scholarly journals Allele-Specific Expression of GATA2 in AML with CEBPA Biallelic Mutations

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1235-1235
Author(s):  
Roger Mulet-Lazaro ◽  
Stanley van Herk ◽  
Claudia Erpelinck-Verschueren ◽  
Mathijs A. Sanders ◽  
Eric Bindels ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Regulatory Elements ◽  
P Value ◽  
Specific Expression ◽  
Allele Specific ◽  
De Novo Aml ◽  
Cebpa Mutations ◽  
Biallelic Mutations ◽  
In Cis

Introduction Transcriptional deregulation is a central event in the development of acute myeloid leukemia (AML), with most mutations occurring in genes related to transcription, chromatin regulation and DNA methylation. Furthermore, alterations involving cis-regulatory elements have been shown to play a critical role in aberrant gene expression in AML. Genetic variation in cis-regulatory regions usually involves a single allele, which results in differential expression of the two alleles. This phenomenon, termed allele-specific expression (ASE), is therefore an accurate marker for cis-regulatory variation (Pastinen, 2010). We propose that a systematic study of genes with aberrant ASE in AML may uncover aberrantly expressed genes caused by abnormalities in cis-regulatory elements. Therefore we aim to 1) chart the landscape of ASE in AML, 2) establish a link between relevant ASE events and AML subtypes, and 3) investigate the mechanisms driving ASE. Methods We performed whole exome sequencing (WES) and RNA-seq on leukemic blasts from 168 de novo AML patients, representing all major subtypes of the disease. Combining both datasets, we assessed ASE in every gene with informative (non-homozygous) single nucleotide variants (SNVs). Results Patients had a median of 37 genes with ASE, several of which were recurrently detected across multiple patients. To shorten the gene list we selected for this study genes known to be involved either in cancer or in myeloid development. The gene most commonly found to show ASE (53/140 cases with SNVs) was GATA2, which encodes a transcription factor crucial for proliferation and maintenance of hematopoietic stem cells with a known involvement in AML. Interestingly, integration with molecularly defined classification of AML revealed that all cases (n=17) with biallelic CEBPA mutations exhibited GATA2 ASE (p-value = 6.00·10-7, Fisher's test). Biallelic CEBPA mutations (CEBPA DM) identify an AML subtype with favorable clinical outcome and frequently co-occur with GATA2 mutations (Greif PA, 2012), pointing to a functional connection between these two genes. Indeed, 44% of the cases in our cohort exhibited a GATA2 mutation, and 27% carried a second, subclonal mutation in the same gene. Importantly, in cases where a GATA2 mutation was found, the mutant allele was always preferentially expressed. These findings were validated in the TCGA dataset, where all four CEBPA DM patients with informative SNVs in GATA2 exhibited GATA2 ASE. Although GATA2 ASE was present in other AML subtypes, none of these subtypes showed a significant association with this finding. Patients with a t(8;21) rearrangement (n=5), which represses CEBPA expression, did not exhibit GATA2 ASE, and we only observed GATA2 ASE in 4 out of 8 CEBPA silenced leukemias (Wouters BJ, 2007). Altogether, this demonstrates the uniqueness of the 1-to-1 relationship between CEBPA DM and GATA2 ASE, and excludes a causative role for inactive CEBPA protein in mediating mono-allelic expression of GATA2. The average expression of GATA2 in CEBPA DM patients was comparable to other AMLs, even in cases with monoallelic GATA2 expression. This suggests that a) ASE was achieved by repression of one allele rather than dramatically increased expression of the other, b) there was a compensation of the non-repressed allele. DNA methylation analysis of the GATA2 promoter did not reveal methylation-mediated gene silencing of the repressed allele. The long-distance +77 kb GATA2 enhancer appears to be involved in ASE, as RNA read-through levels at the enhancer were significantly different in CEBPA DM AMLs (p-value < 10-4, Wald test) in an allele-specific manner. The involvement of the enhancer was further confirmed by differences in H3K27ac levels between the two alleles. Conclusions An unbiased screen of 168 de novo AML cases revealed that all patients (n=17) with CEBPA biallelic mutations display GATA2 ASE. GATA2 mutations were found in 8 of the 17 cases, always in the allele that is preferentially expressed. Since GATA2 ASE is present in all CEBPA DM and GATA2 mutations only in a fraction, we hypothesize that GATA2 ASE is acquired first and mutations are only selected if they occur in the expressed allele. Moreover, given that other subgroups with CEBPA abnormalities do not show a similar pattern, we propose that ASE of GATA2 is not a consequence of CEBPA mutations, but rather a requirement for the development of AML in these patients. Disclosures No relevant conflicts of interest to declare.

scholarly journals Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders

2021 ◽  
Vol 22 (7) ◽  
pp. 3735
Author(s):  
Guillaume Velasco ◽  
Damien Ulveling ◽  
Sophie Rondeau ◽  
Pauline Marzin ◽  
Motoko Unoki ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Catalytic Domain ◽  
De Novo ◽  
Mutation Screening ◽  
Histone H3 ◽  
Regulatory Elements ◽  
Germline Mutations ◽  
Dna Methyltransferases ◽  
Mendelian Disorders ◽  
Epigenetic Machinery

DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.

scholarly journals Genome-Wide Regulatory Interactions in the Early Stages of Drosophila Speciation

2020 ◽  
Author(s):  
◽  
Alwyn Clark Go
Keyword(s):  
Reproductive Isolation ◽  
Expression Analysis ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Interactions ◽  
Early Stages ◽  
Genome Wide ◽  
Allele Specific ◽  
Incomplete Reproductive Isolation

Speciation occurs when reproductive barriers prevent the exchange of genetic information between individuals. A common form of reproductive barrier between species capable of interbreeding is hybrid sterility. Genomic incompatibilities between the divergent genomes of different species contribute to a reduction in hybrid fitness. These incompatibilities continue to accumulate after speciation, therefore, young divergent taxa with incomplete reproductive isolation are important in understating the genetics leading to speciation. Here, I use two Drosophila subspecies pairs. The first is D. willistoni consisting of D. w. willistoni and D. w. winge. The second subspecies pair is D. pseudoobscura, which is composed of D. p. pseudoobscura and D. p. bogotana. Both subspecies pairs are at the early stages of speciation and show incomplete reproductive isolation through unidirectional hybrid male sterility. In this thesis, I performed an exploratory survey of genome-wide expression analysis using RNA-sequencing on D. willistoni and determined the extent of regulatory divergence between the subspecies using allele-specific expression analysis. I found that misexpressed genes showed a degree of tissue specificity and that the sterile male hybrids had a higher proportion of misexpressed genes in the testes relative to the fertile hybrids. The analysis of regulatory divergence between this subspecies pair found a large (66-70%) proportion of genes with conserved regulatory elements. Of the genes showing evidence or regulatory divergence between subspecies, cis-regulatory divergence was more common than other types. In the D. pseudoobscura subspecies pair, I compared sequence and expression divergence and found no support for directional selection driving gene misexpression in their hybrids. Allele-specific expression analysis revealed that compensatory cis-trans mutations partly explained gene misexpression in the hybrids. The remaining hybrid misexpression occurs due to interacting gene networks or possible co-option of cis-regulatory elements by divergent transacting factors. Overall, the results of this thesis highlight the role of regulatory interactions in a hybrid genome and how these interactions could lead to hybrid breakdown by disrupting gene interaction networks.

scholarly journals Genetic influences on cell type specific gene expression and splicing during neurogenesis elucidate regulatory mechanisms of brain traits

2020 ◽  
Author(s):  
Nil Aygün ◽  
Angela L. Elwell ◽  
Dan Liang ◽  
Michael J. Lafferty ◽  
Kerry E. Cheek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Elements ◽  
Regulatory Mechanisms ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Risk Variants ◽  
Allele Specific ◽  
Cell Type Specific ◽  
Regulatory Effects

SummaryInterpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing is mainly performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements of cells present during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs and allele specific expression in primary human neural progenitors (n=85) and their sorted neuronal progeny (n=74). Using colocalization and TWAS, we uncover cell-type specific regulatory mechanisms underlying risk for these traits.

scholarly journals DNA Methylation Contributes to the Differential Expression Levels of Mecp2 in Male Mice Neurons and Astrocytes

2019 ◽  
Vol 20 (8) ◽  
pp. 1845 ◽  
Author(s):  
Vichithra R.B. Liyanage ◽  
Carl O. Olson ◽  
Robby M. Zachariah ◽  
James R. Davie ◽  
Mojgan Rastegar
Keyword(s):  
Dna Methylation ◽  
Current Knowledge ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Autism Spectrum ◽  
Brain Cells ◽  
Specific Expression ◽  
Expression Levels ◽  
Mecp2 Duplication Syndrome ◽  
Cell Type Specific Expression

Methyl CpG binding protein-2 (MeCP2) isoforms (E1 and E2) are important epigenetic regulators in brain cells. Accordingly, MeCP2 loss- or gain-of-function mutation causes neurodevelopmental disorders, including Rett syndrome (RTT), MECP2 duplication syndrome (MDS), and autism spectrum disorders (ASD). Within different types of brain cells, highest MeCP2 levels are detected in neurons and the lowest in astrocytes. However, our current knowledge of Mecp2/MeCP2 regulatory mechanisms remains largely elusive. It appears that there is a sex-dependent effect in X-linked MeCP2-associated disorders, as RTT primarily affects females, whereas MDS is found almost exclusively in males. This suggests that Mecp2 expression levels in brain cells might be sex-dependent. Here, we investigated the sex- and cell type-specific expression of Mecp2 isoforms in male and female primary neurons and astrocytes isolated from the murine forebrain. Previously, we reported that DNA methylation of six Mecp2 regulatory elements correlated with Mecp2 levels in the brain. We now show that in male brain cells, DNA methylation is significantly correlated with the transcript expression of these two isoforms. We show that both Mecp2 isoforms are highly expressed in male neurons compared to male astrocytes, with Mecp2e1 expressed at higher levels than Mecp2e2. Our data indicate that higher DNA methylation at the Mecp2 regulatory element(s) is associated with lower levels of Mecp2 isoforms in male astrocytes compared to male neurons.

scholarly journals Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells

2019 ◽  
Vol 5 (12) ◽  
pp. eaay7246 ◽  
Author(s):  
Zhiyuan Chen ◽  
Qiangzong Yin ◽  
Azusa Inoue ◽  
Chunxia Zhang ◽  
Yi Zhang
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Genetic Manipulation ◽  
Paternal Allele ◽  
Gene Promoters ◽  
Maternal Allele ◽  
Mammalian Development ◽  
Placental Development ◽  
Early Embryos ◽  
Allele Specific

Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation–dependent (canonical) imprinting is relatively stable during development, the recently found oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos, with some genes important for placental development maintaining imprinted expression in the extraembryonic lineage. How these noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here, we report that maintenance of noncanonical imprinting requires maternal allele–specific de novo DNA methylation [i.e., somatic differentially methylated regions (DMRs)] at implantation. The somatic DMRs are located at the gene promoters, with paternal allele–specific H3K4me3 established during preimplantation development. Genetic manipulation revealed that both maternal EED and zygotic DNMT3A/3B are required for establishing somatic DMRs and maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying noncanonical imprinting maintenance but also sheds light on how histone modifications in oocytes may shape somatic DMRs in postimplantation embryos.

scholarly journals Allele-specific expression identified rs2509956 as a novel long-distance cis-regulatory SNP for SCGB1A1, an important gene for multiple pulmonary diseases

2019 ◽  
Vol 317 (4) ◽  
pp. L456-L463
Author(s):  
Xiu-Xiong Li ◽  
Tao Peng ◽  
Jing Gao ◽  
Jia-Gang Feng ◽  
Dan-Dan Wu ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Pulmonary Diseases ◽  
Chronic Obstructive ◽  
Long Distance ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Chromosome Conformation ◽  
Functional Region ◽  
Gene Assay ◽  
Allele Specific

SCGB1A1 (secretoglobin family 1A member 1) is an important protein for multiple pulmonary diseases, especially asthma, chronic obstructive pulmonary disease, and lung cancer. One single-nucleotide polymorphism (SNP) at 5′-untranslated region of SCGB1A1, rs3741240, has been suggested to be associated with reduced protein expression and further asthma susceptibility. However, it was still unclear whether there were other cis-regulatory elements for SCGB1A1 that might further contribute to pulmonary diseases. Allele-specific expression (ASE) is a novel approach to identify the functional region in human genome. In the present study, we measured ASE on rs3741240 in lung tissues and observed a consistent excess of G allele over A ( P < 10−6), which indicated that this SNP or the one(s) in linkage disequilibrium (LD) could regulate SCGB1A1 expression. By analyzing 1000 Genomes Project data for Chinese, one SNP locating ~10.2 kb away and downstream of SCGB1A1, rs2509956, was identified to be in strong LD with rs3741240. Reporter gene assay confirmed that both SNPs could regulate gene expression in the lung cell. By chromosome conformation capture, it was verified that the region surrounding rs2509956 could interact with SCGB1A1 promoter region and act as an enhancer. Through chromatin immunoprecipitation and overexpression assay, the related transcription factor RELA (RELA proto-oncogene, NF-kB subunit) was recognized to bind the region spanning rs2509956. Our work identified a novel long-distance cis-regulatory SNP for SCGB1A1, which might contribute to multiple pulmonary diseases.

Molecular Epidemiological Study in Pediatric Acute Myeloid Leukemia.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2015-2015
Author(s):  
Helene Lapillonne ◽  
S. Lejeune-Dumoulin ◽  
Paola Ballerini ◽  
A.S. Goetgheluck-Gadenne ◽  
Anne Auvrignon ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Type I ◽  
Type Ii ◽  
Monosomy 7 ◽  
Female Ratio ◽  
Ras Mutations ◽  
De Novo Aml ◽  
Cebpa Mutations ◽  
11Q23 Abnormalities

Abstract It is hypothesized that AML arises from two cooperative types of mutations: type I mutations mainly induce proliferation and type II mutations involved in the maturation arrest. AML is a rare disease in children and few molecular data are available on pediatric AML. We therefore studied N-RAS, K-RAS, FLT3-ITD, FLT3 , C-KIT mutations (type I), and CEBPA mutations (type II) as well as FLT3, EVI-1 and WT1 gene expression in 77 de novo AML. Patients and methods: All the patients (aged 1 month-17 years, median age: 6.9 years, male/female ratio 1.26) were treated for de novo AML between 1995 and 2003 in two French institutions and prospectively enrolled in LAM91, LAM01 and APLs French collaborative protocols. According to the FAB classification the repartition was: M0:6.5%, M1: 5.2%, M2: 22%, M3: 13%, M4 :14.3%, M5 :30%, M7: 6.5% and unclassified :2.5%. Cytogenetics features according to the MRC classification were favorable, intermediate or poor in 25% (t(8;21) n=5; t(15,17) n=8, inv(16) n=5), 65% (normal n=20 and 11q23 abnormalities n=15) and 10% (−7, n=4) respectively. With a median follow-up of 26 months (range 2–98 months), Complete Remission was obtained in 92% (71/77) of patients, OS was 71% and EFS 61%. CEBPA, N-RAS, K-RAS, C-KIT and FLT3 mutations detection was performed by direct sequencing. FLT3, EVI-1 and WT1 transcripts were quantified by RQ-PCR. Results: (1) Frequency of N-RAS and K-RAS mutations were 11% (8/75) and 16% (12/75) respectively. RAS-mutated patients belonged to favorable (30%), intermediate (60%) and poor (10%) cytogenetic subgroups. In univariate analysis only N-RAS mutations is associated with adverse outcome (OS 37% vs 79%, p<0.05). (2) CEBPA mutations were found in 8% (6/75), mostly belonged to the intermediate cytogenetic risk subgroup (66%). (3) C-KIT mutations were observed in 4% (4/75) always associated with fusion CBFb/MYH11 transcript and excellent outcome. (4) FLT3-ITD and FLT3 Asp835 mutations were obtained in 12% (9/74) and 4% (3/74) of patients respectively. Cytogenetic subgroups were favorable (33%) and intermediate (67%). (5) At diagnosis FLT3 overexpression was detected in 34% (24/70) and 11q23 abnormalities were associated in 7/24 patients. (6) EVI-1 overexpression was found in 21% (16/76), belonged to intermediate (85%) and poor (15%) cytogenetic subgroups with a significant frequency in monosomy 7 (p<0.025). The EVI-1 expression was specifically expressed (p<0.001) in M5 and M7-FAB subtypes. (7) WT1 overexpression was detected in 81% (62/76). Conclusion: In total, 48% of de novo AML in children had a mutation in N-RAS, K-RAS, FLT3-ITD, FLT3 Asp835, C-KIT or CEBPA with a high frequency of RAS mutations (27%) compared to adult AML and a significantly bad survival. Additional gene expression quantification of EVI-1, FLT3 and WT1 allows MDR detection in 95% of patients.

CEBPA Methylation as a Prognostic Biomarker in Adult Patients with De Novo AML.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1569-1569
Author(s):  
Hsin-Yu Chen ◽  
Tsung-Chin Lin ◽  
Wen-Chien Chou ◽  
Hsin-An Hou ◽  
Hwei-Fang Tien ◽  
...  
Keyword(s):  
Promoter Methylation ◽  
Promoter Region ◽  
De Novo ◽  
Epigenetic Modification ◽  
Core Promoter ◽  
Methylation Status ◽  
Distal Region ◽  
The Core ◽  
De Novo Aml ◽  
Cebpa Mutations

Abstract Abstract 1569 Poster Board I-593 Acute myeloid leukemia (AML) is a clonal disorder characterized by acquired genetic abnormalities in hematopoietic progenitors. CCAAT/enhancer binding protein α (C/EBPα) is a basic leucine zipper transcription factor that regulates differentiation-dependent genes during granulocyte differentiation. CEBPA mutations have been observed in several human malignancies. Epigenetic modification of the distal CEBPA promoter region (-1422 to -896) has been reported to result in down-regulation of CEBPA expression in lung cancer, pancreatic cancer, and head and neck squamous cell carcinoma. Apart from solid tumors, epigenetic modification of CEBPA in AML has also been reported. Chim et al. reported aberrant CEBPA core promoter methylation in a small proportion (2.85%) of patients with AML. Wouters et al. identified a subgroup of AML patients (1.4%) in which the CEBPA gene was silenced in association with CEBPA core promoter methylation. Hackanson et al. observed CEBPA methylation in the distal promoter region in 51% of selected AML patients. Due to the selection of differing patient populations and CEBPA promoter regions for analysis in past studies, the clinical significance of CEBPA methylation in AML remains unclear. To evaluate the CEBPA methylation status of patients with AML, 193 patients with de novo AML were evaluated for CEBPA methylation by bisulfite sequencing and MSP methods. A substantial proportion of patients were noted to have some degree of heterogeneous methylation in the distal region (-1423 to -1121), but not in the proximal region (-1121 to -896) or in the core region (-141 to +103), of the CEBPA promoter. Only one patient was noted to have broad methylation from the distal region to the core of the CEBPA promoter, and extending into exon1 (-25 to +103). This patient was a 61-year-old female with M1 subtype AML, a normal karyotype and an absence of CEBPA, NPM1 or FLT3 mutations. We further correlated the CEBPA methylation levels with CEBPA transcript levels in leukemic cells from 12 patients with AML and found a negative correlation (coefficient of correlation = -0.722, P = 0.017). To clarify the correlation between CEBPA methylation and clinical features in AML, quantitative MassARRAY analyses for CEBPA methylation were performed. Among the 193 patients studied, methylation levels ranged from 0.073 to 0.971 with a median value of 0.229, compared to normal bone marrow cells (NBM) with levels ranging from 0.207 to 0.269 (n=5, median: 0.218) and mature leukocytes (NPB) which ranged from 0.144 to 0.201 (n=5, median 0.161). Using complete linkage clustering, we divided the patients into two groups: one with high CEBPA methylation levels (≥ 0.55, n = 28), and the other with low methylation levels (< 0.55, n = 165). Clinical and laboratory features of these two groups are explored. Gene alteration analysis revealed NPM1 mutation was mutually exclusive with CEBPA methylation (P = 0.004), so was similar trend in CEBPA mutation. Of the 28 patients with high CEBPA methylation, only one patient had a CEBPA mutation. immunophenotyping work revealed that leukemic blasts from patients with high CEBPA methylation were predominately negative for HLA-DR (P = 0.005) and CD56 (P = 0.015) expression. Of the 140 patients receiving standard induction therapy, 110 (79.3%) patients achieved CR. With a median follow-up of 17.5 months, patients with high CEBPA methylation demonstrated a greater probability of survival (median >60 months vs. 20 months, P = 0.020) than those with low CEBPA methylation. In addition, in the subgroup of AML patients without favorable karyotypes as well as NPM1 and CEBPA mutations, patients with high CEBPA methylation (n = 14) still had better five-year survival (median 34 months vs. 11 months, P = 0.048) than those with low CEBPA methylation. Intriguingly, among the cytogenetically normal AML patients, except those with CEBPA and NPM1 mutations, the five-year survival of patients with high CEBPA methylation (n=8) was remarkably better than those with low CEBPA methylation (n=19; median >60 months vs. 11 months, P = 0.002). These results suggest that, in addition to current cytogenetic and molecular markers, CEBPA methylation status could emerge as a prognostic factor for survival advantage in AML patients. Disclosures No relevant conflicts of interest to declare.

Analysis of ASXL1, IDH1, IDH2, c-CBL, and WT1 Mutations in De Novo Acute Myeloid Leukaemia

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1450-1450
Author(s):  
Mariam Ibañez ◽  
Esperanza Such ◽  
Jose Cervera ◽  
Irene Luna ◽  
Sandra Dolz ◽  
...  
Keyword(s):  
De Novo ◽  
Prognostic Impact ◽  
Significant Implication ◽  
Wild Type ◽  
Idh Mutations ◽  
Flt3 Mutations ◽  
Exon 4 ◽  
De Novo Aml ◽  
Cebpa Mutations ◽  
Acute Myeloid

Abstract Abstract 1450 The clinical relevance and prognostic implications of some recently identified mutations in acute myeloid leukemia (AML) is not yet well established. Among them, we have selected to be analyzed those affecting the following genes: Additional Sex Combs-Like 1 (ASXL1), Isocitrate Dehydrogenase (IDH1 and IDH2), Casitas B-lineage Lymphoma (c-CBL), and Wilms Tumor 1 (WT1). They have been previously reported with a variable incidence: ASXL1 mutations in 10.8% patients with normal karyotype (NK), IDH1 and IDH2 mutations in 8 – 33% of de novo AML, c-CBL mutations in 2% of de novo AML, and WT1 mutations in 5–12% of de novo AML patients. In order to know the incidence and prognostic impact of these mutations and their possible cooperative role in leukemogenesis, we have screened for ASXL1, IDH1, IDH2, c-CBL, WT1, FLT3, NPM1 and CEBPa, mutations in a cohort of de novo AML patients from a single centre. We studied 174 de novo AML patients [98M/76F; median age: 62 yr. (range: 16 – 88); favourable (n= 13), intermediate (n= 86) and high (n= 51) cytogenetic risk classification by the MRC group]. DNA was isolated from bone marrow samples obtained at diagnosis. In order to determine cooperating mutations, we developed a new combination of high-resolution melting (HRM) assays on a LightCycler® 480 and lastly direct sequencing, to detect somatic mutations for ASXL1 (exon 12), IDH1 (exon 4), IDH2 (exon 4), WT1 (exons 7, 8 and 9) and c-CBL (exons 8 and 9). All mutations reported in this study were confirmed al least twice. FLT3 (ITD and D835Y), NPM1 (exon 12) and CEBPa were performed as described previously by standard methods. Sequence analysis was checked by its corresponding GeneBank Accession Number. The number of patients found to carry mutations in our series was: 16 patients with ASXL1 mutations (9.2%), 16 patients with IDH mutations (2.9% had a IDH1R132, 12.6% the SNP rs11554137 and 6.3% IDH2R140), 5 patients with WT1 mutations (2.9%), 37 patients with FLT3 mutations (21.3%), 44 patients with NPM1 mutations (25,3%) and 8 patients with CEBPa mutations (4.6%). No mutations where found in c-CBL. We could not found a pattern of cooperating mutations in the studied group of genes. WT1, FLT3 and NPM1 were associated with leukocyte count >30 × 109/L at diagnosis (80% vs. 31% for WT1, P =0,022; 68% vs. 22% for FLT3, P= 0.001; and 50% vs. 24% for NPM1, P= 0.002; in mutated vs. wild-type patients, respectively). WT1 was also associated with a platelet count > 50 × 109/L at diagnosis (100% vs. 57% in mutated vs. wild-type patients, respectively; P =0,048). Besides, FLT3 and NPM1 mutations were more frequent in the intermediate cytogenetic risk group (82% and 74%; P =0.004 and P =0.047; respectively). ASXL1 and IDH mutations were not correlated with any of the clinical and biological features studied. In univariate analysis, only age and cytogenetics had an impact on overall survival (OS, median of 12mo vs. 3mo, for patients < and ≥65 yr., P <0.001 and 24mo, 11mo and 3mo for favourable, intermediate and high risk, P =0.005). Mutational status of ASXL1, IDH1, IDH2, WT1, FLT3, NPM1 and CEBPa did not impact on outcome in the whole series. However, when the analysis was restricted to patients with intermediate cytogenetic risk, patients with FLT3 mutations had a shorter OS (19mo vs. 8mo, wild-type vs. mutated patients; P =0.047) and those with WT1 mutations showed a trend towards an inferior OS (11mo vs. 1mo, wild-type vs. mutated patients; P = 0.066). In multivariate analysis in patients with intermediate cytogenetic risk, the age [HR (95% CI) = 3.3 (1.9 − 5.9) P <0.001], and FLT3 status [HR (95% CI) = 2.2 (1.2–3.9) P =0.008] retained an independent adverse significance for OS. In terms of relapse free survival any of the variables showed a significant implication. To sum up, the incidence found for the studied genes was lower than the previously reported: ASXL1, 9.2%; IDH1R132, 2.9%; IDH2R140, 6.3%; WT1, 2.9%; and c-CBL, 0%. We were unable to find a pattern of cooperating mutations in the studied group of genes or any impact of these mutations on the outcome. Disclosures: No relevant conflicts of interest to declare.

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