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.

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.

scholarly journals The Clinical Features and Prognostic Impact of PRDM16 gene Expression in Adult Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5228-5228
Author(s):  
Genki Yamato ◽  
Hiroki Yamaguchi ◽  
Hiroshi Handa ◽  
Norio Shiba ◽  
Satoshi Wakita ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Risk Group ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Prognostic Impact ◽  
Pediatric Aml ◽  
Prdm16 Gene ◽  
Acute Myeloid

Abstract Background Acute myeloid leukemia (AML) is a complex disease caused by various genetic alterations. Some prognosis-associated cytogenetic aberrations or gene mutations such as FLT3-internal tandem duplication (ITD), t(8;21)(q22;q22)/RUNX1-RUNX1T1, and inv(16)(p13q22)/CBFB-MYH11 have been found and used to stratify the risk. Numerous gene mutations have been implicated in the pathogenesis of AML, including mutations of DNMT3A, IDH1/2, TET2 and EZH2 in addition to RAS, KIT, NPM1, CEBPA and FLT3in the recent development of massively parallel sequencing technologies. However, even after incorporating these molecular markers, the prognosis is unclear in a subset of AML patients. Recently, NUP98-NSD1 fusion gene was identified as a poor prognostic factor for AML. We have reported that all pediatric AML patients with NUP98-NSD1 fusion showed high expression of the PR domain containing 16 (PRDM16; also known as MEL1) gene, which is a zinc finger transcription factor located near the breakpoint at 1p36. PRDM16 is highly homologous to MDS1/EVI1, which is an alternatively spliced transcript of EVI1. Furthermore, PRDM16 is essential for hematopoietic stem cell maintenance and remarkable as a candidate gene to induce leukemogenesis. Recent reports revealed that high PRDM16 expression was a significant marker to predict poor prognosis in pediatric AML. However, the significance of PRDM16 expression is unclear in adult AML patients. Methods A total of 151 adult AML patients (136 patients with de novo AML and 15 patients with relapsed AML) were analyzed. They were referred to our institution between 2004 and 2015 and our collaborating center between 1996 and 2013. The median length of follow-up for censored patients was 30.6 months. Quantitative RT-PCR analysis was performed using the 7900HT Fast Real Time PCR System with TaqMan Gene Expression Master Mix and TaqMan Gene Expression Assay. In addition to PRDM16, ABL1 was also evaluated as a control gene. We investigated the correlations between PRDM16 gene expression and other genetic alterations, such as FLT3-ITD, NPM1, and DNMT3A, and clarified the prognostic impact of PRDM16 expression in adult AML patients. Mutation analyses were performed by direct sequence analysis, Mutation Biased PCR, and the next-generation sequencer Ion PGM. Results PRDM16 overexpression was identified in 29% (44/151) of adult AML patients. High PRDM16 expression correlated with higher white blood cell counts in peripheral blood and higher blast ratio in bone marrow at diagnosis; higher coincidence of mutation in NPM1 (P = 0.003) and DNMT3A (P = 0.009); and lower coincidence of t(8;21) (P = 0.010), low-risk group (P = 0.008), and mutation in BCOR (P = 0.049). Conversely, there were no significant differences in age at diagnosis and sex distribution. Patients with high PRDM16 expression tended to be low frequency in M2 (P = 0.081) subtype, and the remaining subtype had no significant differences between high and low PRDM16 expression. Remarkably, PRDM16 overexpression patients were frequently observed in non-complete remission (55.8% vs. 26.3%, P = 0.001). Patients with high PRDM16 expression tended to have a cumulative incidence of FLT3-ITD (37% vs. 21%, P = 0.089) and MLL-PTD (15% vs. 5%, P = 0.121). We analyzed the prognosis of 139 patients who were traceable. The overall survival (OS) and median survival time (MST) of patients with high PRDM16 expression were significantly worse than those of patients with low expression (5-year OS, 17% vs. 32%; MST, 287 days vs. 673 days; P = 0.004). This trend was also significant among patients aged <65 years (5-year OS, 25% vs. 48%; MST, 361 days vs. 1565 days, P = 0.013). Moreover, high PRDM16 expression was a significant prognostic factor for FLT3-ITD negative patients aged < 65 years in the intermediate cytogenetic risk group (5-year OS, 29% vs. 58%; MST, 215 days vs. undefined; P = 0.032). Conclusions We investigated the correlations among PRDM16 expression, clinical features, and other genetic alterations to reveal clinical and prognostic significance. High PRDM16 expression was independently associated with non-CR and adverse outcomes in adult AML patients, as well as pediatric AML patients. Our finding indicated that the same pathogenesis may exist in both adult and pediatric AML patients with respect to PRDM16 expression, and measuring PRDM16 expression was a powerful tool to predict the prognosis of adult AML patients. Disclosures Inokuchi: Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria; Celgene: Honoraria; Pfizer: Honoraria.

The Prognosis of Karyotypic Subgroups in Pediatric Acute Myeloid Leukemia Depends on the Alterations of KIT, MLL and FLT3 Genes: A Report from Japanese Childhood AML Cooperative Study Group.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2281-2281
Author(s):  
Akira Shimada ◽  
Tomohiko Taki ◽  
Ken Tabuchi ◽  
Ryoji Hanada ◽  
Akio Tawa ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Poor Prognosis ◽  
Tandem Duplication ◽  
Normal Karyotype ◽  
Genetic Alterations ◽  
Kras Mutations ◽  
Childhood Aml ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Karyotypic abnormalities are associated with a prognosis of acute myeloid leukemia (AML). However, there are some patients who had poor prognosis among patients with the same karyotypic abnormalities. Recently, it is revealed that alterations of the genes including tyrosine kinases, lead to poor prognosis in AML. Genetic alterations associated with a poor prognosis remain to be clarified in karytotypic subgroups of AML. We performed the mutation analysis of FLT3, MLL, KIT, RAS and NPM in 158 pediatric AML patients who were enrolled in Japanese Childhood AML Cooperative Treatment Protocol, AML99, including 33 with normal karyotype, 46 with t(8;21), 7 with inv(16), 20 with 11q23 translocations, 13 with t(15;17), 10 with Down syndrome (DS) FAB-M7 and 29 other karyotypic abnormalities. In the 33 patients with normal karyotype, 9 FLT3-internal tandem duplication (ITD), 2 FLT3-D835 mutation (D835Mt), 8 MLL-partial tandem duplication (PTD), 2 KIT, 2 NRAS and 3 KRAS mutations were identified. FLT3-ITD and MLL-PTD were associated with a poor prognosis. Notably, NPM gene mutation was not identified in these patients. In the 46 patients with t(8;21), 2 FLT3-ITD, 1 D835Mt, 4 MLL-PTD, 8 KIT, 4 NRAS and 5 KRAS mutations were found. KIT mutations were associated with a poor prognosis. In the 7 patients with inv(16), 2 FLT3-D835Mt and 1 KIT mutations were identified. Only one patient with KIT mutation relapsed. In the 20 patients with 11q23 translocations, 1 D835Mt and 5 MLL-PTD were identified. MLL-PTD was associated with a poor prognosis in patients with 11q23 translocations. In the 13 patients with t(15;17), 3 FLT3-ITD and 3 D835Mt were found. FLT3-ITD was not associated with a poor prognosis. In the 10 patients with DS-M7, KIT and KRAS mutations were found in each one patient, showing no prognostic significance. In the 29 patients with other karyotypic abnormalities, 6 FLT3-ITD, 2 D835Mt, 4 MLL-PTD, 0 KIT, 2 NRAS and 2 KRAS mutations were found. FLT3-ITD and MLL-PTD were associated with a poor prognosis. Fifteen patients (9.5%) who had alterations of 2 of these 4 genes showed a poor prognosis. RAS gene mutations were found in 26 (16.5%) of 158 patients, but were not associated with the prognosis. These results suggest that a new different therapeutic strategy for the patients with these gene alterations in each subgroup, for example KIT mutations in t(8;21)-patients and MLL-PTD in patients with 11q23 translocation, is needed to improve the prognosis of pediatric AML.

FLT3, NPM1 and MLL Mutations Help Risk Stratification in Pediatric Acute Myeloid Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1574-1574
Author(s):  
Shuhong Shen ◽  
Yin Liu ◽  
JingYan Tang ◽  
Long-Jun Gu
Keyword(s):  
Acute Myeloid Leukemia ◽  
Risk Stratification ◽  
Myeloid Leukemia ◽  
Tandem Duplication ◽  
De Novo ◽  
Genetic Alterations ◽  
Npm1 Mutation ◽  
De Novo Aml ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Abstract 1574 Poster Board I-600 Introduction Acute myeloid leukemia (AML) is a heterogeneous disease which harbors various genetic alterations. Among theses genetic events, Mutations of FLT3, NPM1, MLL and other genes often predict prognosis, particularly in cases cytogenetic normal (CN-AML). Could these be criteria for risk stratification in Pediatric AML ? Patients and Methods 155 cases of de novo AML were diagnosed routinely according to morphology, immunology, cytogenetics, and molecular biology examination on bone marrow (BM) aspirates between Jan. 2002 and Dec. 2008. All patients received chemotherapy according to the AML-XH-99 protocol, which consist of Daunorubicin, Cytosine arabinoside, Etoposide, Homoharringtonine. For acute promyelocytic leukemia, all-trans retinoic acid and Arsenic trioxide were also included. Meanwhile, total RNA of leukemic cells form all diagnostic BM samples were extracted, and then reverse transcribed. MLL partial tandem duplication (MLL/PTD) fusion transcripts were screened by real-time quantitative polymerase chain reaction. FLT3 internal tandem duplication (FLT3/ITD), FLT3 tyrosine kinase domain mutation (FLT3/TKD) and NPM1 mutation were examined by High resolution melting analysis. Results Of the 155 children with de novo AML, 121(78.1%) had received chemotherapy for more than one week with data available for analysis. Among them, 55(45.5%) was cytogenetically normal (CN-AML). In this total cohort of patients 49(27.09%) had FLT3/ITD (32.70% in CN-AML), 14 (9.03%) had FLT3/TKD (7.30% in CN-AML), 62 (40%) had NPM1 mutation (49% in CN-AML), and additional 8 (5.16%) had MLL/PTD (5.50% in CN-AML). In this cohort of patients 98 (63.22%) had at least one mutation. The clinical outcomes were listed in table 1. Generally, patients with FLT3 mutation (ITD or TKD mutation) usually have worse results after chemotherapy, as reported previously by other researchers. Meanwhile, NPM1 mutations usually predict better prognosis in our cohort of AML patients. MLL/PTD always predicts the worst outcome in AML as other MLL rearrangements in leukemia. Among CN-AML patients, 5-year EFS and OS were similar to whole cohort of patients according to those mutations. Cox regression analysis in a univariate model revealed that the presence of FLT3/ITD and NPM1 was significant prognostic factor of EFS, (P<0.05). We therefore proposed a molecular-risk classification of pediatric AML patients based on the data we got in this study. For the newly classified groups of low, medium and high risk groups, EFS rate was 62.03%±8.42%, 45.42%±4.52%, and 14.85%±2.99%, respectively, P=0.00. CRD for the 3 groups was 27.69±21.34 months, 22.62±19.64 months, 13.26±11.95 months, respectively, p=.022. Our results indicate that combinations of these couple of molecular events may be the useful tool for further classify AML in children. Disclosures No relevant conflicts of interest to declare.

Heterogeneity in Infants with Acute Myeloid Leukemia: Retrospective Analysis of a Japanese Nationwide Survey

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1477-1477
Author(s):  
Akira Shimada ◽  
Daisuke Tomizawa ◽  
Akitoshi Kinoshita ◽  
Kazuko Hamamoto ◽  
Ichiro Tsukimoto ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Survival Rate ◽  
Retrospective Analysis ◽  
Myeloid Leukemia ◽  
Genetic Alterations ◽  
Fish Analysis ◽  
Prognostic Impact ◽  
Hematopoietic Stem ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Abstract 1477 Introduction: When compared to older patients, infants with acute leukemia exhibit distinct cytogenetic features, such as higher prevalence of MLL gene rearrangement (MLL-R), and are known to have higher vulnerability to intensive cytotoxic therapy, such as hematopoietic stem cell transplantation. In contrast to acute lymphoblastic leukemia (ALL), there have been few reports on acute myeloid leukemia (AML) in infants. To develop more appropriate therapeutic strategies for infants with AML, it is necessary to elucidate the distinct clinical features of this subgroup. We therefore performed a retrospective analysis on infant AML in Japan. Patients: Infants with AML, aged less than 1 year at diagnosis, registered in any of the 6 Japanese AML clinical trials between 1991 and 2010 (TCCSG M91-13, TCCSG M96-14, AML99, CCLSG9805, CCLSG9805RE, and JPLSG AML-05) were included in this study. Patients with Down syndrome were excluded. Results: A total of 122 infant AML patients were included in the present analysis, which comprised approximately 10% of all pediatric AML patients. The most frequent FAB classification type was M5 (28.7%), followed by M7 (22.9%) and M4 (10.8%). About 30% of patients had 11q23 abnormalities/MLL -R, but there was no impact on prognosis. Several cases with normal karyotype were revealed to be MLL -R on FISH analysis or on MLL -fusion chimeric transcript analysis by RT-PCR. t(8;21), inv(16) and t(15;17) cases were very rare among the infant cohorts. Furthermore, 7.8% had t(1;22)(p13;q13), and 2.5% had t(7;12)(q36;p13). Genetic mutation results could be obtained in 11 cases in the AML99 study; only one case each was confirmed to have NRAS, KRAS or KIT gene mutation. No cases with FLT3-ITD were detected among the 11 cases in the AML99 or the 44 cases in the AML-05 study. Survival rate varied based on treatment received; 5-year OS rate was 58.3% to 71.4%, and 5-year EFS rate was 49.4% to 64.2%. Discussion: Survival rate in infant AML was identical to that in older pediatric AML. However, there was a possible underestimation of MLL -R patients based on sole chromosome analysis; the prevalence of MLL -R was less than 50% in infant AML patients, without any prognostic impact. Other well-known genetic alterations in pediatric AML also had no effect on outcome of infant AML. Infant AML is a heterogeneous subgroup of pediatric AML, and further studies, as well as novel biomarkers, will be necessary to fully understand its biology. Disclosures: No relevant conflicts of interest to declare.

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 &lt;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&lt;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).

Rearrangements in Nucleoporin Family of Genes in Childhood Acute Myeloid Leukemia: A Report from Children Oncology Group and NCI/COG Target AML Initiative

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 169-169
Author(s):  
Fabiana Ostronoff ◽  
Rhonda E. Ries ◽  
Robert B. Gerbing ◽  
Marco A Marra ◽  
Ma Yussanne ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Poor Prognosis ◽  
Genetic Alterations ◽  
Inverse Association ◽  
Post Induction ◽  
Asian Descent ◽  
Pediatric Aml ◽  
The Impact ◽  
Acute Myeloid

Abstract Genetic alterations in the Nucleoporin (NUP) family of genes are involved in myeloid leukemogenesis and are associated with poor prognosis. We previously showed that NUP98-NSD1 is prevalent in acute myeloid leukemia (AML) and is highly associated with FLT3-ITD and dismal outcome. As genetic alterations in the NUP family are frequently cryptic by conventional karyotyping, their incidence has been underestimated. The COG/NCI TARGET AML initiative has performed comprehensive genome-wide characterization of diagnostic specimens from 200 pediatric AML cases in order to identify novel genetic lesions with prognostic and therapeutic significance. The interrogation of the whole genome and RNA sequencing data generated by this initiative identified numerous fusion transcripts involving the NUP family of genes, including NUP98-NSD1, NUP98-KDM5A, NUP98-HOXA9, NUP98-HMG3, NUP98-HOXD13, NUP98-PHF23, NUP98-BRWD3, CLINT-NUP98 and DEK-NUP214. All computationally identified NUP fusions were verified by orthogonal methodology and high-throughput screening assay was developed for frequency determination. The verified NUP fusions were screened in children treated on COG AAML0531 and AAML03P1 to define their prevalence, clinical characteristics and association with clinical outcome. The impact of NUP fusions was initially evaluated in patients with cytogenetically normal AML (CN-AML). NUP fusions were observed in 14.5% (35 of 242) patients: NUP98-NSD1 (N=21), DEK-NUP214 (N=3), NUP98-HMG3 (N=3), NUP98-HOXD13 (N=2), NUP98-PHF23 (N=2) and NUP98-KDM5A (N=4). The NUP fusions NUP98-BRWD3, NUP98-HOXA9 and CLINT-NUP98 were not found in CN-AML patients. Demographics and disease characteristics of CN-AML patients with and without NUP fusions were compared. Although patients of Asian descent comprised only 7% of the study population, they harbored significantly higher number of NUP fusions (29% vs 5%, P =0.002). Among those of Asian descent with CN-AML, 35% harbored a NUP fusion. We also noted an inverse association between NUP fusions and African-Americans where NUP fusions were not identified in any of African-American patients (P =0.031). NUP fusions were correlated with other common mutations in AML. NPM1 (9% vs 28%, P =0.007) and CEBPA (6% vs 19%, P =0.06) were rare in patients with NUP fusions, whereas FLT3/ITD (62% vs 34%, P =0.002) and WT1 (32% vs 8%, P <0.001) were significantly more prevalent in patients harboring NUP fusions. Patients with NUP fusions had a significantly lower complete remission (CR) rate (53% vs. 77%, P =0.004) and 5-year event free survival (EFS, 32% vs 53%, P =0.003) than those without N UP fusions. Given the high co-occurrence of NUP fusions and FLT3-ITD, we investigated the prevalence and clinical correlation of NUP fusions in all FLT3-ITD-positive patients. The prevalence of NUP fusions in FLT3-ITD patients was 26% (43 of 164). The CR rate was lower in patients co-expressing the NUP fusion and FLT3-ITD (40% vs 71%, P <0.001) than in those with FLT3-ITD alone. In addition, minimal residual disease (MRD) was more common in patients co-expressing NUP fusions and FLT3-ITD (68% vs 42%, P =0.008) than in those with FLT3-ITD alone. Finally, patients co-expressing FLT3-ITD and NUP fusions had a 5-year EFS of 28% vs 35% (P =0.093) for those with FLT3-ITD only. Next, we investigated the prevalence of NUP fusions in specific cytogenetic groups and found that NUP fusions were rare in patients with core binding factor and were not observed in patients with MLL rearrangements. In this study we report on the discovery, verification and frequency validation of NUP fusions, a new class of genetic alterations in AML. We demonstrate that NUP fusionsare common in pediatric patients and patients with CN-AML harboring NUP fusions have poor outcome and are more likely to have post-induction MRD than those without thesefusions. Furthermore, there is a high co-occurrence of FLT3-ITD and NUP fusions and patients harboring both genetic lesions have a lower CR rate and high post-induction MRD than those with FLT3-ITD alone. NUP fusions define a new subgroup of pediatric AML patients with an overall poor prognosis. AML harboring NUP fusions likely share similar mechanisms of leukemogenesis and targeting these genetic lesions will likely improve outcome in a significant subset of pediatric AML patients. Disclosures No relevant conflicts of interest to declare.

Uncommon cytogenetic abnormalities identifying high-risk acute myeloid leukemia in children

2020 ◽  
Vol 16 (33) ◽  
pp. 2747-2762
Author(s):  
Riccardo Masetti ◽  
Salvatore Nicola Bertuccio ◽  
Vanessa Guidi ◽  
Sara Cerasi ◽  
Annalisa Lonetti ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
High Risk ◽  
Myeloid Leukemia ◽  
Large Scale ◽  
Risk Groups ◽  
Prognostic Impact ◽  
Treatment Protocols ◽  
Genomic Landscape ◽  
Pediatric Aml ◽  
Acute Myeloid

Pediatric acute myeloid leukemia (AML) represents an aggressive disease and is the leading cause of childhood leukemic mortality. The genomic landscape of pediatric AML has been recently mapped and redefined thanks to large-scale sequencing efforts. Today, understanding how to incorporate the growing list of genetic lesions into a risk stratification algorithm for pediatric AML is increasingly challenging given the uncertainty regarding the prognostic impact of rare lesions. Here we review some uncommon cytogenetic lesions to be considered for inclusion in the high-risk groups of the next pediatric AML treatment protocols. We describe their main clinical characteristics, biological background and outcome. We also provide some suggestions for the management of these rare but challenging patients and some novel targeted therapeutic options.

scholarly journals Genomic and Transcriptomic Characterization of Adult and Pediatric Relapsed Acute Myeloid Leukemia Reveals Novel Therapeutic Targets

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 37-38
Author(s):  
Svea Stratmann ◽  
Sara A Yones ◽  
Jitong Sun ◽  
Aron Skaftason ◽  
Markus Mayrhofer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Gene Expression Analysis ◽  
Gene Fusions ◽  
Rna Seq ◽  
Differential Gene ◽  
Pediatric Aml ◽  
Acute Myeloid ◽  
Novel Therapeutic

Acute myeloid leukemia (AML) is the overall most common form of acute leukemia, characterized by a high relapse frequency and low long-term survival rate especially for adults. Even though children with AML have a better prognosis than adults, patients with recurrent AML - independent of age - show poorer overall survival, accelerated disease progression and they often do not respond to conventional treatment. Therefore, a more personalized treatment approach is required to prolong event free survival (EFS) and expand treatment options for relapse and primary resistant (R/PR) AML patients. During the last decade, AML research has largely been focused on improving diagnostic and prognostic tools in AML by investigating data derived from whole genome- and whole exome sequencing (WGS and WES, respectively), gene panels or differential expression analyses of individual genes and gene-fusions. Nevertheless, studies on relapsing AML incorporating WGS data are rare, although necessary to investigate the full repertoire of genetic aberrations underlying AML progression and therapy resistance. To this end, we applied a combination of WGS (WES for a subset of cases) and RNA-seq of longitudinal samples from 48 adult and 21 pediatric R/PR AML cases from the Nordic countries. These comprised tumor samples collected at diagnosis (n=49) and relapse (n=76), as well as PR specimens (n=6). Normal bone marrow (BM) derived stromal cells were cultivated from leukemic BM as a source of patient-matched constitutional DNA, while CD34+ BM cells from five healthy donors were used as a source of normal control RNA. Our findings reveal recurrent relapse specific mutations in CSF1R (2.9% of relapse cases) not previously reported in de novo AML, suggesting the use of receptor tyrosine kinase inhibitors as a novel therapeutic option for a subset of AML relapse cases. Further, we report specific differences in the mutational spectrum between adult and pediatric R/PR AML. In adults, we detected higher mutational frequencies of, for instance, ARID1A (6.3%), H3F3A (6.3%) and MGA (10.4%) compared with previous AML studies of only specimens from initial diagnosis, while these mutations were not seen in pediatric AML. In contrast, internal tandem duplications (ITDs) in UBTF were detected solely in pediatric relapsing AML (n=3 [14.3%]). IKZF1 was more frequently mutated in pediatric R/PR AML (14.3%) than previously reported (0.5-2.7%; Bolouri et al., Nat Med. 2018; Shiba et al., Br J Haematol, 2016). Also, differential gene expression analysis identified IKZF1 as downregulated in pediatric chemotherapy resistant samples in comparison with treatment responsive counterparts, independent of IKZF1 mutational status. By investigating differential gene expression patterns of longitudinal samples, we found lower expression of the complement inhibitor CR1/CD35 at relapse compared to their patient matched diagnostic samples in both adults and children. Additionally, IL1R1, encoding a key regulator of inflammation and immune response, was upregulated in both adult and pediatric diagnosis specimens from cases with short EFS, indicating a pronounced role of chronic inflammation during disease progression and AML cell survival. Finally, our findings reveal overexpression of GLI2 and SGMS2 among samples associated with short EFS. Overexpression of these genes may prevent excessive cell proliferation while increasing stemness and dormancy, leading to increased chemotherapy resistance and shorter EFS. Taken together, our results emphasize the advantage of applying a combination of WGS and RNA-seq, to be able to gain a more complete picture of alterations, including mutations, gene fusions and copy number alterations combined with gene expression analysis, when attempting to characterize AML at relapse. This is the first study of both adult and pediatric AML incorporating WGS and RNA-seq analyses on sequential AML samples. Knowledge gathered from this study has provided critical new insights into the biologic basis of this complex disease and will hopefully help to pave the way for improved and individualized treatment strategies. Disclosures No relevant conflicts of interest to declare.

Prevalence & Prognosis Value of TET2 Gene Polymorphisms in Childhood Acute Myeloid Leukemia in Taiwan

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1551-1551 ◽  
Author(s):  
Meng-Ju LI ◽  
Yung-Li Yang ◽  
Shiann-Tarng Jou ◽  
Meng-Yao Lu ◽  
Hsiu-Hao Chang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Myeloid Leukemia ◽  
Clinical Characteristics ◽  
Event Free Survival ◽  
Free Survival ◽  
Kaplan Meier ◽  
Childhood Aml ◽  
Pediatric Aml ◽  
Gene Alterations ◽  
Acute Myeloid

Abstract Abstract 1551 Introduction: Acute myeloid leukemia (AML) is a phenotypically and genetically heterogeneous disease, accounts for 10% of childhood leukemia. The prognosis of children with AML has improved greatly over the past 30 years, and the Taiwan Pediatric Oncology group (TPOG) AML 97A and B protocols had been designed and explored in 1997 for the treatment of AML in Taiwan with complete remission (CR) and overall survival (OS) rates as high as 80–90% and 50–60%. In recent years, molecular research identified an increasing panel of genetic markers in AML, enhancing better risk stratification, modify treatment strategy and improving prognosis. The tet oncogene family member 2 (TET2) gene, a candidate tumor suppressor gene, and the mutations are found in adult AML with prevalence of around 10–20% and is associated to prognosis. However, the report in childhood AML is limited. Here, we assess the prevalence of TET2 gene alterations in childhood AML and to identify its association with prognosis. Method: We enrolled children who were diagnosed AML and visited national Taiwan university hospital between Jan, 1997 to June, 2010. The patients with APL (acute promyeloid leukemia) were excluded due to different treatment protocol. All the children were treated by TPOG AML 97 protocol. The induction therapy consist two courses of cytarabine (Ara-C) and idarubicin (IDR). Patients who achieved CR subsequently received four courses of consolidation therapy consisted of high-dose Ara-C and mitoxantrone or etoposide. The clinical characteristics, such as age, sex, laboratory data, cytogenetics information, relapse, survival time were all collected from TPOG database. DNA was isolated from bone marrow cells at diagnosis and sequence analysis was carried out for TET2 gene. The all data of eligible cases will be collected and analyzed for estimating EFS (event free survival), and OS (overall survival). Survival curves will be estimated by the Kaplan-Meier method. Comparisons were made by Chi-square test for binary variables and t test for continuous variables. For all analyses, the P-values were two-tailed, and a P < 0.05 was considered statistically significant. Results: Total of 56 pediatric AML patients were enrolled. The mean age is 9.07 ± 5.4 (0.01∼17.54) years. There are 34 (60.7%) males. Twenty-four (42.9%) patients had relapse and the overall survival rate is 44.6% (25/56). In this study, there was no nonsense or frameshift mutation, which is frequently identified in adult AML. Total 44 patients (78.6%) present TET2 SNP (single nucleotide polymorphism) and the details are listed in Table 1. There are 18 SNP, and 3 of them (rs72224084, rs58201766, rs59046770) are located in intron. Other 15 SNP are all located in exon. Most of them are located in exon 3 (27 events) and exon 11 (32 events). Only SNP rs3733609 is located in exon 9, and this is synonymous mutation. There are 9 SNP located in exon are not reported in reference yet. Among these, 4 SNP is synonymous mutation. All SNPs are heterozygous, except 4 SNP are homozygous, which are all SNP rs2454206 (I1762V). The clinical characteristics between patients with or without TET2 SNP, including sex, age, white count while diagnosis, chromosome abnormalities, death and relapse are not different between this 2 groups. Kaplan–Meier survival analysis is used to test the correlation between TET2 gene polymorphism to prognosis, including overall survival and event free survival. There was no difference. Conclusion: As we know, we are the first group to publish TET2 gene alterations in childhood AML in Asian. We conclude the prevalence of TET2 mutations in pediatric AML patients is far lower than in adults and the TET2 polymorphisms are not associated with prognosis. Disclosures: No relevant conflicts of interest to declare.

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