scholarly journals The Molecular Characteristics and Clinical Relevance of NUP98-Other Translocations in Pediatric Acute Myeloid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 36-37
Author(s):  
Eline J.M. Bertrums ◽  
Jenny L. Smith ◽  
Rhonda E. Ries ◽  
Todd A. Alonzo ◽  
Fabiana Ostronoff ◽  
...  
Keyword(s):  
High Risk ◽  
Myeloid Leukemia ◽  
Clinical Characteristics ◽  
Adverse Outcomes ◽  
Clinical Implications ◽  
Pediatric Acute Myeloid Leukemia ◽  
The Past ◽  
Pediatric Aml ◽  
Wt1 Mutation ◽  
Reference Cohort

Background Cytogenetic and molecular aberrations are important prognostic factors in pediatric acute myeloid leukemia (AML). NUP98 translocations with more than 30 different partner genes have been identified in pediatric AML. The 2 most common fusions, NUP98-NSD1 and NUP98-KDM5A, have been shown to have distinct characteristics and are both associated with adverse outcomes. Although NUP98 fusions with less common fusion partners have been identified, the biological and clinical implications of these variants are unknown. Methods To determine the biological and clinical implications of the less common "other" NUP98 translocations (NUP98-X), we evaluated the clinical characteristics and transcriptome and genome sequencing data from 2396 children and young adults with AML within 4 consecutive Children's Cancer Group (CCG) and Children's Oncology Group (COG) trials CCG-2961, AAML03P1, AAML0531 and AAML1031. All NUP98-X translocations were confirmed by RNA sequencing. Results Of the 2396 patients screened, 164 patients (6.8%) had a NUP98 translocation. We identified 20 patients with a NUP98-X fusion (0.83%) and compared them with those with NUP98-NSD1 (n=110, 4.5%), NUP98-KDM5A(n=34, 1.4%), and a reference cohort without NUP98 translocations (n=2232). Translocation partners identified in the NUP98-X group were HOXA9 (n=4), HOXD13 (n=3), PHF15 (n=2), PHF23 (n=2), and single cases of BPTF, BRWD3, DDX10, HMGB3, HOXA13, KAT7, PRRX1, SET and TOP1. Besides the distinct characteristics of NUP98-NSD1 and NUP98-KDM5A, the NUP98-X group showed high inter-patient variance in clinical characteristics compared to our reference cohort. NUP98-X patients showed a clear bimodal age distribution with half of the patients being in the older age category and a similar number in the category <3 years (Figure 1). White blood cell count and blast percentages were in line with those of the reference cohort. We investigated the co-occurrence of common pediatric AML mutations within our cohort (Figure 2). There was a lack of additional driving mutations with the exception of WT1 mutations that are significantly more prevalent in the NUP98-X group compared to the reference cohort (25% vs 8%, p=0.018). NUP98-X patients with a WT1 mutation have a median age of 16.3 years compared to 2.3 years for those without a WT1 mutation. Also, in contrast to NUP98-NSD1 translocated patients, the co-occurrence of FLT3-ITD did not occur in NUP98-X translocated patients. Further, NUP98-X patients had a more varied transcriptome profile than did patients with NSD1 or KDM5A translocations (Smith J, et al. ASH abstract 2020). We evaluated the impact of NUP98-X translocations in response to the initial induction therapy. The morphological complete remission (CR) rate after course 1 was 65% in the NUP98-X cohort versus 76% in the reference cohort (p=0.266). NUP98-NSD1 patients had an inferior CR rate (36%, p<0.001), but the CR rate in NUP98-KDM5A patients was similar (77%) to the reference cohort. Of all NUP98-X patients, 11% underwent stem cell transplantation (SCT), compared to 17% in the reference cohort, 40% in the NUP98-NSD1 and 23% in the NUP98-KDM5A cohort. Outcome analysis for NUP98-X patients demonstrated that despite differences in disease characteristics, they have similar adverse outcomes as patients with NSD1 or KDM5A translocations (Figure 3). Overall survival (OS) at 5 years from diagnosis was 35% compared to 65% in the group without NUP98 translocations (p=0.006, Figure 3). Event-free survival was 35% for NUP98-X patients, compared to 48% for those without NUP98 translocations (p=0.282). These adverse outcome rates are comparable to those reported in studies on high-risk pediatric AML patients. Conclusion NUP98-X translocated pediatric AML patients represent a rare cohort with a high variability in both translocation partners and other clinical characteristics. Despite this heterogeneity, the OS of these patients is comparable to high-risk pediatric AML patients, which justifies a high-risk stratification of these patients and emphasizes the need for developing new treatment strategies. Further research within large patient cohorts is needed to investigate the biologic and clinical characteristics of these rare translocations and potential differences between the different NUP98-X fusion partners. Disclosures Kaspers: AbbVie: Ended employment in the past 24 months; Helsinn Healthcare: Ended employment in the past 24 months; Boehringer Ingelheim: Membership on an entity's Board of Directors or advisory committees; Janssen R&D: Ended employment in the past 24 months. Cooper:Celgene: Other: Spouse was an employee of Celgene (through August 2019).

High BMP2 Expression Is a Poor Prognostic Factor and a Good Candidate to Identify CBFA2T3-GLIS2-like High-Risk Subgroup in Pediatric Acute Myeloid Leukemia

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2583-2583 ◽  
Author(s):  
Yusuke Hara ◽  
Genki Yamato ◽  
Norio Shiba ◽  
Kentaro Ohki ◽  
Myoung-Ja Park ◽  
...  
Keyword(s):  
High Risk ◽  
Myeloid Leukemia ◽  
Gene Mutations ◽  
Fusion Genes ◽  
Gene Expressions ◽  
Poor Prognostic Factor ◽  
Pediatric Acute Myeloid Leukemia ◽  
Expression Levels ◽  
Pediatric Aml ◽  
Induction Failure

Abstract <Background> Recent molecular analyses have identified novel inv(16)(p13.3q24.3)/CBFA2T3-GLIS2 in 13-27% of pediatric acute megakaryoblastic leukemia with non-Down syndrome. Some previous studies reported a poor prognosis of CBFA2T3-GLIS2, and one of them reported that all CBFA2T3-GLIS2-positive patients had high BMP2 expression. BMP2 belongs to the TGF-β family and plays essential roles in the regulation of cell proliferation, differentiation, and motility. Besides, new information about the relationship of BMP2 with oncogenesis has been determined in some cancers. Thus, we examined molecular and clinical significance of high BMP2 expression in pediatric acute myeloid leukemia (AML) to identify whether high BMP2 expression was useful for the detection of "CBFA2T3-GLIS2-like" high-risk subgroup. <Patients and Methods> We analyzed 369 cDNA samples of de novo pediatric AML patients who enrolled in the AML-05 study conducted by Japanese Pediatric Leukemia/Lymphoma Study Group. We examined fusion genes of CBFA2T3-GLIS2, NUP98-JARID1A, RBM15-MKL1, MLL-MLLT3, MLL-MLLT10, NUP98-NSD1, FUS-ERG, DEK-NUP214, RUNX1-RUNX1T1, and CBFB-MYH11, gene mutations of KIT, NRAS, KRAS, WT1, NPM1, MLL-PTD, and FLT3-ITD, and gene expressions of BMP2, PRDM16, and EVI1. Fusion genes and gene mutations were analyzed by PCR and/or RT-PCR, and gene expressions by realtime quantitative PCR. These expression levels were calculated relative to ABL1 expression, and high expression of each gene was defined by ROC analysis. <Results> CBFA2T3-GLIS2 gene fusions were identified in 11 patients (3.0%), all of whom were diagnosed as FAB-M7. Their 4-year overall survival probability (4-pOS) and event-free survival probability (4-pEFS) were significantly poorer than those of CBFA2T3-GLIS2-negative patients (36.4% vs 67.9%, p = 0.003, and 9.1% vs 53.7%, p < 0.001, respectively). Besides, 18 patients (4.9%), including 7 CBFA2T3-GLIS2-positive patients, exhibited high BMP2 expression (BMP2/ABL1 ratio ≥ 1.12). BMP2 expression levels of CBFA2T3-GLIS2-positive patients(range 0.494-3.608, median 1.274) were significantly higher than those of CBFA2T3-GLIS2-negative patients (range 0-3.653, median 0.044) (p < 0.001). Notably, 4-pOS and 4-pEFS of the patients with high BMP2 expression were significantly much lower than those of the patients with low BMP2 expression (25.0% vs 69.3%, p < 0.001, and 16.7% vs 54.3%, p < 0.001, respectively). Age at diagnosis of the patients with high BMP2 expression was significantly lower than that of the patients with low BMP2 expression (median, 2.3 vs 8.3 years, p = 0.047), whereas WBC count was not significantly different between 2 groups (median, 40,850 vs 19,700/µl, p = 0.113). FAB classifications of the patients with high BMP2 expression were as follows: M1 (n = 1), M2 (n = 3), M5a (n = 4), M7 (n = 8), and RAEB-T (n = 2). Cytogenetic and molecular analyses of the patients with high BMP2 expression revealed the presence of CBFA2T3-GLIS2 (n = 7), FUS-ERG (n = 3), MLL-rearrangements (n = 2), RUNX1-RUNX1T1 (n = 1), inv(3)(q21q26.2) (n = 1), t(8;16)(p11.2;p13.3) (n = 1), monosomy 7 (n = 2), NRAS (n = 3), KRAS (n = 1), KIT (n = 1), FLT3-ITD (n = 1), high PRDM16 expression (n = 3), and high EVI1 expression (n = 2). Even if we exclude patients with RUNX1-RUNX1T1 (n = 106) and CBFB-MYH11 (n = 31) from all 369 patients (a total of 232 patients), 4-pOS and pEFS of the patients wtih high BMP2 expression (n = 17, one RUNX1-RUNX1T1-positive patient was excluded) were significantly lower than those of the patients with low BMP2 expression (20.2% vs 56.8%, p < 0.001, and 17.6% vs 45.1%, p = 0.002, respectively). As for the risk stratification, one, 9, and 4 patients were classified into low, intermediate, and high-risk group, respectively, and 4 patients had induction failure. Concerning CBFA2T3-GLIS2-positive patients, all of 3 patients with induction failure had high BMP2 expression, and 5 of 7 patients with high BMP2 expression died, whereas 2 of 4 patients with low BMP2 expression died. <Conclusions> High BMP2 expression was considered as a poor prognostic factor in pediatric AML. When compared with CBFA2T3-GLIS2-negative patients, BMP2 expression levels of CBFA2T3-GLIS2 -positive patients were extremely high, indicating that high BMP2 expression might be a good candidate to identify high-risk CBFA2T3-GLIS2-like patients. Therefore, investigation of BMP2 inhibitors for these patients will be expected. Disclosures No relevant conflicts of interest to declare.

Telomere Length and Telomerase Complex Mutations in Pediatric Acute Myeloid Leukemia

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1482-1482
Author(s):  
Anna M. Aalbers ◽  
Rodrigo T. Calado ◽  
Neal S. Young ◽  
Christian M. Zwaan ◽  
Colin O. Wu ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
High Risk ◽  
Telomere Length ◽  
Carrier Frequency ◽  
Myeloid Leukemia ◽  
Clinical Characteristics ◽  
Leukemic Cells ◽  
Npm1 Mutation ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Abstract 1482 Inherited loss-of-function mutations in the telomerase complex gene TERT have recently been implicated as risk factors for acute myeloid leukemia (AML) in adults. The telomerase complex is expressed in highly proliferative cells, and is responsible for maintaining telomeres, which cap the ends of chromosomes and protect genomic DNA from eroding during cell division. Impaired telomerase function can result in extremely short telomeres, which limits the proliferative capacity of progenitor cells, and can also lead to chromosomal instability, thus predisposing to malignant transformation. In pediatric AML, the frequency of such mutations, and the association of telomere length with cytogenetic, molecular, and clinical characteristics and outcome, are unknown. In a cohort of 168 pediatric AML patients, we determined the frequency of telomerase complex gene mutations and leukemic cell telomere length, and correlated this with prognostic cytogenetic characteristics (inv(16), t(8;21), MLL rearrangements, normal karyotype, other aberrations), molecular aberrations (CEBPA double mutations, NPM1 mutations, FLT3/ITD, WT1 mutations), clinical characteristics, and outcome. No mutations were present in TERC. Three heterozygous variants in TERT, E327D, T726M, and A1062T, were identified in eight of 168 pediatric AML patients (carrier frequency 0.048). In three of six patients carrying A1062T, remission material was available, in which germ-line origin of the variant was confirmed. The variants E327D and T726M were absent, but A1062T was present in a cohort of 406 geographically matched controls (carrier frequency 0.049). Telomerase activity, as determined by TRAP assay in reconstitution experiments, of the novel E327D variant was unaffected, as was the previously published activity of T726M; the earlier reported activity of A1062T was reduced to 60%. Telomere length of leukemic cells was not associated with age, sex, prognostic cytogenetic subgroup, complex karyotype, or expression levels of telomerase and shelterin complex genes. However, patients carrying the high-risk molecular aberration FLT3/ITD had significantly shorter telomeres than did patients with favorable NPM1 mutation or CEBPA double mutations. Telomere length was not associated with overall survival, event-free survival, or cumulative incidence of relapse. We conclude that, in pediatric AML, telomerase complex mutations do not confer a risk for leukemia development, and although short telomeres correlate with the high-risk molecular aberration FLT3/ITD, telomere length of leukemic cells obtained at diagnosis does not correlate with adverse outcome in this pediatric AML cohort. Disclosures: No relevant conflicts of interest to declare.

Molecular Profiling of High-Risk Pediatric Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5250-5250
Author(s):  
Lianna J Marks ◽  
Jennifer A Oberg ◽  
Julia L Glade-Bender ◽  
Susan J Hsiao ◽  
Danielle Pendrick ◽  
...  
Keyword(s):  
High Risk ◽  
Myeloid Leukemia ◽  
Clinical Characteristics ◽  
Molecular Profiling ◽  
Genetic Alterations ◽  
Genomic Profiling ◽  
Gene Fusions ◽  
Ras Pathway ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Background: Several landmark genomic profiling studies have dramatically advanced our understanding of the origin, progression and clonal evolution of adult acute myeloid leukemia (AML) and directly impacted clinical care. However, very little is known about the mutational landscape of pediatric AML, a distinct entity that shares few genetic and clinical characteristics with adult AML. To investigate potential drivers of high-risk pediatric AML, comprehensive genomic profiling was performed on high-risk AML samples as part of a prospective clinical next-generation sequencing program. Methods:Samples obtained from patients with known high-risk features at diagnosis or with refractory or relapsed AML were selected for molecular profiling. Comprehensive testing included whole-exome sequencing (WES) of matched tumor (bone marrow or chloroma tissue) and normal tissue (peripheral blood or buccal swab) samples and transcriptome analysis (RNAseq). Targeted sequencing of 467 cancer-associated genes was used when tumor tissue was limited. Sequencing was performed on Illumina's HiSeq 2500 with 150X and 500X average coverage for WES and targeted sequencing, respectively. Variants were filtered to select alterations in cancer-related genes or genes relevant for patient care. Results:Fifteen patients with AML (mean age 7.7 yrs; range 0.75-19 yrs) met high-risk criteria (high-risk features at diagnosis = 4, relapsed disease = 8, refractory disease = 3) and were selected for profiling. WES and RNAseq were performed on 11 samples, WES only on 3 samples and targeted DNA sequencing on 1 sample. The median number of variants was 60 (range 14- 5950) per case. After filtering, 54 mutations were identified in 35 genes with a mean of 3.6 mutated genes per patient sample (range 0-14); two samples only carried a fusion gene with no other genetic alterations. At least one driver genetic alteration was detected in each patient sample. Thirteen samples carried mutations in at least one gene known to be altered in AML (e.g. IDH1, WT1, TP53, NRAS) (mean, 2; range, 1-6) and 5 samples carried novel mutations in 15 genes not previously implicated in AML (e.g. CARD9, CHD9, Axin1). Mutations in 11 AML related genes were detected in more than one sample including NRAS in 4, TP53 in 3 and KRAS, PTPN11 PHF6, JAK3 in 2 samples each; genes not previously implicated in AML were only mutated in single patients. Of note, mutations in genes encoding members of the RAS pathway occurred in 60% of cases (9/15 samples). RNAseq identified gene fusions in 7/11 samples (63%). Four fusions involving KMT2A and core binding factor genes were also detected by FISH while three fusions were detected by RNAseq only: NUP98-NSD1 in two patients and CBFA2T3-GLIS2 in one patient. Samples carrying driver gene fusions had the lowest number of mutated genes (0-1) compared to samples lacking a gene fusion (1-5 mutated genes), with one exception of a patient with history of infant ALL who later developed KMT2A-AFF1AML with the highest number of mutated genes (n=14). There was no correlation between the number of mutated genes and age, clinical characteristics, initial risk classification at diagnosis or intensity of therapy prior to sequencing. Conclusion:Our study provides an initial overview of the genetic alterations that characterize high-risk, chemo-resistant pediatric AML. Analysis of the data highlights the overall low genetic complexity of high-risk AML despite the aggressive clinical behavior and exposure to intense chemotherapy, including stem cell transplant. Of interest, similar to adult AML, we found that mutations leading to aberrant activation of the RAS pathway were also very frequent in our cohort of pediatric high-risk AML, while genes typically mutated early in the process of leukemogenesis in adult AML, such as NPM1, DNMT3A, FLT3, IDH1, IDH2 were not affected. Such findings suggest that distinct, age-specific mechanisms of leukemogenesis might exist. Furthermore, our data also highlights the important role of RNA sequencing in complementing current standard diagnostic tools, allowing the identification of driver fusion genes in samples for which no other driver event is detected. Larger studies, preferably including diagnostic samples and utilizing broader approaches, are needed to better understand the mechanisms responsible for the initiation and progression of childhood AML. Disclosures No relevant conflicts of interest to declare.

scholarly journals Duplex Sequencing with Patient-Specific Hybrid Capture Panels Reveals Ultra-Low Frequency Measurable Residual Disease in Pediatric Acute Myeloid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 31-32
Author(s):  
Jacob Higgins ◽  
Fang Yin Lo ◽  
Michael J. Hipp ◽  
Charles C. Valentine ◽  
Lindsey N. Williams ◽  
...  
Keyword(s):  
Myeloid Leukemia ◽  
Residual Disease ◽  
Limit Of Detection ◽  
Low Frequency ◽  
Patient Specific ◽  
Pediatric Acute Myeloid Leukemia ◽  
Hybrid Capture ◽  
Pediatric Aml ◽  
Duplex Sequencing ◽  
Measurable Residual Disease

Sensitive and specific detection of measurable residual disease (MRD) after treatment in pediatric acute myeloid leukemia (AML) is prognostic of relapse and is important for clinical decision making. Mutation-based methods are increasingly being used, but are hampered by the limited number of common driver gene mutations to target as clone markers. Additional targets would greatly increase MRD detection power. However, even in cases with many AML-defining mutations, it is the limited accuracy of current molecular methods which establishes the lower bounds of sensitivity. Here we describe an ultrasensitive approach for disease monitoring with personalized hybrid capture panels targeting hundreds of somatic mutations identified by whole genome sequencing (WGS), and using extremely accurate Duplex Sequencing (DS) in longitudinal samples. In a pilot cohort of 13 patients we demonstrate detection sensitivities several orders of magnitude beyond currently available single locus testing or less accurate sequencing. With multi-target panels, overall power for MRD detection is cumulative across sites. For example, if a patient has MRD at a true frequency of 1/30,000, sequencing a single mutant site to 10,000x molecular depth would be unlikely to detect MRD. However, sequencing 10 sites each to 10,000x would effectively total 100,000x informative site depth, increasing power to &gt;95%. However, standard sequencing assays are insufficiently accurate to achieve this theoretical limit of detection (LOD). DS enables accurate detection of individual variants to &lt;10-5 with an error rate &lt;10-7 and, thus, can achieve MRD sensitivities below one-in-one-million. Marrow aspirates were collected from 13 uniformly treated pediatric AML patients at time of diagnosis (TOD), during treatment (end of induction, EOI), in remission (end of therapy, EOT), and at relapse. 9/13 patients relapsed. DNA from TOD was analyzed by WGS. Germline variants were excluded and somatic single nucleotide variants (SNVs) were targeted by a custom probe panel designed for each patient. An average of 170 SNVs were targeted per patient (range 53-200). More than 90% of the SNVs were noncoding. Longitudinal samples were then analyzed with DS, which compares sequences from both strands of each DNA molecule to eliminate technical noise and reveal biological mutation signal with extreme accuracy and sensitivity. A median of 82% of WGS SNVs were validated by DS in the TOD DNA, and the vast majority of those were also present at relapse. Relapsers had more SNVs at diagnosis than non-relapsers. EOT samples were sequenced to an average Duplex molecular depth of 29,400x, with a maximum of 61,283x. The figure below shows time course plots tracking SNVs at diagnosis, EOT and relapse for 2 patients. Among mutations validated in TOD samples, a median of only 8 (5%) were detected per EOT sample (range 0-66 mutations). MRD was detected in 8/9 relapsers. Targeting 1 or even 10 SNVs would therefore have missed MRD in the majority of these patients. Among relapsers, median EOT SNV VAF was 0.069%. The lowest single VAF detected per EOT sample ranged from 0.036% to 0.002%. The presence of an SNV at diagnosis and relapse implies that it must truly be present at EOT, whether or not it is detected. Therefore, if a small minority of leukemic mutations are detected at EOT, the true overall MRD frequency is much lower than the LOD at any single site. In the only relapser where MRD was not detected, targeted SNVs were present at diagnosis and relapse, so additional sequencing depth at EOT would eventually reveal ultra-low frequency mutations. Among patients that did not relapse by the end of the study, median VAF at EOI (the latest time point DNA available) was 0.0258%. Therefore, non-relapsers have a lower median VAF at EOI than relapsers do even later at EOT, potentially indicating very early on that treatment is more successful. This study shows excellent performance of DS-based assays for detecting MRD with patient-specific panels. We have demonstrated that among large panels of validated somatic SNVs present at time of diagnosis, a median of 5% are identified at EOT in eventual relapsers. DS detected MRD in 8/9 patients, and at a median VAF well below the limit of detection of any other sequencing technology. Comprehensive personalized hybrid selection panels coupled with DS represents a powerful option for MRD monitoring in pediatric AML and potentially other cancers. Figure Disclosures Higgins: TwinStrand Biosciences: Current Employment. Lo:TwinStrand Biosciences: Current Employment. Hipp:TwinStrand Biosciences: Current Employment. Valentine:TwinStrand Biosciences: Current Employment. Williams:TwinStrand Biosciences: Current Employment. Radich:TwinStrand Biosciences: Research Funding. Salk:TwinStrand Biosciences: Current Employment.

scholarly journals An Immune Checkpoint-Related Gene Signature for Predicting Survival of Pediatric Acute Myeloid Leukemia

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Feng Jiang ◽  
Xin-Yu Wang ◽  
Ming-Yan Wang ◽  
Yan Mao ◽  
Xiao-Lin Miao ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Immune Checkpoint ◽  
Myeloid Leukemia ◽  
Immune Cell ◽  
Cox Regression ◽  
Secondary Data ◽  
Gene Signature ◽  
Pediatric Acute Myeloid Leukemia ◽  
Pediatric Aml ◽  
Acute Myeloid

Objective. The aim of this research was to create a new genetic signature of immune checkpoint-associated genes as a prognostic method for pediatric acute myeloid leukemia (AML). Methods. Transcriptome profiles and clinical follow-up details were obtained in Therapeutically Applicable Research to Generate Effective Treatments (TARGET), a database of pediatric tumors. Secondary data was collected from the Gene Expression Omnibus (GEO) to test the observations. In univariate Cox regression and multivariate Cox regression studies, the expression of immune checkpoint-related genes was studied. A three-mRNA signature was developed for predicting pediatric AML patient survival. Furthermore, the GEO cohort was used to confirm the reliability. A bioinformatics method was utilized to identify the diagnostic and prognostic value. Results. A three-gene (STAT1, BATF, EML4) signature was developed to identify patients into two danger categories depending on their OS. A multivariate regression study showed that the immune checkpoint-related signature (STAT1, BATF, EML4) was an independent indicator of pediatric AML. By immune cell subtypes analyses, the signature was correlated with multiple subtypes of immune cells. Conclusion. In summary, our three-gene signature can be a useful tool to predict the OS in AML patients.

Apoptosis: A biomarker of high-risk phenotype in pediatric acute myeloid leukemia?

2018 ◽  
Vol 41 (1) ◽  
pp. 141-147 ◽  
Author(s):  
Anudishi Tyagi ◽  
Raja Pramanik ◽  
Radhika Bakhshi ◽  
Sreenivas Vishnubhatla ◽  
Sameer Bakhshi
Keyword(s):  
Acute Myeloid Leukemia ◽  
High Risk ◽  
Myeloid Leukemia ◽  
Pediatric Acute Myeloid Leukemia ◽  
Acute Myeloid

Acute Differentiated Dendritic Cell Leukemia: A New Form of Pediatric Acute Myeloid Leukemia (AML) with MLL Translocations.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3263-3263
Author(s):  
Luca Lo Nigro ◽  
Laura Sainati ◽  
Anna Leszl ◽  
Elena Mirabile ◽  
Monica Spinelli ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Dendritic Cells ◽  
Dendritic Cell ◽  
Myeloid Leukemia ◽  
Fusion Transcript ◽  
Fish Analysis ◽  
Rt Pcr ◽  
Pediatric Acute Myeloid Leukemia ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Background: Myelomonocytic precursors from acute or chronic leukemias can differentiate to dendritic cells in vitro, but leukemias with a dendritic cell immunophenotype are rare, have been reported mainly in adults, and their molecular pathogenesis is unknown. Dendritic cells are classified as Langherans, myeloid and lymphoid/plasmacytoid cells, but leukemias arising from dendritic cells are unclassified in the FAB system. We identified a new entity of pediatric acute myeloid leukemia (AML) presenting with morphologic and immunophenotypic features of mature dendritic cells, which is characterized by MLL gene translocation. Methods and Results: Standard methods were used to characterize the morphology, immunophenotype, karyotype and MLL translocations in 3 cases of pediatric AML. The patients included two boys and one girl diagnosed with AML between 1–6 years old. Their clinical histories and findings included fever, pallor, abdominal and joint pain, adenopathy, hepatosplenomegaly, normal WBC counts but anemia and thrombocytopenia. and no evidence of CNS disease. The bone marrow aspirates were hypocellular and replaced completely by large blasts with irregular nuclei, slightly basophilic cytoplasm, and prominent cytoplasmic projections. There were no cytoplasmatic granules or phagocytosis. Myeloperoxidase and alpha napthyl esterase reactions were negative, excluding FAB M5 AML, and the morphology was not consistent with any standard FAB morphologic diagnosis. The leukemic blasts in all three cases were CD83+, CD86+, CD116+, consistent with differentiated myeloid dendritic cells, and did not express CD34, CD56 or CD117. MLL translocations were identified in all 3 cases. In the first case FISH analysis showed t(10;11)(p12;q23) and RT-PCR identified and a ‘5-MLL-AF10-3’ fusion transcript. In the second case FISH analysis showed t(9;11)(p22;q23) and RT-PCR identified and a ‘5-MLL-AF9-3’ fusion transcript. In the remaining case, the MLL gene rearrangement was identified by Southern blot analysis and RT-PCR showed an MLL-AF9 fusion transcript. The fusion transcripts in all 3 cases were in-frame. Remission induction was achieved with intensive chemotherapy, and all three patients have remained in durable remission for 30–60 months after hematopoietic stem cell transplantation. Conclusions. We have characterized a new pediatric AML entity with features of mature dendritic cells, MLL translocation and an apparently favorable prognosis. The in-frame MLL fusion transcripts suggest that chimeric MLL oncoproteins underlie its pathogenesis. The partner genes in all 3 cases were known partner genes of MLL that encode transcription factors. This study increases the spectrum of leukemias with MLL translocations. Comprehensive morphological, immunophenotypic, cytogenetic and molecular analyses are critical for this diagnosis, and will reveal its frequency and spectrum as additional cases are uncovered.

scholarly journals Distinct Genomic Landscape of Chinese Pediatric Acute Myeloid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 38-38
Author(s):  
Ting Liu ◽  
Jianan Rao ◽  
Wenting Hu ◽  
Yuhan Liu ◽  
Huiying Sun ◽  
...  
Keyword(s):  
Myeloid Leukemia ◽  
Mutation Frequency ◽  
Chinese Patients ◽  
Rna Seq ◽  
Pediatric Acute Myeloid Leukemia ◽  
Genomic Landscape ◽  
Mutation Profile ◽  
Genomic Aberrations ◽  
Pediatric Aml ◽  
Acute Myeloid

Although comprehensive genomic studies have revealed key genomic aberrations in pediatric acute myeloid leukemia (AML), knowledge about Chinese patients remains lacking. Here we report the genomic landscape of Chinese pediatric AML by analyzing the sequence mutations and fusions from transcriptome sequencing (RNA-seq) of 292 cases diagnosed through 2009 to 2018 in Shanghai Children's Medical Center. Informed consents were obtained from parents for all patients. A total of 1831 non-synonymous mutations that were predicted somatic and/or associated to pediatric cancer were identified in 972 genes, including 1597 single nucleotide variants (SNV), 210 insertion/deletion (indels) and 24 internal tandem duplications (ITD), with a median of 6 mutations per case (ranging 0 to 15). Among these abnormalities, 7 aberrations occurred in more than 5% of cases in current cohort, including mutations in KIT (n=54, 18.5%), FLT3 (n=46, 15.8%), NRAS (n=28, 9.6%), CEBPA (n=23, 7.9%), ASXL2 (n=20, 6.8%), KRAS (n=16, 5.5%) and CSF3R (n=15, 5.1%). 444 potential driver variations were identified affecting 66 genes by a combined strategy of mutation pathogenicity and hotspot analysis. Each patient carried a median of one driver mutations per case (ranging 0 to 7). In addition, RNA-seq identified 227 fusions involving 99 genes in 203 out of 292 patients (69.5%), and CBL exon8/9 deletion in 12 patients (4.1%). The most prevalent fusions detected in current cohort included RUNX1-RUNX1T1 (n=82, 28.1%), KMT2A rearrangements (n=45, 15.4%) and NUP98 rearrangements (n=17, 5.8%). Furthermore, novel gene rearrangements were identified in current study, including PTPRA-FUS, ZEB2-ATIC, MSI2-UBE3C (n=1 each). Distinct genomic aberration profile was revealed while comparing our results to the mutation profile characterized in Children's Oncology Group (COG)-National Cancer Institute (NCI) TARGET AML initiative representing the Western pediatric AML cohort. A total of 16 recurrently mutated genes were identified with significantly (two-sided fisher exact test) different mutation frequency. Among these, 7 genes mutated more frequently in Chinese patients, including KIT (18.5% vs 12.8% in Chinese and Western cohort, respectively. p=0.027), ASXL2 (6.8% vs 3.6%, p=0.043), CSF3R (5.1% vs 2.4%, p=0.044), JAK2 (3.4% vs 0.0%, p&lt;0.001), DNM2 (2.7% vs 0.0%, p&lt;0.001), KDM6A (2.1% vs 0.0%, p&lt;0.001) and KMT2C (1.7% vs 0.0%, p=0.003). On the other hand, mutations in FLT3 (15.8% vs 33.0%, p&lt;0.001), NRAS (9.6 vs 30.9%, p&lt;0.001), KRAS (5.5% vs 12.8%, p&lt;0.001), WT1 (2.4% vs 13.6%, p&lt;0.001), NPM1 (2.4% vs 10.3%, p&lt;0.001), PTPN11 (3.8% vs 8.1%, p=0.016), TET2 (1.0% vs 5.2%, p=0.001), CBL sequence mutation (0.0% vs 3.0%, p&lt;0.001) and IKZF1 (0.3% vs 2.7%, p=0.018) were occurred less frequently in Chinese patients. Notably, the RAS signaling pathway as a whole was significantly less frequently mutated in Chinese patients (35.6% vs 71.0%, p&lt;0.001). Furthermore, distinct associations between mutations and FAB subtypes were also observed. For example, NF1 mutations were significantly enriched with subtype M5 in Chinese patients (p=0.003), which was previously reported as co-mutated with CBFB-MYH11 fusion with associated with subtype M4. Survival analysis revealed key genomic aberrations associated with patient prognosis. Variants significantly (log-rank test) associated with better event free survival rate included mutations in CEBPA (p=0.023), NPM1 (p=0.026) and GATA2 (p=0.016). On the other hand, CBFA2T3-GLIS2 (p=0.028), nucleoporin gene family related fusions (including NUP98, NUP214 and NUP153, p&lt;0.001), FUS related fusions (p=0.030), mutations in RUNX1 (p&lt;0.001) and FLT3 (p=0.003) were associated with worse prognosis. A revised risk stratification model was proposed based on these associations observed. Characterized a first comprehensive genomic landscape of Chinese pediatric AML, our results reveal a distinct mutation profile as compared to the Western cohort, in terms of both mutation frequency and patterns of mutation co-occurrence. These findings further reveal the complexity of pediatric AML and highlight the importance of tailored risk stratification for Chinese patients in clinical management. Disclosures No relevant conflicts of interest to declare.

scholarly journals Evaluating the Efficacy of PRMT5 Inhibitor C220 in Patient-Derived Xenograft Models of Pediatric Acute Myeloid Leukemia

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1170-1170
Author(s):  
Anilkumar Gopalakrishnapillai ◽  
Anne Kisielewski ◽  
Yang Zhang ◽  
Bruce Ruggeri ◽  
Peggy Scherle ◽  
...  
Keyword(s):  
Median Survival ◽  
Peripheral Blood ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Publicly Traded ◽  
Pediatric Acute Myeloid Leukemia ◽  
Patient Derived Xenograft ◽  
Pediatric Aml ◽  
Pdx Models ◽  
Acute Myeloid

Abstract Pediatric acute myeloid leukemia (AML) is the deadliest malignancy in children. Despite maximally intensive therapy, inclusive of chemotherapy and hematopoietic stem cell transplant, approximately 20% of patients experience recurrent disease. These patients are also burdened with treatment-related toxicities. Significant improvements in survival in pediatric AML patients necessitate the incorporation of rational targeted therapies with reduced toxicity. Recent studies demonstrate that PRMT5 knockout or inhibition in syngeneic mouse models of KMT2A (MLL) rearranged leukemic cells increased disease latency (Serio et al., Oncogene, 37:450, 2018; Kaushik et al., Leukemia, 32:499, 2018), indicating that PRMT5 is a potential therapeutic target in pediatric AML. However, there are no reports testing the efficacy of PRMT5 in PDX models of pediatric AML. We evaluated the preclinical efficacy of C220, a potent and selective PRMT5 inhibitor (PRMT5i) (Pastore et al., Cancer Discovery, 10:1742, 2020) in three distinct patient-derived xenograft (PDX) models of KMT2A rearranged AML. Based on the model used for the study, 3-5 million AML cells were injected intravenously in NSG-B2m mice. Disease progression was monitored by evaluating the percentage of human cells in mouse peripheral blood at periodic intervals by flow cytometry. At 2-3 weeks post transplantation, when human cells were detectable in peripheral blood, mice were randomly assigned to control (n=4-5) or treatment (n=2) groups. C220 was administered daily p.o. at a dose of 15 mg/kg for seven days with a break of two days. Mice were dosed with 2-3 additional cycles (indicated in the figure by shaded areas) based on their health status. Mice were monitored daily for experimental endpoints that included body condition score and human cell percentages in peripheral blood. Kaplan-Meier survival plots were generated based on the time when mice were euthanized because they met experimental endpoints. Chronic dosing of C220 prolonged survival and delayed the rise in percentage of human AML cells in mouse peripheral blood in all 3 PDX models (Fig. 1B, D, F). In the NTPL-146 model (KMT2A-MLLT1 fusion), a 135-day improvement in median survival was observed with C220-treatment (Fig. 1A). In the DF-2 (KMT2A-MLLT10 fusion) and DF-5 (KMT2A-MLLT4 fusion) models, which showed a faster engraftment compared to NTPL-146, there was a 5.5-day and 18-day improvement in median survival respectively (Fig. 1C, E). The improvement in median survival was statistically significant in all models (*P&lt;0.05). In conclusion, C220 was effective in controlling leukemia progression and improving survival in KMT2A rearranged PDX models of pediatric AML. Figure 1 Figure 1. Disclosures Gopalakrishnapillai: Geron: Research Funding. Zhang: Prelude Therapeutics: Current Employment. Ruggeri: Prelude Therapeutics: Current Employment, Current equity holder in publicly-traded company. Scherle: Prelude Therapeutics: Current Employment, Current equity holder in publicly-traded company. Barwe: Prelude Therapeutics: Research Funding.

scholarly journals Transcriptome Analysis Revealed the Entire Genetic Understanding of Pediatric Acute Myeloid Leukemia with a Normal Karyotype

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2850-2850
Author(s):  
Norio Shiba ◽  
Kenichi Yoshida ◽  
Yuichi Shiraishi ◽  
Shiraishi Yuichi ◽  
Yusuke Hara ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Normal Karyotype ◽  
Gene Rearrangements ◽  
Pediatric Leukemia ◽  
Pediatric Acute Myeloid Leukemia ◽  
Recurrent Mutations ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Background: Pediatric acute myeloid leukemia (AML) comprises approximately 20% of pediatric leukemia, representing one of the major therapeutic challenges in pediatric oncology with a current overall survival rate of less than 70%. The pathogenesis of AML is heterogeneous and can be caused by various chromosomal aberrations, gene mutations/epigenetic modifications, and deregulated/overregulated gene expressions, leading to increased proliferation and decreased hematopoietic progenitor cell differentiation. Recurrent chromosomal structural aberrations [e.g., t(8;21), inv(16), and MLL-rearrangements] have been well established as diagnostic and prognostic markers of AML. Furthermore, recurrent mutations in FLT3, KIT, NPM1, and CEBPA have been reported in both adult and pediatric AML. Recently, massively parallel sequencing enabled the discovery of recurrent mutations in DNMT3A, TET2, and IDH, which are clinically useful for the prediction of the prognosis. However, these mutations are rare in pediatric AML, suggesting that other genetic alterations exist in pediatric AML. In contrast, recent reports have described NUP98-NSD1 fusion as an adverse AML prognostic marker and PRDM16 (also known as MEL1) as the representative overexpressed gene in patients harboring NUP98-NSD1 fusion. Intriguingly, PRDM16 overexpression occurs in nearly one-quarter of all children, with AML involving NUP98-NSD1-negative patients. Moreover, this overexpression is enriched in specimens with other high-risk lesions (e.g., FLT3-ITD, NUP98-NSD1, and MLL-PTD). Patients and Methods: To reveal a complete registry of gene rearrangements and other genetic lesions in pediatric AML with a normal karyotype, we performed transcriptome analysis (RNA sequencing) of 61 of 70 de novo pediatric AML patients with a normal karyotype using Illumina HiSeq 2000. We could not perform RNA sequencing in nine patients because of a lack of RNA quantity or quality. Among the 70 AML patients with a normal karyotype, 33 patients overexpressed PRDM16, which was found to be strongly associated with a poor prognosis in our previous studies. All patients were enrolled and treated with AML-05 in the study conducted by the Japan Pediatric Leukemia/Lymphoma Study Group (JPLSG). We also analyzed the known genetic mutations associated with these patients using the data derived from RNA sequencing. Results: A total of 144 candidate gene rearrangements, which were not observed in normal samples, were identified in 51 of 61 samples. Many of the recurrent gene rearrangements identified in this study involved previously reported targets in AML, including NUP98-NSD1, NUP98-JARID1A, CBFA2T3-GLIS2, MLL-MLLT10, and MLL-MLLT3. However, several gene rearrangements were newly identified in the current study, including MLL-SEPT6, HOXA10-HOXA-AS3, PRDM16-SKI, and CUL1-EZH2. We have also performed the validation of these novel gene rearrangements using Sanger sequencing. Most of these gene rearrangements were found in patients with a high expressionof PRDM16. In contrast, CEBPA mutations were frequently observed in patients with a low expression of PRDM16. Known gene alterations, such as FLT3-ITD and MLL-PTD, and mutations of the RAS, KIT, CEBPA, WT1, and NPM1genes were also detected using RNA sequencing. Conclusion: RNA sequencing unmasked a complexity of gene rearrangements and mutations in pediatric AML genomes. Our results indicate that a subset of pediatric AML represents a discrete entity that could be discriminated from adult counterparts, regarding the spectrum of gene rearrangements and mutations. In the present study, we identified at least one potential gene rearrangement or driver mutation in nearly all AML samples, including some novel fusion genes. These findings suggest that gene rearrangements in conjunction with mutations also play essential roles in pediatric AML. Disclosures Ogawa: Kan research institute: Consultancy, Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

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