scholarly journals Polymorphisms at microRNA binding sites of Ara-C and anthracyclines-metabolic pathway genes are associated with outcome of acute myeloid leukemia patients

2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Hai-xia Cao ◽  
Chao-feng Miao ◽  
Liang Yan ◽  
Ping Tang ◽  
Li-rong Zhang ◽  
...  
Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5130-5130
Author(s):  
Juan Eduardo Megías-Vericat ◽  
Montesinos Pau ◽  
María José Herrero ◽  
Federico Moscardó ◽  
Virginia Bosó ◽  
...  

Abstract Background: Cytarabine (Ara C) is considered the most effective chemotherapeutic agent in acute myeloid leukemia (AML) treatment. Several studies suggest that single nucleotide polymorphisms (SNPs) within the genes involving metabolic pathway of Ara C could influence in treatment outcomes, although their clinical relevance remains undetermined. Methods: The SNPs of cytarabine pathway (DCK: rs2306744, rs11544786, rs4694362; CDA: rs2072671, rs3215400, rs532545, rs602950; NT5C2: rs11598702; RRM1: rs9937; NME1: rs2302254) were evaluated in 225 adult patients at initial diagnosis from AML using a mass spectrometry-based multiplex genotyping assay (Sequenom®). All patients received induction chemotherapy consisting of idarubicin plus cytarabine (PETHEMA 99, 2007 and 2010 trials). Efficacy of first induction cycle was evaluated comparing complete remission (CR) vs. partial remission (PR) or resistance (patients dying during induction excluded); and overall survival (OS). Induction death was defined as patients dying during induction against CR, excluding these patients with PR or resistance. Based on WHO grading scale, toxicities were grouped as binary variables (grades 0-1 vs. 2-4; or 0 vs. 1-4), assigning the maximum grade of all the specific toxicities within that group (evaluated in all patients). Genotypes were studied with co-dominant model. Association between variables was assessed using linear and logistic regression adjusting for age, gender, cytogenetic risk, ECOG, leukocyte and platelet count, hemoglobin, creatinine, bilirubin, albumin and LDH level at diagnosis (R® version 3.1.2). Kaplan-Meier method and Cox proportional were employed to OS estimates with the same covariates. Results: The median age of patients was 51.1 years (16-78 years). The variant allele of DCK SNP rs2306744, enzyme that catalyzes the limiting first phosphorylation in activation of Ara C, showed higher CR (OR:6.3; 95%CI 1.3-31.1; P=0.024), as well as higher mucositis (OR:3.3; 95%CI 1.1-10.0; P=0.038). CDA is the main inactivating enzyme of Ara C. The variant allele of rs602950 was related to higher CR (OR:3.0; 95%CI 1.02-8.8; P=0.045) and OS at 5 years (HR:0.4; 95%CI 0.2-0.9; P=0.012; Figure 1) and the variant homozygous of rs2072671 to higher OS at 5 years (HR:0.3; 95%CI 0.1-0.96; P=0.018; Figure 2), whereas the wild-type allele of rs532545 was associated to higher OS at 3 years (HR:1.5; 95%CI 1.01-2.4; P=0.039; Figure 3). In addition, variant alleles of rs532545 and rs602950 were related to skin toxicity (OR:2.2; 95%IC 1.1-4.3; P=0.033; OR:2.1; 95%IC 1.01-4.5; P=0.047, respectively). Variant allele of RRM1 (rs9937), enzyme directly associated with Ara C sensitivity, was associated to induction death (OR:0.2; 95%IC 0.03-0.9, P= 0.034). Variant allele of NT5C2 (rs11598702), responsible of nucleotide pools balance, showed higher hepatotoxicity (OR: 4.1; 95%IC 1.1-14.5; P=0.032). Conclusions: This study reveals the influence in Ara C efficacy of DCK and CDA polymorphisms in AML adult patients, previously suggested in other studies. In addition, novel associations between SNPs in metabolic Ara C genes and toxicities were detected. Further studies with larger population are needed to validate these associations. Figure 1 Figure 1. Figure 3 Figure 3. Figure 2 Figure 2. Disclosures Boluda: Instituto de Investigación Sanitaria La Fe: Employment.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3545-3545
Author(s):  
Kristine Baraoidan ◽  
Vinzon Ibanez ◽  
Chetna Mittal ◽  
Habte Yimer ◽  
Suman Chakraborty ◽  
...  

Abstract AML1 and PU.1, important regulators of hematopoietic differentiation, interact with each other and are known to synergize in transcriptional activation (Zhang et al, 1996). PU.1 and AML1 also interact with mSin3, a component of a co-repressor complex that can include N-CoR, HDAC and CBFA2T1 (ETO, MTG8) or CBFA2T3 (ETO2, MTG16). CBFA2T3 is highly expressed in hematopoietic cells and is a target of a chromosomal translocation found in acute myeloid leukemia (t(16;21)). In transfected 293T cells, we demonstrate that both AML1 and PU.1 co-immunoprecipitate with the conserved N-terminal TAFH domain of CBFA2T3 but not the C-terminal MYND domain. Although AML1 and PU.1 independently co-immunoprecipitate with CBFA2T3, when all three proteins are over-expressed in 293T cells, AML1 and PU.1 co-immunoprecipitate with each other while excluding CBFA2T3. CBFA2T3 interacts with the non-runt portion of AML1 (AML1 C-terminus) while PU.1 can interact with both the runt domain of AML1 and AML1 C-terminus. Presumably, the interaction between AML1 and PU.1 shields the CBFA2T3 binding sites on both proteins. Since this region includes the binding site for mSin3, other co-repressors may also be excluded from an AML1/PU.1 complex. This may be one basis for the co-operation between AML1 and PU.1 in transcriptional activation.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3811-3811 ◽  
Author(s):  
Amanda J Favreau ◽  
Fariba Shaffiey ◽  
Erin Cross ◽  
Pradeep Sathyanarayana

Abstract The recent discovery of new molecular lesions with prognostic significance in acute myeloid leukemia (AML) is enhancing our understanding of leukemia biology and our ability to identify new therapeutic targets. Previously, using the unique leukemic myeloid progenitor line AML-193, we profiled IL-3-, GM-CSF-, and G-CSF-regulated miRNA signatures. 301 miRNAs were commonly regulated by these three cytokines, and the most highly induced miRNA was miR-590-5p. Herein, we have attempted to define the functional role and clinical relevance of miR-590 in AML. We first examined the relative miR-590 expression in steady state hematopoiesis and showed it was highest at CD34+ and declined its expression through myeloid lineage differentiation (ANOVA, p<0.0001). To functionally determine the role of increased miR-590 expression, we generated a gain-of-function model in human CD34+ hematopoietic stem cells (HSC) via lentivirus transduction. Increased expression of miR-590 in CD34+ cells resulted in significant increases in CFU-GM colonies, strongly suggesting that dysregulation of miR-590 expression may be myeloproliferative. In AML (n=33) and control (n=9) bone marrow samples, miR-590 expression was determined via RT-qPCR. miR-590-5p expression was highly upregulated in 22 of the samples (67%) compared to control subjects. In silico analysis of the miR-590-5p promoter revealed three potential binding sites for STAT5 (-249, -749, -1499). To functionally determine whether STAT5 directly regulates miR-590-5p expression, we performed a ChIP assay, which showed that STAT5 binds to the -749 region of miR-590-5p promoter. To conclusively determine the STAT5 binding sites, we cloned the miR-590 promoter in a luciferase vector and performed site directed mutagenesis for each potential binding site. This assay confirmed that the -749 binding site was the major STAT5 regulatory site for miR-590 (p<0.002). Importantly, constitutive activation of STAT5 is a hallmark of AML associated with FLT3 mutations, therefore, we set out to determine if specific STAT5 and FLT3 inhibitors could decrease miR-590 expression. We pretreated MV4-11 cells, which harbors the FLT-ITD mutation and has increased STAT5 activation, with 100uM STAT5 inhibitor (N′-((4-Oxo-4H-chromen-3-yl)methylene)nicotinohydrazide) for 90 minutes or 100nM FLT3 inhibitor (EMD Millipore, 343020) for 12 hours, both of which resulted in significant inhibition of miR-590-5p expression (p<0.05). To evaluate whether the AML samples with high miR-590 expression also possess elevated phospho-STAT5 or phospho-FLT3 levels, we performed immunohistochemistry analysis on a custom-made tissue microarray. In AML samples with high miR-590 levels, increased activation of FLT3 and STAT5 was observed compared to controls. Since FLT3 mutations result in decreased survival and poorer prognosis in AML, it may be that miR-590-5p plays an important role in the pathology of AML associated with dysregulated FLT3 and STAT5. To understand the complete functional role of miR-590 in AML, the predicted targets need to be identified and validated for their roles in leukemogenesis. Upon molecular screening of several predicted targets, FasL was experimentally found to be a conserved target of miR-590. More specifically, 3’UTR analysis of FasL revealed three potential seed sequences for miR-590 which have been verified experimentally via luciferase assay. Furthermore, significantly increased levels of FasL protein and transcript expression was detected in the MV4-11 cells stably expressing anti-miR-590 compared to control cells. Additionally, we identified the levels of Fas/CD95 (FasL receptor) on AML-193 and MV4-11 cell lines and found these cells had high Fas/CD95 expression on the cell surface as analyzed via flow cytometry. In order to determine the physiological significance of Fas/FasL, these cells were treated with soluble FasL (100ng) for 24 hours and apoptosis was analyzed via Annexin V staining. FasL treatment induced increased apoptosis compared to the untreated cells. Taken together, we have identified miR-590 as a candidate oncomiR that is regulated via the STAT5 pathway and targets FasL to promote cell survival. Thus, our data suggests that further understanding of miR-590’s role in AML may lead to development of novel anti-miR-590 therapeutic strategies in AML associated with dysregulated STAT5. Disclosures: No relevant conflicts of interest to declare.


2018 ◽  
Vol 2 (3) ◽  
pp. 271-284 ◽  
Author(s):  
Justin Loke ◽  
Paulynn Suyin Chin ◽  
Peter Keane ◽  
Anna Pickin ◽  
Salam A. Assi ◽  
...  

Key Points C/EBPα directly represses the leukemia maintenance program; however, the pattern of repressed genes is specific for each type of AML. Overexpression of C/EBPα does not globally displace these proteins from their binding sites, but overrides their repressive activity.


Blood ◽  
2012 ◽  
Vol 120 (15) ◽  
pp. 3058-3068 ◽  
Author(s):  
Sadia Saeed ◽  
Colin Logie ◽  
Kees-Jan Francoijs ◽  
Gianmaria Frigè ◽  
Mauro Romanenghi ◽  
...  

Abstract Chromatin accessibility plays a key role in regulating cell type specific gene expression during hematopoiesis but has also been suggested to be aberrantly regulated during leukemogenesis. To understand the leukemogenic chromatin signature, we analyzed acute promyelocytic leukemia, a subtype of leukemia characterized by the expression of RARα-fusion proteins, such as PML-RARα. We used nuclease accessibility sequencing in cell lines as well as patient blasts to identify accessible DNA elements and identified > 100 000 accessible regions in each case. Using ChIP-seq, we identified H2A.Z as a histone modification generally associated with these accessible regions, whereas unsupervised clustering analysis of other chromatin features, including DNA methylation, H2A.Zac, H3ac, H3K9me3, H3K27me3, and the regulatory factor p300, distinguished 6 distinct clusters of accessible sites, each with a characteristic functional makeup. Of these, PML-RARα binding was found specifically at accessible chromatin regions characterized by p300 binding and hypoacetylated histones. Identifying regions with a similar epigenetic make up in t(8;21) acute myeloid leukemia (AML) cells, another subtype of AMLs, revealed that these regions are occupied by the oncofusion protein AML1-ETO. Together, our results suggest that oncofusion proteins localize to accessible regions and that chromatin accessibility together with p300 binding and histone acetylation characterize AML1-ETO and PML-RARα binding sites.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3641-3641 ◽  
Author(s):  
Maya D. Hughes ◽  
Valerie A. Morris ◽  
Carrie Cummings ◽  
Soheil Meshinchi ◽  
Vivian G. Oehler

Abstract Acute myeloid leukemia (AML) is a heterogeneous disease that develops secondary to the acquisition of mutations that disrupt cell differentiation, proliferation and survival. MicroRNAs (miRNAs or miRs) are short non-coding RNA molecules that modulate post-transcriptional gene expression by either cleaving or repressing translation of target mRNA transcripts. Differential expression of miRNAs has been identified in AML and noted to correlate with specific disease characteristics, cytogenetic abnormalities and prognosis. MiR-155 expression is upregulated in both adult and pediatric patients with cytogenetically normal AML (CN-AML) and correlates with adverse clinical outcomes. Specifically, we have shown that high miR-155 expression is associated with an increased incidence of induction chemotherapy failure and inferior overall and event free survival. However, how miR-155 up-regulation contributes mechanistically to adverse clinical outcomes is poorly understood. In prior work, we correlated the expression of predicted or validated miR-155 target genes with miR-155 expression in a gene expression profiling (GEP) dataset of pediatric AML samples. We identified 22 candidates with inversely correlated expression by GEP for further validation in diagnostic bone marrow specimens from children with the highest miR-155 expression levels (n=9) vs. children with the lowest miR-155 expression levels (n=9). Although the expression of miR-155 inversely correlated with 9 target genes, only expression of the putative target KDM7A demonstrated a statistically significant difference in expression between low and high miR-155 expressing cases (p = 0.03). KDM7A is a lysine-specific histone demethylase enzyme that may play a role in regulating differentiation by impacting transcriptional elongation. Computational software programs, i.e. TargetScan, identified two predicted miR-155 binding sites in the KDM7A 3'UTR. To evaluate whether miR-155 directly binds to the KDM7A 3'UTR, we cloned two regions of the KDM7A 3'UTR containing predicted miR-155 binding sequences into luciferase reporter vectors and then mutated the binding sites by site-directed DNA mutagenesis. We validated that both predicted binding sites in KDM7A 3'UTR were direct miR-155 targets using HEK293T cells. Next, we examined the impact of miR-155 overexpression in K562 cells, an acute leukemia cell line that express very low levels of endogenous miR-155, and can be differentiated along the erythroid lineage after hemin exposure. KDM7A RNA expression was decreased 16-fold in miR-155 versus control lentivirally transduced K562 cells as detected by qPCR. KDM7A protein expression was also decreased in miR-155 versus control expressing K562 cells as measured via Western blot. These data demonstrate that KDM7A is a previously uncharacterized target of miR-155. Next, we explored the effect of differential KDM7A expression on cell differentiation, and cell death and apoptosis after exposure to daunorubicin chemotherapy. For this work we used GFP-labeled miR-155 and YFP-labeled KDM7A lentiviral constructs and labeled control constructs. To examine differentiation we used benzidine staining of hemin-exposed K562 cells transduced with empty control vector (ECV), miR-155, KDM7A, or both constructs. The lowest percentage of benzidine staining, consistent with limited erythroid differentiation, was seen in K562 cells with miR-155 overexpression compared to ECV (28.2% vs. 39.8% positive). This effect on blocked erythroid differentiation was fully reversed with overexpression of KDM7A in miR-155 overexpressing cells (41.4% positive). Confirming these observations, we also observed decreased benzidine staining in hemin exposed K562 cells that were transduced with KDM7A shRNA versus control (28.9% versus 42.7%). Together, these data support that KDM7A plays a role in cell differentiation that is in part controlled by miR-155 expression. Preliminary data also support that re-expression of KDM7A in miR-155 overexpressing cells promotes cell death after exposure to daunorubicin. Further work is ongoing. In conclusion, we have identified a new target of miR-155, KDM7A. Our data suggest that KDM7A plays a role in cell differentiation and that decreased KDM7A expression in AML cells that overexpress miR-155 contributes to blocked differentiation, and may also contribute to resistance to chemotherapy. Disclosures No relevant conflicts of interest to declare.


2017 ◽  
Vol 58 (12) ◽  
pp. 2880-2894 ◽  
Author(s):  
Juan Eduardo Megías-Vericat ◽  
Pau Montesinos ◽  
María José Herrero ◽  
Federico Moscardó ◽  
Virginia Bosó ◽  
...  

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 319 ◽  
Author(s):  
Bhise ◽  
Elsayed ◽  
Cao ◽  
Pounds ◽  
Lamba

Nucleoside analog, cytarabine (ara-C) is the mainstay of acute myeloid leukemia (AML) chemotherapy. Cytarabine and other nucleoside analogs require activation to the triphosphate form (ara-CTP). Intracellular ara-CTP levels demonstrate significant inter-patient variation and have been related to therapeutic response in AML patients. Inter-patient variation in expression levels of drug transporters or enzymes involved in their activation or inactivation of cytarabine and other analogs is a prime mechanism contributing to development of drug resistance. Since microRNAs (miRNAs) are known to regulate gene-expression, the aim of this study was to identify miRNAs involved in regulation of messenger RNA expression levels of cytarabine pathway genes. We evaluated miRNA and gene-expression levels of cytarabine metabolic pathway genes in 8 AML cell lines and The Cancer Genome Atlas (TCGA) data base. Using correlation analysis and functional validation experiments, our data demonstrates that miR-34a-5p and miR-24-3p regulate DCK, an enzyme involved in activation of cytarabine and DCDT, an enzyme involved in metabolic inactivation of cytarabine expression, respectively. Further our results from gel shift assays confirmed binding of these mRNA-miRNA pairs. Our results show miRNA mediated regulation of gene expression levels of nucleoside metabolic pathway genes can impact interindividual variation in expression levels which in turn may influence treatment outcomes.


Blood ◽  
2010 ◽  
Vol 116 (24) ◽  
pp. 5316-5326 ◽  
Author(s):  
Giridharan Ramsingh ◽  
Daniel C. Koboldt ◽  
Maria Trissal ◽  
Katherine B. Chiappinelli ◽  
Todd Wylie ◽  
...  

Abstract MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and have been implicated in the pathogenesis of cancer. In this study, we applied next generation sequencing techniques to comprehensively assess miRNA expression, identify genetic variants of miRNA genes, and screen for alterations in miRNA binding sites in a patient with acute myeloid leukemia. RNA sequencing of leukemic myeloblasts or CD34+ cells pooled from healthy donors showed that 472 miRNAs were expressed, including 7 novel miRNAs, some of which displayed differential expression. Sequencing of all known miRNA genes revealed several novel germline polymorphisms but no acquired mutations in the leukemia genome. Analysis of the sequence of the 3′-untranslated regions (UTRs) of all coding genes identified a single somatic mutation in the 3′-UTR of TNFAIP2, a known target of the PML-RARα oncogene. This mutation resulted in translational repression of a reporter gene in a Dicer-dependent fashion. This study represents the first complete characterization of the “miRNAome” in a primary human cancer and suggests that generation of miRNA binding sites in the UTR regions of genes is another potential mechanism by which somatic mutations can affect gene expression.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1353-1353
Author(s):  
Christian Bach ◽  
Philipp B. Staber ◽  
Min Ye ◽  
Pu Zhang ◽  
Alan D. Friedman ◽  
...  

Abstract Abstract 1353 The transcription factors PU.1 and C/EBPα are key regulators of hematopoietic cell differentiation. Tight and coordinated regulation of these factors is essential for normal hematopoiesis and even moderate alterations can lead to acute myeloid leukemia (AML). Previous studies established that in PU.1 knockout mice myeloid differentiation is blocked at an earlier stage compared to C/EBPα knockouts, consistent with PU.1 acting upstream of C/EBPα during hematopoietic differentiation. Recently, however, we and others identified a PU.1 upstream regulatory element (URE) which contains potential C/EBP binding sites. C/EBPα binds to the PU.1 URE in vitro and in vivo. Furthermore, C/EBPα transactivated the PU.1 proximal promoter in a URE dependent manner. We, therefore, hypothesized that PU.1 is a target gene of C/EBPα in hematopoietic cells. To assess the role of PU.1 as a downstream target of C/EBPα in normal hematopoiesis we performed gene expression analysis in immature hematopoietic cells of conditional C/EBPα knockout mice (Mx1-Cre). Of note, we observed a strong reduction of PU.1 expression in hematopoietic stem cells (HSCs: CD150+CD48-LSK) after excision of C/EBPα, corroborating that PU.1 is a target of C/EBPα in murine HSCs in vivo. Moreover, lentiviral PU.1 expression alleviated the myeloid differentiation block of C/EBPα−/− KSL cells as evidenced by the differentiation to Gr-1 and Mac1 positive myeloid cells. Targeted deletion of the PU.1 URE reduces PU.1 expression and induces myeloid leukemia. Additionally, inactivation of C/EBPα by various mechanisms is a common observation in many AML subtypes. Therefore, we tested if dysregulation of C/EBPα is associated with decreased PU.1 expression. Gene expression studies in several human AML cell lines revealed a positive correlation between C/EBPα and PU.1 expression. Furthermore, we analyzed expression of C/EBPα and PU.1 in a well characterized cohort of 285 AML patients. Importantly, PU.1 expression was strongly reduced in cases with either C/EBPα mutations or C/EBPα promoter silencing compared to other AML subtypes. Taken together, our data support that PU.1 is a downstream target gene of C/EBPα in normal hematopoiesis as well as human leukemia. We currently develop a mouse model containing targeted mutations of three C/EBP binding sites in the PU.1 URE. This model will help to further pinpoint the functional impact of C/EBPα mediated regulation of PU.1 in different hematopoietic populations and to determine how this regulation may contribute to leukemia development in vivo. The first two authors contributed equally to this work. Disclosures: No relevant conflicts of interest to declare.


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