnosed Acute Myeloid Leukemia

Genetic aberrations in leukemic blasts are associated with clinical outcomes in patients with AML. However, the role of inherited genetic variants with regards to variation in AML treatment outcome remains obscure. To that end, we conducted a genome wide association study (GWAS) on 400 newly diagnosed pediatric AML patients to identify single nucleotide polymorphism (SNPs) that may be associated with minimal residual disease (MRD1) after induction 1 chemotherapy, event-free survival (EFS) and overall survival (OS). In this study, we utilized whole-genome genotyping with Illumina's Omni2.5Exome-8 BeadChip array to investigate SNPs for association with clinical outcome in 2 pediatric AML cohorts: the multi-site AML02 [NCT00136084, n=167] and AML08 [NCT00703820, n=233] trials. Post GWAS quality control, 1,365,439 unphased SNP genotypes were selected for imputation using TOPMed Imputation Server. Following imputation and additional quality control filtering, 6,741,200 SNPs evaluated for association with clinical outcomes (MRD1, EFS and OS). To improve statistical rigor, two GWAS approaches were utilized: i) A one-stage GWAS with both clinical trial cohorts combined (n=400) and ii) A two-stage GWAS where we utilized a two-step iterative resampling procedure (PMID: 26377241) by splitting the cohort at a 70:30 ratio into discovery and replication cohorts, balanced by clinical trial, treatment arm and initial risk group at diagnosis (100 randomizations performed). For each of the 100 iterations of the two-stage GWAS, we used the discovery cohort to perform a genome-wide analysis, followed by a replication screen. SNPs replicated in at least 20 of 100 rounds of discovery-replication were prioritized. A comparison of the two approaches showed all significant SNPs in the two-stage GWAS were also captured in the one-stage GWAS. For EFS, a Bonferroni-adjusted genome-wide significant association was observed for a SNP in CSMD1 and this SNP was replicated in 83 out of 100 discovery-replication rounds for two-stage GWAS. For CSMD1 SNP, presence of variant A allele has significantly reduced EFS (HR=3.29, 95% CI (2.177-4.975), P=1.61x10-8, Figure 1A). CSMD1 is a membrane-bound complement inhibitor that has been shown to act as a putative tumor suppressor gene in other malignancies (PMIDs:27764775, 35623420). Another significant marker worth mentioning was an intronic SNP in CDKN2B-AS1 that associated with poor outcome [EFS: HR=2.37, 95% CI (1.700-3.317), P=4.40x10-7] and [OS: HR=2.87, 95% CI (1.954-4.225), P=8.06x10-8, Figure 1B]. This marker is in high linkage disequilibrium with 26 other SNPs within the CDKN2B and CDKN2B-AS1 cluster. The product of this gene is an RNA molecule that interacts with polycomb repressive complex-1 (PRC1) and -2 (PRC2) involved in silencing other genes within this cluster through epigenetic mechanisms (PMID: 20716771). CDKN2B-AS1 has been reported to play a role in tumorigenesis and chemoresistance in pediatric T-cell acute lymphoblastic leukemia and with the risk of chronic lymphocytic leukemia (PMIDs: 32976214/23770605). Though limited by numbers, this is one of the largest GWAS conducted in pediatric AML to identify SNPs associated with clinical outcomes. Our top results show that genetic variation in several genes of biological relevance may impact MRD1, EFS and OS. Future studies are aimed at looking at SNP/gene and association with gene expression collected from leukemic cells at time of diagnosis to establish AML-specific eQTLs and functional validation of the most promising candidates. Additionally, future analyses will include other subgroups such as cytogenetic risk group and validation of these findings in larger cohort of patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Proteomic Analysis Identifies Epigenetic Modifiers and Potential Negative Regulators of Leukemogenesis KMD6A and SETDB1 to be Induced Post In Vivo Decitabine Exposure in Pediatric AML

Deregulation of epigenetic mechanisms has been associated with AML pathogenesis. In an integrated transcriptomic and DNA methylation evaluation in pediatric AML, we demonstrated that reduced methylation and increased expression of DNMT3B were associated with greater genome-wide methylation and worse outcome in pediatric AML patients treated on St Jude AML02 and COG clinical trials. This epigenetic deregulation has been leveraged through use of DNA methylation inhibitors (DMTis) such as azacytidine and decitabine for treatment of MDS and AML. Given promising results in adults and relapsed pediatric AML, the multi-site AML16 clinical trial (NCT03164057) evaluated single agent DMTi "priming” followed by standard chemotherapy for the treatment of pediatric AML. Despite the use of DMTi to treat heme-malignancies, the underlying molecular mechanisms are still under investigation. Thus, we evaluated molecular in vivo response of pediatric AML cells to decitabine by evaluating paired specimens obtained at diagnosis and after five days of single agent decitabine therapy for global proteomic profiling. In a pilot study we previously showed modest correlation (10.7%) between transcript and protein levels, suggesting that the transcriptome may not be a reliable surrogate for proteomics in pediatric AML. Additionally, given that the majority of biological functions within cells are operated by proteins and most drugs target the proteome rather than the genome or transcriptome, understanding the proteomic signatures is critical. Thus, in this evaluation, we focused on decitabine-induced alterations in cellular proteomic profiles of paired diagnostic leukemic samples and 5 days post in vivo decitabine exposure from 9 patients treated on AML16. Completely automated high-resolution TMT (tandem-mass-tag) -LC/LC-MS/MS system was utilized to capture high resolution proteomic data and 10,471 proteins were detected in samples. At p<0.01, 109 proteins increased and 41 decreased post decitabine exposure. In vivoexposure to decitabine resulted in increased levels of several epigenetic regulators, including KMD6A and SETDB1. KMD6A, a histone3 lysine 27 demethylase, was recently shown to be mutated in relapsed AML and loss of KMD6A has been associated with resistance to cytarabine and daunorubicin (PMID: 31201358). SETDB1 is a methyltransferase that suppresses leukemogenesis and higher SETB1 expression has been shown to alter the promoter epigenome and reduce expression of AML associated genes such as DOCK1, HOXA9, SIX1. A recent study demonstrated SETDB1 to be negatively regulating pro-leukemic target genes thereby suppressing AML (PMID: 33054052). Among the top genes that were reduced at protein levels was DNMT3A, which is a well-established prognostic marker in adult AML. Combined, alterations in these protein levels suggest that decitabine exposure may increase sensitivity of AML blasts to chemotherapy and interfere with the leukemia program. Of particular interest were proteins that are targetable by drugs and demonstrated increased expression post decitabine exposure such as dihydrofolate reductase (DHFR), which is essential for cellular metabolism and growth. DHFR is inhibited by the antileukemic agent methotrexate and our data suggest that DNMTi priming might increase sensitivity of leukemia cells to methotrexate. Other targetable proteins are listed in Table 1. In summary, this pilot study provides significant insight into the DMTi-mediated proteomics changes that hold prognostic and therapeutic relevance in AML. Ongoing studies are focused on expanding the cohort size and evaluate association of proteomics with clinical outcome. Additionally, we plan to perform a multi-omics analysis by integrating proteomics with DNA methylation, RNAseq and metabolomics. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Clinical and Functional Implications of MYC Variants As a New Class of Pathogenic Variants in AML

MYC, a well-known oncogene, is implicated in a majority of cancers, but there is little data on its role in myeloid malignancies. We recently described a novel internal tandem duplication of MYC gene (MYC-ITD) in a subset of patients with AML. As the prevalence of MYC aberrations have not been well documented in AML, we interrogated the genome, transcriptome and associated clinical and laboratory data from the largest cohort of pediatric AML patients to define the prevalence, frequency of co-occurring cytomolecular alterations and outcomes associated with MYC variants. Mutation Profiling: Diagnostic specimens from 1,806 patients with AML (age 0-29 years) enrolled on COG Phase III trials were retrospectively interrogated using contemporary NGS techniques or a PCR based "Tandem Repeat" assay for MYC-ITD. Conventional karyotyping and mutational analysis, including NGS, were used to determine additional cytogenetic and molecular abnormalities. Of the 1,806 patients studied, MYC aberrations were identified in 58 patients (3.2%) with 50% (N=29) harboring MYC-ITD, 46.5% (N=27) with a SNV or indel (MYCSNV/indel) and 2 patients (3.5%) with dual MYC-ITD and SNV. For MYC-ITD, tandem duplications occurred in exon 3 (Max binding domain) with ITD lengths ranging from 252-588 bp. The majority of MYCSNV/indel (77%) were identified at the P72-P78 hotspot with 33.3% (N=9) harboring the P74>L mutation and 18.5% (N=5) having the T73>N mutation. Functional Studies: Given the novelty of the ITD variant, we initially characterized the functional properties of MYC-ITD in vitro. Similar to wild-type (MYCWT), MYC-ITD is localized to the nucleus and requires Max to bind to specific DNA sequences (E-boxes). However, in contrast to MYCWT, MYC-ITD fails to recognize sequences containing a single E-box in vitro, but exhibits higher affinity toward sequences with two or more E-boxes. MYC-ITD is consistently more efficient in activating promoters with multiple E-boxes than MYCWT. Thus, MYC-ITD may possess different DNA-binding and protein-interacting properties, potentially leading to altered transcriptional regulation and biological output. Given the alterations in DNA binding properties, we evaluated the functional consequences of MYC-ITD in our cord blood stem cell/endothelial cell (EC) co-culture system. Normal cord blood stem cells were transduced with MYC-ITD vs. MYCWT and grown in an EC co-culture system. MYC-ITD transduced cord blood stem cells showed significantly higher proliferation compared to MYCWT or control GFP-transduced cells with proliferation advantage of 37-and 45-fold after 14 and 21 days in co-culture, respectively (p<0.001). Clinical Impact: Analysis of cooperating cytomolecular lesions revealed a striking difference between MYC-ITD and MYCSNV/indel. MYC-ITD was highly enriched in core-binding factor (CBF) AML found in 86% (N=25)[(N=18, 62%) with inv(16) and (N=7, 24%) with t(8;21)] (Figure 1A), vs. 26% in the MYCWT cohort and had a paucity of somatic mutations. Conversely, MYCSNV/indel was enriched in NUP98-NSD1 fusions (N=7, 27%), FLT3-ITD (N=10, 38%) and NPM1 mutations (N=9, 33%) (Figure 1A), which was significantly higher than the WT cohort. Patients with MYC-ITD had a morphologic CR rate after course 1 of 92.3% vs. 80% (p=0.249) in patients with MYCSNV/indel with a corresponding relapse rate of 24% and 52% (p=0.046). Lower CR and higher relapse reflects the higher proportion of patients with high-risk lesions (FLT3-ITD, NUP98-NSD1 and WT1) in MYCSNV/indel and favorable CBF in MYCITD. Those with MYC-ITD and MYCSNV/indel had a 5-year event free survival (EFS) of 70% vs. 38.5%, respectively (p=0.018) with a corresponding overall survival (OS) of 76% and 47% (p=0.023) similar to patients with favorable or high risk disease (Figure 1B). Conclusion: Here we define MYC aberrations as a new class of pathogenic variants in childhood AML. We demonstrate functional and clinical characterization of a novel MYC-ITD and contrast this novel variant to that of established pathogenic MYCSNV/indel. We show the high prevalence of co-occurring core-binding factor fusions with MYC-ITD, and high frequency of co-occurring NUP98-NSD1, FLT3-ITD and NPM1 mutations in MYCSNV/indel. Patients with MYC-ITD have superior clinical outcomes while patients with MYCSNV/indel have clinical outcomes similar to high-risk patients, likely due to the associations with the disease associated fusions. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Genomic alterations in a cohort of pediatric acute myeloid leukemia patients at two cancer centers in Colombia

Few studies identifying genomic aspects in pediatric acute myeloid leukemia patients in Latin American countries have been reported. The aim of this study was to identify genomic alterations, clinical characteristics and outcomes in a cohort of pediatric AML patients. This descriptive observational cohort study included patients with confirmed de novo acute myeloid leukemia up to 18 years of age. Cytogenetics and conventional FISH analysis, next-generation sequencing and PCR testing were performed. The correlation of genomic data with treatment response and outcomes were analyzed. Of the 51 patients analyzed, 67.4% had a cytogenetic abnormality and 74.5% had a genetic variant. FLT3 variants (ITD or TKD D835) were found in 27.4%, followed by NRAS (21.6%), KRAS (13.7%) and WT1 and KIT (11.8%). Patients were stratified by risk (66.6% high-risk) after the end of induction. FLT3-ITD was associated with relapse (OR 11.25; CI 1.89–66.72, p 0.006) and NRAS with death during induction (OR 16.71; CI 1.51–184.59, p 0.022). Our study highlights the importance of rapid incorporation of genetic testing in pediatric AML in Colombia, as it directly affects treatment decisions and outcomes. Incorporation of targeted therapies with conventional chemotherapy is an increasingly urgent need in pediatric patients.

High CX3CR1 expression predicts poor prognosis in paediatric acute myeloid leukaemia undergoing hyperleukocytosis.

Paediatric AML patients with hyperleukocytosis have a poor prognosis and higher early mortality. Therefore, more studies are needed to explore relevant prognostic indicators and develop effective prevention strategies for this type of childhood AML. All original data were obtained from the TARGET database. First, we explored meaningful differentially expressed genes (DEGs) between the hyperleukocytosis group and the non-hyperleukocytosis group. Next, we screened and identified valuable target genes using univariate Cox regression, Cytoscape software, and Kaplan-Meier survival curves. Finally, the coexpressed genes, functional networks, and immune-related activities associated with the target gene were deeply analysed by the GeneMANIA, LinkedOmics, GEPIA2021, TISIDB, and GSCA databases. We selected 1229 DEGs between the hyperleukocytosis group and the non-hyperleukocytosis group in paediatric AML patients. Among them, 495 DEGs were significantly linked with the overall survival of paediatric AML patients. Further, we discovered that CX3CR1 was a promising target gene. Meanwhile, we identified CX3CR1 as an independent prognostic predictor. Besides, we showed that CX3CR1 had strong physical interactions with CX3CL1. Additionally, functional network analysis suggested that CX3CR1 and its coexpressed genes modulated immune response pathways. Subsequent analysis found that immune cells with a high median value of CX3CR1 were monocytes, resting NK cells and CD8 T cells. Finally, we observed that CX3CR1 expression correlated with infiltrating levels of immune cells and immune signatures. Elevated CX3CR1 expression may be an adverse prognostic indicator in paediatric AML patients undergoing hyperleukocytosis. Moreover, CX3CR1 may serve as an immunotherapeutic target for AML with hyperleukocytosis in children.

Respiratory Viral Infections in Pediatric Acute Leukemia Patients Presenting with Febrile Neutropenia in a Tertiary Hospital in Ankara, Turkey

Background: The prevalence and roles of respiratory viral pathogens in pediatric acute leukemia patients with febrile neutropenia is not well understood and laboratory tests to detect viral agents are not a routine practice in the investigation of these patients.Patients and methods: The medical records of 50 neutropenic episodes in pediatric acute leukemia patients in the Hacettepe University Children’s hospital, Ankara-Turkey, were reviewed. Blood samples were obtained for blood culture, aspergillus antigen and other routine tests. Nasopharyngeal aspirate samples were collected and transferred to the laboratory in a viral transport medium. Therapy for febrile neutropenia was initiated according to our institution’s protocols.Results: Fifty (50) consecutive febrile neutropenic episodes in 44 pediatric ALL and AML patients were included in the study between 1st October 2009 and 31st August 2010. Microbiologically documented infections were found in 36% of the episodes, clinically documented infections in 16% of the episodes and 48% of the episodes were accepted as Fever of Unknown Origin. Twenty-two percent (22%) of the microbiologically documented infections were due to viral agents, 56 % were due to Gram positive bacteria, 21% were due to Gram negative bacteria (E. coli) and only one episode of fungemia was documented.Conclusions: Fever of Unknown Origin constituted nearly 50% of the febrile neutropenic episodes in this study despite the availability of advanced laboratory diagnostic methods. Among the episodes with microbiologically documented infections, bacterial pathogens were especially common. Presenting complaints like cough and rhinorrhea are not specific to a viral etiology and care should be taken not to miss potentially threatening bacterial pathogens in such episodes.

P464: COMPARED TO CLASSICAL CYTOGENETICS OPTICAL GENOME MAPPING (OGM) DETECTS MULTIPLE ADDITIONAL STRUCTURAL CHROMOSOMAL ABERRATIONS IN PEDIATRIC ACUTE MYELOID LEUKEMIA (AML)

Background: AML is the 2nd most frequently diagnosed blood cancer in children affecting approximately 130 patients annually in Germany. Pediatric AML is a heterogeneous malignancy that has multiple genetic aberrations. This is relevant for classification, prognosis and selection of optimal therapy. To detect these alterations established procedures (karyotyping, FISH, RNA-based techniques) are used with well-known limitations (resolution of karyotyping and FISH, respectively; cell cultivation is necessary to generate metaphases; cost-intensiveness; necessity of experienced and intensively trained staff). OGM is an emerging technique addressing these limitations. Based on extraction of ultra-high weight DNA followed by fluorescent labelling at the sequence CTTAAG a barcode-like pattern of the genomic DNA is created. The DNA strands labelled in this way are stretched and drawn as single ultra-long fragments through nanochannels. The results are translated into molecule maps which are compared to the reference genome (resolution down to 500 bp) allowing the identification of genetic alterations. This method combines high resolution with picturing almost whole chromosomes without cell cultivation. Aims: The aim of this study was to test to what extend OGM might supplement classical cytogenetics (CCG) to detect risk defining genetic aberrations at initial diagnosis in pediatric patients with AML. Methods: We analyzed 24 specimen of pediatric AML, MPAL and bilineage leukemia patients by OGM starting from stored frozen material (bone marrow, peripheral blood) obtained at initial diagnosis. Results of OGM were compared with karyotyping and FISH. Primer walking and breakpoint spanning PCR were used to validate newly detected aberrations by OGM in selected cases. Applying breakpoint-spanning PCR, validated aberrations were used as markers for assessment of minimal residual disease (MRD) in selected cases during AML treatment. Results: Overall, we detected discrepant results between CCG and OGM in 17/24 (70%) cases including 9 cases in which karyotyping detected aberrations which were not found by OGM. However, these aberrations were not relevant for risk stratification. In general, focusing on genetic aberrations important for risk stratification the results between CCG and OGM were concordant in 23/24 (96%) cases. In a single case OGM was able to detect a high-risk aberration which was missed by CCG. In total, 33 previously unknown genetic alterations were identified by OGM. Out of these four newly detected variants (2 deletions, 2 translocations) were validated by PCR. The translocations t(2;12) and t(8,12) both affected gene ETV6 on chr. 12 with different fusion partners (chr. 2: AC064875.1; chr. 8: NSMCE2). In both translocations sequences at the breakpoints were determined. Two deletions affecting genes RNF157 on chr. 17 and MEF2B on chr. 19 were validated. These aberrations had not been described before in pediatric AML. In 2 cases - both without a previously identified MRD marker – the newly detected translocations by OGM were used for MRD monitoring. Summary/Conclusion: OGM considerably expands the range of techniques to optimize the diagnosis of pediatric AML and has much potential to omit limitations of classical cytogenetics. Furthermore, the results will contribute to a better understanding of the leukemogenesis of pediatric AML. In addition, OGM offers the possibility to identify new aberrations which can serve as patient specific MRD markers especially in cases without a previously known MRD marker.