Ectopic Expression of CDX2 Perturbs HOX Gene Expression in Murine Progenitors Depending on Its N-Terminal Transactivation Domain and Is Closely Correlated with Deregulated HOX Gene Expression in Human Acute Myeloid Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2125-2125
Author(s):  
Vijay P.S. Rawat ◽  
Silvia Thoene ◽  
Vegi M. Naidu ◽  
Natalia Arseni ◽  
Bernhard Heilmeier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myeloid Leukemia ◽  
Hox Genes ◽  
Ectopic Expression ◽  
Normal Karyotype ◽  
Transactivation Domain ◽  
Aberrant Expression ◽  
Npm1 Mutation ◽  
Hox Gene ◽  
Cdx2 Expression

Abstract Deregulated homeobox gene expression characterizes more than 60% of all acute myeloid leukemia (AML) patients, particular in patients with normal karyotype (NK). So far it is largely unknown how the aberrant expression of homeobox genes is initiated in the malignant clone. The ParaHox gene Cdx2 was shown to act as positive upstream regulator of Hox genes in embryogenesis. We have previously shown that ectopic Cdx2, which normally is not expressed in hematopoietic cells, can be the key event in the development of AML in mice (Rawat et al., PNAS 2004). In our present study we now demonstrate that ectopic expression of Cdx2 in murine hematopoietic progenitors induced significant up-regulation of Hox genes with leukemogenic potential such as HoxA9, Hoxa10, HoxA5, Hoxa7, Hoxb6, Hoxb8. Deletion of the N-terminal transactivation domain of Cdx2 abrogated its ability to perturb Hox gene expression and eliminated its leukemogenic potential in vivo (n=13), whereas inactivation of the putative Pbx binding site of the protein did not prevent Cdx2 induced leukemogenesis. As we showed that Cdx2 upregulated leukemogenic Hox genes and caused AML in the murine model we analyzed 115 AML patients for a correlation between the expression levels of CDX2 and deregulated HOX gene expression. A total of 71 patients with normal karyotype (AML NPMc+ = 45 cases; NPMc– = 26 cases) was analyzed for CDX2 expression. 89% of the AML NPMc+ cases showed ectopic expression of CDX2 as well as 88% of the cases without the NPM1 mutation. We extended this analysis to 44 patients with abnormal karyotype and detected ectopic CDX2 expression in 64% (28 out of 44) of the cases: 12 of 24 patients with t(8;21), 10 of 10 patients with t(15;17). Importantly, when the expression level of CDX2 was compared between AML cases with normal and abnormal karyotype, there was 14fold higher expression level in the patient group with NK (n=63) compared to the group with aberrant karyotype (n=28) (ØΔCT 7.72 vs. ØΔCT 11.62, respectively; p>0.001). By using oligonucleotide microarray analysis, we confirmed that high Cdx2 expressing AML-NK patients with (n=12) or without NPM1 mutation (n=12) were characterized by aberrant expression of multiple HOXA and B cluster genes such as HOXA10, HOXA9 and HOXB3, HOXB6 in contrast to AML cases expressing the PML-RARA or AML1-ETO fusion gene or normal healthy donors. Three NPMc- cases with normal karyotype showed the same low level of expression of CDX2 (ΔCT 10.55–11.55) as AML cases with aberrant karyotype. Of note, these three cases did not show any perturbation of HOX gene expression and thereby fell into the same cluster as AML cases with t(8;21) or t(15;17) in the microarray data set evaluating HOX gene expression in the different AML subtypes. All AML-NK patients tested were negative for CDX1 and CDX4 expression. These data link the leukemogenic potential of Cdx2 to its ability to dysregulate Hox genes. They furthermore correlate the level of CDX2 expression with HOX gene expression in human AML and support a potential role of CDX2 in the development of human AML with aberrant Hox gene expression.

Overexpression of CDX2 perturbs HOX gene expression in murine progenitors depending on its N-terminal domain and is closely correlated with deregulated HOX gene expression in human acute myeloid leukemia

Blood ◽  
2008 ◽  
Vol 111 (1) ◽  
pp. 309-319 ◽  
Author(s):  
Vijay P. S. Rawat ◽  
Silvia Thoene ◽  
Vegi M. Naidu ◽  
Natalia Arseni ◽  
Bernhard Heilmeier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Hox Genes ◽  
Constitutive Expression ◽  
Normal Karyotype ◽  
Parahox Gene ◽  
Hox Gene ◽  
Terminal Domain ◽  
Acute Myeloid

The mechanisms underlying deregulation of HOX gene expression in AML are poorly understood. The ParaHox gene CDX2 was shown to act as positive upstream regulator of several HOX genes. In this study, constitutive expression of Cdx2 caused perturbation of leukemogenic Hox genes such as Hoxa10 and Hoxb8 in murine hematopoietic progenitors. Deletion of the N-terminal domain of Cdx2 abrogated its ability to perturb Hox gene expression and to cause acute myeloid leukemia (AML) in mice. In contrast inactivation of the putative Pbx interacting site of Cdx2 did not change the leukemogenic potential of the gene. In an analysis of 115 patients with AML, expression levels of CDX2 were closely correlated with deregulated HOX gene expression. Patients with normal karyotype showed a 14-fold higher expression of CDX2 and deregulated HOX gene expression compared with patients with chromosomal translocations such as t(8:21) or t(15;17). All patients with AML with normal karyotype tested were negative for CDX1 and CDX4 expression. These data link the leukemogenic potential of Cdx2 to its ability to dysregulate Hox genes. They furthermore correlate the level of CDX2 expression with HOX gene expression in human AML and support a potential role of CDX2 in the development of human AML with aberrant Hox gene expression.

Mutation in the Nucleophosmin Gene (NPM1) Is a Stable Marker for Minimal Residual Disease Monitoring in Acute Myeloid Leukemia Patients with Increased Sensitivity and Specificity Compared to Expression of the Wilms Tumor (WT1) Gene.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1602-1602
Author(s):  
Thomas Kristensen ◽  
Birgitte Strange Preiss ◽  
Lone Friis ◽  
Michael B. Møller
Keyword(s):  
Gene Expression ◽  
Myeloid Leukemia ◽  
Residual Disease ◽  
Wilms Tumor ◽  
Normal Karyotype ◽  
Leukemia Cells ◽  
Mutational Load ◽  
Wt1 Gene ◽  
Npm1 Mutation ◽  
Minimal Residual

Abstract Abstract 1602 Poster Board I-628 Mutation in exon 12 of the nucleophosmin (NPM1) gene occurs in approximately 60% of acute myeloid leukemia (AML) patients with normal karyotype. To date, molecular minimal residual disease (MRD) monitoring in this patient group has primarily been based on expression of the Wilms tumor gene (WT1), although expression of WT1 in non-leukemia cells limits the specificity of this marker. Mutation in the NPM1 gene is potentially a superior MRD marker compared to WT1 gene expression by being specific to the malignant clone. The use of NPM1 mutation as a MRD marker would furthermore be in line with the widespread use of leukemia cell specific fusion-genes as MRD markers in AML patients with balanced translocations. In the present study, we therefore evaluated NPM1 mutation as a MRD marker with respect to stability, sensitivity and specificity in direct comparison to WT1 gene expression. A total of 13 relapsed AML patients with normal karyotype that were positive for mutation in NPM1 and WT1 gene expression at the time of diagnosis were included in the study. The NPM1 mutational load and WT1 gene expression was analyzed by real-time qPCR in up to 22 peripheral blood mononuclear cell samples per patient from the time of primary diagnosis to latest follow-up to compare the kinetics of the two markers during periods of morphological remission and relapse events. The 13 patients experienced a total of 18 morphological relapses which were all accompanied by high levels of NPM1 mutation, along with high WT1 mRNA levels, thus demonstrating complete stability of NPM1 mutation during relapse in the present material. During periods of complete morphological remission, the NPM1 mutational load was below detection limit (< 1/1000 cells) in all samples. In contrast, WT1 gene expression was detectable in 70% of these samples, thus demonstrating the limited specificity of this marker. This background WT1 expression in non-leukemia cells reached levels of up to 1% of the levels detected at the time of diagnosis thus limiting the de facto MRD marker sensitivity of WT1. All samples with detectable levels of NPM1 mutation after a period of complete molecular remission were followed by a morphological relapse within weeks. The present study therefore shows that mutation in NPM1 is a stable and more sensitive and specific, and therefore superior, molecular MRD marker than WT1. Disclosures No relevant conflicts of interest to declare.

Global and HOX Gene DNA Methylation In Normal Karyotype Acute Myeloid Leukemia: Clinical Implications and Molecular Correlations

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 231-231
Author(s):  
Stefan Deneberg ◽  
Andreas Lennartsson ◽  
Bertil Uggla ◽  
Verena Gaidzik ◽  
Andrea Corbacioglu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bone Marrow ◽  
Hox Genes ◽  
Normal Karyotype ◽  
Global Methylation ◽  
Hox Gene ◽  
Mutational Status ◽  
Average Methylation ◽  
Wbc Count

Abstract Abstract 231 Background: DNA methylation induces gene silencing in a nonrandom fashion in many types of malignancies. In AML there is no consensus regarding the clinical implications of DNA methylation on a global level. Normal karyotype AML (NK AML) can be prognostically stratified by molecular mutations in genes such as FLT3 and NPM1. We have previously reported that increased gene promoter methylation levels may have positive prognostic implications in AML. Now we have focused and expanded our analysis in a homogenous group of NK AML in an effort to illuminate these issues. Methods and patients: We analyzed genome wide DNA methylation signatures from the diagnostic bone marrow samples of 58 de novo NK AML with the IlluminaHuman27 Methylation array, covering 27000 CpG sites, mainly located in the promoter regions of 15000 individual genes. Global methylation was defined as the average methylation values of all measured CpG sites in the specific sample. All patients were between 18 and 67 years of age and received standard induction chemotherapy. All were eligible for intensive consolidation therapy including allogeneic transplantation. FACS sorted normal bone marrow separated into four stages of myeloid differentiation were analyzed as normal controls. Methylation data were correlated to clinical outcomes and molecular mutational status of NPM1 and FLT3. Functional annotation analyses were performed on differentially methylated genes to find epigenetically perturbed pathways. Further molecular analysis of CEBPA, IDH1 and IDH2 is currently performed. Results and discussion: Global methylation levels varied substantially between AML samples but remained mainly unchanged during normal myeloid differentiation. Methylation levels were significantly higher in AML cases than in the normal myeloid progenitors (p<0.001). There were no correlations between methylation levels, age, white blood cell (WBC) count or bone marrow blast percentage at diagnosis. Increased global methylation correlated significantly to increased in vivo chemosensitivity and to patient survival. CR rates after one course of induction chemotherapy were 64% in the quartile of patients with the highest level of global DNA methylation compared to 32% in others (HR 3.9, p=0.04). Median overall survival of patients of the most methylated quartile was not reached and significantly longer than the 16 months median survival of the least methylated quartile (p=0.001) (see figure below). In a Cox Regression model stratified for FLT3-mutational status, methylation level was an independent prognostic factor for survival (p=0.01) together with WBC count (p=0.01). A functional annotation analysis revealed that NPM1 wild type samples had an enrichment of Homeobox (HOX) gene methylation as compared to NPM1 mutated cases (p=1.7×10−11), providing a mechanism for the previously described difference in HOX gene expression in NPM1 wt vs. NPM1 mutated AML. The average methylation levels of all HOX genes were higher in wild type NPM1 cases compared to NPM1 mutated cases (p=0.02). Additional gene expression array data in our cohort of patients also showed methylation levels of individual HOX genes to be correlated inversely with expression. HOX genes were also enriched in non-FLT3ITD cases compared to FLT3ITD-cases, however, not to a statistically significant degree. In conclusion we show that global DNA methylation levels are predictive of response to chemotherapy and an independent prognostic factor for survival in normal karyotype AML. Furthermore, our results suggest that HOX gene methylation may be the mechanism underlying the previously known difference in HOX-gene expression between NPM1 mutated and unmutated AML cases. Disclosures: Nahi: Jansen-Cilag: Honoraria; Celgene: Honoraria.

scholarly journals Methylation in HOX Clusters and Its Applications in Cancer Therapy

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1613 ◽  
Author(s):  
Ana Paço ◽  
Simone Aparecida de Bessa Garcia ◽  
Renata Freitas
Keyword(s):  
Gene Expression ◽  
Cancer Therapy ◽  
Hox Genes ◽  
Treatment Options ◽  
Chemotherapy Resistance ◽  
Migration And Invasion ◽  
Aberrant Expression ◽  
Hox Gene ◽  
Positional Identity ◽  
Near Future

HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.

Comprehensive Analysis Of HOX Gene Expression and DNA Methylation From 189 Primary AMLs Demonstrates Canonical Patterns Associated With Hematopoietic Stem/Progenitors and Recurrent AML Mutations

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2496-2496 ◽  
Author(s):  
David H Spencer ◽  
Margaret A. Young ◽  
Jeffery M. Klco ◽  
Timothy J. Ley
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Hox Genes ◽  
Embryonic Stem ◽  
Normal Karyotype ◽  
Hematopoietic Stem ◽  
Hox Gene ◽  
Cd34 Cells ◽  
Methylation Patterns

Abstract HOX genes encode a family of homeodomain transcription factors with important roles in hematopoiesis. Expression of HOX genes is also a common feature of acute myeloid leukemia (AML), and functional studies have suggested that HOX-dependent pathways may contribute to leukemogenesis. Although HOX expression is known to correlate with specific AML mutations, the patterns of expression of all 39 HOX genes in primary AML samples, and their relationships with recurrent AML mutations, are incompletely understood. In addition, little is known about the influence of AML mutations on DNA methylation at the HOX loci, and the relationship between HOX gene expression and methylation in AML. In this study, we carried out a combined analysis of gene expression data from microarray and RNA-sequencing platforms and genome-wide DNA array-based methylation from 189 primary AML samples that have been previously characterized by either whole-genome or whole exome sequencing. We also measured expression and methylation using the same platforms from normal bone marrow subsets, including CD34+ cells, promyelocytes, monocytes, neutrophils and lymphocytes, and obtained expression data from CD34+ hematopoietic precursors generated from in vitro differentiation of human embryonic stem cells. Our analysis confirmed previous work on the general patterns of HOX expression in AML. The HOXA and HOXB genes showed variation both within each cluster and across the AMLs, although high level expression was restricted to a subset of these genes, including HOXA3, HOXA5, HOXA7, HOXA9, HOXA10, HOXB2-HOXB4, and HOXB6, as well as HOX cofactor MEIS1; HOXC and HOXD genes were minimally expressed in all of the samples. These observations were orthogonally validated by RNA-seq, and with a targeted Nanostring expression platform. Consistent with previous studies, MLL-positive AML samples (n=11) expressed only HOXA genes and MEIS1. AML samples with CBFB-MYH11 rearrangements (n=12) showed expression of only MEIS1, and HOXB2-HOXB4 at moderate levels; RUNX1-RUNX1T1 (n=7) and PML-RARA (n=19) samples did not detectably express any HOX genes. In AMLs with a normal karyotype (n=85), we observed two distinct patterns; one pattern displayed little or no HOX gene expression (7/85; 8%), and another displayed canonical expression of a specific subset of the HOXA and HOXB genes and MEIS1 (78/85; 92%) with similar relative HOX gene expression levels in all cases. Comparison of this pattern with normal bone marrow revealed the same HOX expression pattern in normal CD34+ cells; additional analysis showed that this pattern was confined to hematopoietic stem/progenitor cells, but was not seen in more mature cells, including other CD34+ subsets, promyelocytes, monocytes and neutrophils. We also measured HOX gene expression in CD34+ hematopoietic precursors generated from in vitro differentiation of human embryonic stem cells, which revealed expression of only MEIS1 and the canonical HOXB genes, suggesting that activation of these genes may represent the earliest events in the HOX pathway of hematopoietic development. Correlation of HOX expression with recurrent AML mutations by gene set enrichment analysis demonstrated a significant association with NPM1 (P<10-4) and DNMT3A (P<10-2) mutations, but not with other recurrent somatic mutations, including FLT3,IDH1/IDH2, and TET2. Methylation at the HOX loci demonstrated patterns that correlated with HOX expression, including hypomethylation at HOX promoters in samples with high expression. However, additional mutation-specific patterns were apparent. For example, NPM1-mutant AMLs demonstrated a distinct methylation pattern that included hypomethylation at the HOXB3 promoter, which was not shared with CBFB-MYH11 cases or other AMLs with HOXB3 expression. In summary, our comprehensive analysis demonstrates canonical expression and methylation patterns at the HOX loci in AML. These patterns correspond to specific recurrent AML mutations, and the dominant pattern in most normal karyotype AMLs mimics the signature of hematopoietic stem cells. This supports previous observations of developmental regulation of HOX genes in hematopoiesis, and implies that this normal stem cell signature is “captured” in the majority of AMLs with normal karyotype. In addition, distinct methylation patterns at HOX loci suggest that multiple regulatory mechanisms are involved in HOX expression in AML. Disclosures: No relevant conflicts of interest to declare.

AML with mutated NPM1 carrying a normal or aberrant karyotype show overlapping biologic, pathologic, immunophenotypic, and prognostic features

Blood ◽  
2009 ◽  
Vol 114 (14) ◽  
pp. 3024-3032 ◽  
Author(s):  
Claudia Haferlach ◽  
Cristina Mecucci ◽  
Susanne Schnittger ◽  
Alexander Kohlmann ◽  
Marco Mancini ◽  
...  
Keyword(s):  
Chromosomal Aberrations ◽  
Myeloid Leukemia ◽  
Who Classification ◽  
Hox Genes ◽  
Normal Karyotype ◽  
Abnormal Karyotype ◽  
Npm1 Mutation ◽  
Prognostic Features ◽  
Genetic Lesion ◽  
Additional Chromosome

Acute myeloid leukemia (AML) with mutated NPM1 usually carries normal karyotype (NK), but it may harbor chromosomal aberrations whose significance remains unclear. We addressed this question in 631 AML patients with mutated/cytoplasmic NPM1. An abnormal karyotype (AK) was present in 93 of 631 cases (14.7%), the most frequent abnormalities being +8, +4, −Y, del(9q), +21. Chromosome aberrations in NPM1-mutated AML were similar to, but occurred less frequently than additional chromosome changes found in other AML with recurrent cytogenetic abnormalities according to WHO classification. Four of the 31 NPM1-mutated AML patients karyotyped at different time points had NK at diagnosis but AK at relapse: del(9q) (n = 2), t(2;11) (n = 1), inv(12) (n = 1). NPM1-mutated AML with NK or AK showed overlapping morphologic, immunophenotypic (CD34 negativity), and gene expression profile (down-regulation of CD34 and up-regulation of HOX genes). No difference in survival was observed among NPM1-mutated AML patients independently of whether they carried a NK or an AK, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Findings in our patients point to chromosomal aberrations as secondary events, reinforce the concept that NPM1 mutation is a founder genetic lesion, and indicate that NPM1-mutated AML should be clinically handled as one entity, irrespective of the karyotype.

scholarly journals The LincRNA HOTAIRM1, Located in the HOXA genomic Region, impacts Prognosis in Acute Myeloid Leukemia and Is Associated with a Distinctive microRNA Signature

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1003-1003
Author(s):  
Marina Díaz-Beyá ◽  
Alfons Navarro ◽  
Salut Brunet ◽  
Josep F Nomdedeu ◽  
Anna Cordeiro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Prognostic Value ◽  
Hox Genes ◽  
Genomic Region ◽  
Expression Level ◽  
Molecular Characteristics ◽  
Npm1 Mutation ◽  
Acute Myeloid

Abstract Background: Non-coding RNAs (ncRNAs) have recently emerged as key regulators of diverse cellular processes, including leukemia. ncRNAs are classified according to their size as short (eg, microRNAs) or long ncRNAs. lincRNAs are long ncRNAs located in intergenic regions and have multiple regulatory functions, including gene expression regulation. Interestingly, active crosstalk between microRNAs and lincRNAs has been observed. lincRNAs are known to be deregulated in some cancers but their importance in acute myeloid leukemia (AML) is so far unknown. HOX genes play an important role in hematopoiesis and are deregulated in AML. lincRNAs are especially abundant in the clusters of HOX genes. HOTAIRM1, a myeloid lineage-specific lincRNA, is located at the 3’end of the HOXA cluster and seems to play a regulatory role in myelopoiesis. However, to date the potential prognostic role of HOTAIRM1 expression in AML has not been examined. Aims: To investigate first whether the expression of the lincRNA HOTAIRM1 is associated with the clinical, cytogenetic and molecular characteristics and microRNA expression in AML patients. Secondly, since intermediate risk (IR) AML patients have a highly diverse prognosis, we analyzed the potential prognostic value of HOTAIRM1 expression in IR-AML patients. Methods: To explore the expression level of HOTAIRM1 among different AML subtypes, we analyzed samples from 244 AML patients including CBF-rearranged AML (n=5), APL (n=4), MLL-rearranged AML (n=3), EVI1-rearranged AML (n=3), t(6;9) AML (n=9), AML with monosomal karyotype (n=3), and a large cohort of IR-AML (described below). For the analysis of prognostic value of HOTAIRM1, we analyzed specifically the outcome of 217 IR-AML patients (median age, 52; 51% males) sequentially included in CETLAM trials during the period 1995-2009. Molecular genotyping of this group identified NPM1 mutation (NPM1mut), FLT3-ITD, and biallelic CEBPA mutation (CEBPA mut) in 99 (45%), 79 (36%) and 17 (11%), respectively. The expression of HOTAIRM1 was analyzed using TaqMan® Gene Expression Assays (Applied Biosystems). microRNA and mRNA expression data were obtained in previous studies (Díaz-Beyá, Leukemia 2013). Statistical analyses were performed with BRB Array Tools, SPSS v20 and R v3.0. MaxStat package from R software was used to determine the optimal cutoff point of HOTAIRM1 expression. Results: Among all 244 patients, HOTAIRM1 expression was significantly different among the 7 included genetic subgroups (ANOVA p=0.0024), with the lowest levels observed in APL-AML patients and the highest in the t(6;9)AML patients. Within the IR-AML group, HOTAIRM1 overexpression was observed in NPM1mut patients (p<0.001). The prognostic study showed that high HOTAIRM1 expression was associated with shorter 5-year overall survival (OS) (27+11% vs.47+8%; p=0.009) shorter 5-year disease-free survival (LFS) (22+12% vs. 53+9%; p<0.001), and a higher cumulative incidence of relapse (CIR) at 5 years (55+15% vs. 34+8%; p=0.004). The effect on outcome was maintained within the subgroup with favorable molecular features (i.e., NPM1mut and CEBPAmut without FLT3-ITD) (OS: 75+11% vs. 39+29%; p=0.026). In the multivariate analysis including age, sex, WBC, NPM1mut, FLT3-ITD and number of treatment cycles for CR achievement as covariates, HOTAIRM1 expression emerged as an independent prognostic marker in OS (HR=2.44; 95% CI: 1.51-3.93; p<0.0001), LFS (HR=2.07; 95% CI: 1.31-3.24; p=0.002) and CIR (HR=2.05; 95% CI: 1.18-3.55; p=0.01). Supervised analysis by means of t-test based on multiple permutations revealed a distinctive 33-microRNA signature which correlated with HOTAIRM1 expression including miR-196b (p<0.001) located in the HOXA genomic region. Moreover, we correlated the expression of HOX genes and HOTAIRM1 and observed a positive correlation with HOXA4 gene expression (R2= 0.6; p=0.001). Conclusion: The expression level of the lincRNA HOTAIRM1 varied among different molecularly-defined AML. Interestingly, HOTAIRM1 expression level showed independent prognostic value within the IR-AML group. Moreover, HOTAIRM1 expression strongly correlates with its neighboring HOXA4 gene and harbors a distinctive microRNA signature. Our findings can pave the way for further studies of HOX-related lincRNAs and microRNAs regulatory networks and their influence on clinical outcome. Acknowledgments: ISCIII RH13/00205, SEHH, FIS13/00999 Disclosures No relevant conflicts of interest to declare.

Cdx4 Upregulates Hox Gene Expression and Generates Acute Myeloid Leukemia Alone and in Cooperation with Meis1a in a Murine Model.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 10-10
Author(s):  
Dimple Bansal ◽  
Claudia Scholl ◽  
Stefan Frohling ◽  
Elizabeth Mcdowell ◽  
Benjamin H. Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Acute Leukemia ◽  
Myeloid Leukemia ◽  
Hox Genes ◽  
Function Analysis ◽  
Marrow Transplant ◽  
Hox Gene ◽  
Acute Myeloid

Abstract HOX genes have emerged as critical effectors of leukemogenesis, but the mechanisms that regulate their expression in leukemia are not well understood. Recent data suggest that the caudal homeobox transcription factors CDX1, 2 and 4, developmental regulators of HOX gene expression, may contribute to HOX gene dysregulation in leukemia. We report here that CDX4 is normally expressed in early hematopoietic progenitors, and is aberrantly expressed in~25% of AML patient samples. Cdx4 regulates Hox gene expression in the adult murine hematopoietic system, and upregulates Hox genes that are implicated in leukemogenesis. Furthermore, bone marrow progenitors that are retrovirally engineered to express Cdx4 serially replate in methylcellulose cultures, grow in liquid culture and generate a partially penetrant, long-latency acute myeloid leukemia (AML) in bone marrow transplant recipients. Co-expression of the Hox co-factor Meis1a accelerates the Cdx4 AML phenotype and renders it fully penetrant. Structure -function analysis demonstrates that leukemic transformation requires intact Cdx4 transactivation and DNA-binding domains, but not the Pbx co-factor interaction motif. Taken together, these data indicate that Cdx4 regulates Hox gene expression in adult hematopoiesis and may serve as an upstream regulator of Hox gene expression in the induction of acute leukemia. Inasmuch as many human leukemias show dysregulated expression of a spectrum of HOX family members, these collective findings also suggest a central role for CDX4 expression in the genesis of acute leukemia.

Gene Expression Profiling in AML with Normal Karyotype: A Multicenter Study Investigating Molecular Markers in 252 Cases

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 751-751 ◽  
Author(s):  
Alexander Kohlmann ◽  
Lars Bullinger ◽  
Christian Thiede ◽  
Markus Schaich ◽  
Susanne Schnittger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Supervised Classification ◽  
Cross Validation ◽  
Hox Genes ◽  
Normal Karyotype ◽  
Npm1 Mutation ◽  
Mutation Status ◽  
Gene Expression Signatures ◽  
Fold Cross Validation

Abstract Acute myeloid leukemia (AML) is a heterogeneous disease and AML with normal karyotype (AML-NK) is a subgroup with intermediate prognosis. Over the past years molecular analyses have led to the identification of multiple molecular biomarkers that will further allow to dissecting clinically meaningful subgroups in this disease. Here, we present a multicenter study investigating whole-genome expression profiles of 252 cases of AML-NK. In three centers (Dresden, n=78; Munich, n=97; Ulm, n=77) Affymetrix HG-U133 Plus 2.0 microarray analyses were performed according to a standardized protocol. In a first series of analyses we focused on nucleophosmin gene (NPM1) mutations, the most common genetic lesion described in adult de novo AML to date. Gene expression signatures for 138 NPM1-mutated cases were compared to the profiles of 114 NPM1-unmutated cases. Supervised classification analyses resulted in >95% prediction accuracy of NPM1 mutation status (10-fold cross-validation). The sensitivity was very high for the positive detection of NPM1-mutated cases (>97%). Using a resampling approach (100 iterations) and splitting the complete data into a training set (n=168) and test set (n=84) the following genes were amongst the most frequently selected with higher expression in NPM1-mutated cases: HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB9, MEIS1, and PBX3. Lower expression in NPM1-mutated cases was observed for ABCB1, BAALC, MN1, MLLT3, or SPARC. Furthermore, our signature also showed a strong overlap to predictive NPM1 mutation signatures as published by Verhaak et al., and Alcalay et al., with 16/20 common genes and 15/18 common genes, respectively. Interestingly, some few NPM1-unmutated cases were repeatedly classified as being NPM1-mutated suggesting mutations in gene sequences not routinely screened. A strong HOXA-cluster signature is clearly dominant as well in these cases, whereas HOXB-cluster genes demonstrated a similar expression as compared to NPM1-unmutated cases. With respect to the robustness of differential gene expression signatures in NPM1 mutated cases across the laboratories using the top 300 differentially expressed genes, an overlap of 67 (22.3%) probe sets was observed between all three laboratories (NPM1-mutated vs. NPM1-unmutated: Dresden: 36 vs. 42; Munich: 42 vs. 55; Ulm: 36 vs. 41). In a second series of analyses we investigated cases with CCAAT/enhancer binding protein alpha (CEBPA) gene mutations. Gene expression signatures for 26 CEBPA-mutated cases were compared to the profiles of 132 CEBPA-unmutated cases. Supervised classification analyses resulted in >90% prediction accuracy of CEBPA mutation status (10-fold cross-validation) and frequently selected genes included HOXA2, HOXA3, HOXA5, HOXA7, HOXA9, HOXA10, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, and HOXB9. Thus, several HOX genes were overlapping to the NPM1 signature, albeit with an inverse correlation, i.e., HOX genes with relative overexpression expression in NPM1-mutated AML-NK demonstrated low expression in CEBPA-mutated cases. Finally, all 252 cases have also been characterized according to their fms-related tyrosine kinase 3 gene (FLT3) internal tandem duplication mutation status and this data is currently being integrated with the obtained signatures from above to develop a multi-gene prognostic model for AML-NK. In conclusion, our gene expression profiling study demonstrates robust signatures for AML-NK with NPM1 or CEBPA mutations. As our knowledge of this heterogeneous disease is increasing it seems possible to refine the classification of AML by incorporating molecular risk-based gene expression signatures.

Analysis of Hox gene expression in the chick limb bud

Development ◽  
1996 ◽  
Vol 122 (5) ◽  
pp. 1449-1466 ◽  
Author(s):  
C.E. Nelson ◽  
B.A. Morgan ◽  
A.C. Burke ◽  
E. Laufer ◽  
E. DiMambro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Sonic Hedgehog ◽  
Hind Limb ◽  
Hox Genes ◽  
Expression Patterns ◽  
Limb Bud ◽  
Posterior Portion ◽  
Hox Gene ◽  
Hoxd Gene

The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3′ genes are expressed in the fore limb bud while the 5′ genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.

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