Differential Gene and MicroRNA Expression In a HOXA9-MEIS1 Model of Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 64-64
Author(s):  
Joanne Margaret Ramsey ◽  
Glenda Joanne Dickson ◽  
Janetta Jacoba Bijl ◽  
Ken I. Mills ◽  
Terence R.J. Lappin ◽  
...  
Keyword(s):  
Target Genes ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Normal Karyotype ◽  
Retroviral Infection ◽  
Appreciable Change ◽  
Inhibition Of Proliferation ◽  
Altered Expression ◽  
Expression Levels ◽  
Blast Cells

Abstract Abstract 64 Altered expression of the HOX-MEIS axis is associated with leukemia, particularly AML, where it plays a role in increased proliferation and impaired differentiation. Particular focus has been placed on the role of HOX-MEIS in leukemia with MLL gene rearrangements and MLL-fusion induced models that represent this poor prognostic subgroup. However more recently, we and others have identified altered expression of HOX-MEIS in AML with normal karyotype (AML-NK) that accounts for the vast majority of patients with this disease. The prognostic outcome of this large subgroup of patients is varied and may depend on other molecular aberrations such as NPM-1 mutation, FLT3-ITD or CEBPB status. A murine model of leukemia using co-overexpression of HOXA9-MEIS1 was developed to investigate their role in an AML-NK setting. Expression levels of the collaborating oncogenes was limited by combination of a bicistronic ires targeting vector, low titre retroviral infection and limiting dilution assay (LDA). HOXA9 and MEIS1 expression was measured using quantitiative PCR (qPCR) and levels obtained in the mouse were similar to those observed for AML-NK patients. The resultant leukemia was transplantable leading to premature death in non-irradiated recipient mice within 30 days (104 cells transplanted). Observed pathology included circulating blasts in the periphery, splenomegaly, tissue infiltration of blast cells (kidney, lung, liver) and enlarged lymph nodes, indicative of leukemia. Blast cells were identified as Kit+, Gr-1+, Mac-1+, CD150lo consistent with a myeloid progenitor phenotype. To evaluate downstream events associated with the leukaemic phenotype TaqMan-based Low Density Arrays (TLDAs) and Open Arrays (Biotrove) were used to obtain gene and microRNA (mIR) expression profiles. The majority of genes assayed 699/821 were either not expressed or showed no appreciable change in expression (ΔΔCT < 2) between the leukaemic and normal bone marrow control samples. Of those genes that showed a measurable change in expression, 111/122 assessed in the pluripotent stem cell, transcription factor and immune arrays were downregulated in the HOXA9-MEIS1 induced leukemia samples compared to control mice (n=4 per group). Individual assays were designed for a subset of candidate genes and validated against the TLDA results. Several genes identified as consistently downregulated in the leukaemic cells, including Smad1 and E2f7, were associated with negative regulation of cell proliferation using DAVID Bioinformatics Resources 6.7. Consistent increased expression of HOXA9 and MEIS1 was confirmed by individual assays as was elevated Elf5, Cd34 and Cd28 levels. mIRs regulate the expression of protein-coding genes in part through cleavage of targeted transcripts by partial or complete base pairing. A growing number of mIRs are differentially regulated in normal and malignant hematopoiesis, where increased mIR levels are associated with downregulation of target gene subsets. mIR expression profiles were compared between leukemic and control mice to investigate their association with the global downregulation of gene expression observed in the leukaemic model. Approximately 16% (48/303) of the mIRs showed measurable changes in expression levels (ΔΔCT >2) between the two models, with >70% (34/48) demonstrating increased expression, up to 360-fold, in the leukemia samples. Candidate mIRs were further examined using the mirDB and/or miRecords target prediction databases. Several of the leukaemia-associated upreglated mIRs putatively target members of the validated subset of downregulated genes e.g. mIR-466c and mIR-181c are predicted to target Smad1 and E2F7 respectively. This study suggests that HOXA9-MEIS1 leukemogenesis occurs in part due to increased expression of a subset of mIRs that are predicted to target genes associated with inhibition of proliferation in an AML-NK model. Disclosures: No relevant conflicts of interest to declare.

Expression Patterns of Hoxa4 and Meis1 Genes Are Regulated by Promoter Hypermethylation and When Combined Predict Survival in AML.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1204-1204
Author(s):  
Lykke Christina Grubach ◽  
Mike Zangenberg ◽  
Hans Beier Ommen ◽  
Anni Aggerholm ◽  
Peter Hokland
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Expression Patterns ◽  
Group Identification ◽  
Normal Karyotype ◽  
Promoter Hypermethylation ◽  
Melting Curve Analysis ◽  
Altered Expression ◽  
Expression Levels ◽  
Prognostic Group

Abstract INTRODUCTION: Acute myeloid leukemia (AML) is a heterogeneous disease with varying survival rates depending mostly upon the molecular phenotype of the single leukemic clone. The most powerful predictor for the outcome of the individual patient is the cytogenetic profile at the time of diagnosis, dividing the patients into good, intermediate and adverse prognostic group. However, given that 40–60 percent of patients exhibits a normal karyotype and are assigned to an intermediate prognostic group, identification of biologic parameters, which either alone or in combination, predict disease outcome more precisely are needed. We have previously performed a gene expression profiling study (Grubach et al, Eur J. Hematol. 2008 Apr 10. [Epub ahead of print]) on a series of Polycomb, Hox and Meis genes expressed in hematopoietic cells. AIM: Based on the finding that HOXA4 could be used as a predictor for outcome in AML patients with a normal karyotype, we hypothesized that combining the gene expression of the HOXA4 gene and co-factor MEIS1 might unravel a leukemogenic impact in other cytogenetic prognostic groups (Grimwade et al. Blood. 1998 Oct 1;92(7):2322–33). In addition, given that epigenetic events might contribute to the regulation of these genes, we determined whether promoter hypermethylation of CpG islands in the promoter regions were of relevance to the expression levels of HOXA4 and MEIS1. MATERIALS & METHODS: Diagnosis samples from 248 AML patients were analyzed by RQ-PCR for expression levels of HOXA4 and MEIS1. 157 of these patients were further analyzed for promoter hypermethylation of the same genes by bisulphite treatment of DNA followed by methylation-specific melting curve analysis (MS-MCA). RESULTS: When combining the gene expression levels of HOXA4 with MEIS1 into the three main groups (low HOXA4/low MEIS1, low HOXA4/high MEIS1 and normal-high HOXA4/high MEIS1; (the latter pooled to enable statistical calculations)), clear differences in overall survival were found (Fig. 1). Thus, within the group of patients exhibiting low levels of HOXA4 transcript, those with a high expression of MEIS1 had a significantly worse outcome than those having low MEIS1 expression (p=0.025). Importantly, in a multiparameter regression analysis, the prediction was independent of the cytogenetic grouping, of mutations in NPM1 and FLT3 genes, WBC and age. Given the efficacy of demethylating therapy, we also considered the mechanism of HOXA4 and MEIS1 gene regulation. Thus, when promoter methylation of HOXA4 and MEIS1 in 157 patients was investigated, we found that 15 % of the patients had hypermethylation of the promoter region of MEIS1 and 77% of the patients showed hypermethylation of HOXA4. Importantly, a significant correlation for both of the genes between the expression level and methylation state was observed (MEIS1, p=0.001 and HOXA4, p=0.007). CONCLUSION: The altered expression levels of HOXA4 and MEIS1 in AML reflect, at least partly, an epigenetic regulation by virtue of promoter hypermethylation. The level of transcripts of HOXA4 and MEIS1 seem to contribute to the leukemogenesis in AML and can serve as independent prognostic variables regardless of their cytogenetic and molecular background. Fig. 1. Overall survival of AML patients-stratified by cytogenetics, mutations in NPM1 and FLT3, WBC and age. By combination of HOXA4 and Meis1 expression a significant better survival is linked to those with a low HOXA4/low MEIS1 compared to those with a low HOXA4/high MEIS1 expression. Fig. 1. Overall survival of AML patients-stratified by cytogenetics, mutations in NPM1 and FLT3, WBC and age. By combination of HOXA4 and Meis1 expression a significant better survival is linked to those with a low HOXA4/low MEIS1 compared to those with a low HOXA4/high MEIS1 expression.

Molecular Determinants of Lymph Node Microenvironment Induced Host Immune Tolerance In CLL: Role for CAV1, PTPN6, and PKCβ In the Process

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1367-1367
Author(s):  
Christine Gilling ◽  
Amit Mittal ◽  
Vincent Nganga ◽  
Vicky Palmer ◽  
Dennis D. Weisenburger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mouse Model ◽  
Immune Tolerance ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Aggressive Disease

Abstract Abstract 1367 Previously, we have shown that gene expression profiles (GEP) of CLL cells from lymph nodes (LN), bone marrow (BM), and peripheral blood (PB) are significantly different from each other. Among the major pathways associated with differential gene expression, a “tolerogenic signature” involved in host immune tolerance is significant in regulating CLL progression. The genes associated with the tolerogenic signature are significantly differentially expressed in patient LN-CLL compared to BM-CLL and PB-CLL, suggesting that LN-CLL cells induce this immune tolerance. From 83 differentially expressed genes identified by GEP that are associated with immune dysregulation, we selected eleven genes (CAV1, PTPN6, PKCb, ZWINT, IL2Ra, CBLC, CDC42, ZNF175, ZNF264, IL10, and HLA-G) for validation studies to determine whether these genes are also dysregulated in the Emu-TCL1 mouse model of CLL. The results demonstrate a trend of upregulation of these genes as determined by qRT-PCR in the LN-tumor microenvironment. To further evaluate the kinetics of selected gene expression during tumor progression, we determined the expression levels of Cav1, Ptpn6, and Pkcb at 12, 24, and 36 weeks of CLL development in the Em-TCL1 mouse model. We found that the expression of all three genes increased as a function of age, indicating a correlation of gene expression with disease progression. In addition, as CLL progressed in these mice there was a marked decrease in CD4+ and CD8+ T cells. The murine data were further validated using CLL cells from the same patients with indolent versus aggressive disease indicating a similar trend in expression as CLL progressed (n=4). Furthermore, patient data analyzed by Kaplan Meier analyses of the expression levels of the selected genes indicated a significant association between down-regulation of PTPN6 (p=0.031) and up-regulation of ZWINT (p<0.001) with clinical outcome as determined by a shorter time to treatment (p<0.05). Functional analysis by knockdown of CAV1 and PKCb in primary patient CLL cells determined by MTT assay showed a decrease in proliferation following knockdown of these genes (p<0.005). Protein-interaction modeling revealed regulation of CAV1 and PTPN6 by one another. Additionally, the PTPN6 protein regulates B cell receptor (BCR) signaling and subsequently the BCR regulates PKCb. Therefore, these data from both mice and humans with CLL, argue that an aggressive disease phenotype is paralleled by expression of genes associated with immune suppression. In particular, evidence presented here suggests, dysregulation of CAV1, PTPN6, ZWINT, and PKCb expression promotes CLL progression. Disclosures: No relevant conflicts of interest to declare.

Analysis of Microvesicle Microrna Expression Profiles and Their Functional Roles in ALL Subtypes

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1488-1488
Author(s):  
Xiaomei Chen ◽  
Wei Xiong ◽  
Xiangjun Chen ◽  
Cong Lu ◽  
Fang Liu ◽  
...  
Keyword(s):  
Cell Line ◽  
Mirna Expression ◽  
Target Genes ◽  
Expression Profiles ◽  
Jurkat Cells ◽  
Negative Regulator ◽  
Altered Expression ◽  
Normal Peripheral Blood ◽  
Potential Target ◽  
Mirna Expression Profiles

Abstract Abstract 1488 Microvesicles (MVs) released by leukemia cells constitute an important part of the leukemia microenvironment. As a cell-to-cell communication tool, MVs transfer microRNA(miRNA) between cells. MVs miRNAs may be valuable not only as a diagnostic tool but may also provide an insight in the role of miRNAs playing in the underlying of pathophysiologic processes of various leukemia. It is worth evaluating whether MVs possess some unique miRNA content depending on their corresponding leukemia origin that could be applicable in diagnosis. Hence, we determined the miRNA expression profiles of ALL-derived MVs using Agilent miRNA microarray analysis. The five miRNAs obtained by microarray profiling were validated using real-time PCR. The putative target genes were predicted by bioformation software. Here, we provided MVs miRNA patterns derived from the healthy controls, B-ALL cell line Nalm 6 cells and T-ALL cell line Jurkat cells. We identified 182 dysregulated miRNAs in MVs derived from Nalm 6 cells as compared with MVs from normal controls (P<0.05); both up regulated(123/182) and down regulated(59/182) expressions were observed. Likewise 166 miRNAs were significantly differentially expressed in MVs derived from Jurkat cells versus MVs from normal peripheral blood (P<0.05), 114 miRNAs of which (114/166) were up expression and 52 miRNAs (52/166) were down expression. We also fould that 44 miRNAs were only detected in B-ALL-derived MVs. MiR-1290, miR-1246, miR-1268, miR-1226, and miR-424 were top 5 expressed in Nalm 6 derived MVs, suggesting that those miRNAs may play an important role in B-ALL. We observed that 16 miRNAs detected only in T cell derived MVs. MiR-96 is up regulated in MVs from T-ALL cells but not expressed in B-ALL. Specific and functional target sites for miR-96, exist in the 3'-UTR of the miRNA that encodes the putative tumor suppressor transcription factor FOXO1. The expression signatures of miR-96 could discriminate B-ALL from T-ALL. In contrast, the MVs from B-ALL cell line, shared 100 miRNAs with MVs from T-ALL cell line, suggestting that those miRNAs play roles in both B-and T-ALL. Of 100 miRNAs, 99 miRNAs were high expression, indicating that miRNAs were active in ALL. This obsearvation suggusted that miRNA differential expression in MVs were partially significantly related to subtypes of acute lymphoblastic leukemia. Intriguing is that miR1290 is top higher expression both in MVs derived from Nalm6 cells and from Jurkat cells; miR-1290 is 475-fold higher expressed in Nalm 6 derived MVs versus MVs from normal cells, whereas this miRNA is 245-fold higher expressed in Jurkat cells. Five of these miRNAs were selected to be further assayed and validated by PCR. The qRT-PCR results correlated well with the microarray data. In addition, we found seven miRNAs(miR-148b, miR-484, miR-let-7f, let-7a, miR-223, miR16 and miR-27b) were located near the 11q23 chromosomal region. With bioinformatic tools (TargetScan), we predicted potential target genes for those miRNAs that exhibited altered expression in MVs from B-ALL and T-ALL. The p85 subunit of phosphatidylinositol 3-kinase (PI3-K) was found to be a potential target of miR-320. Of particular interest, we found that protein tyrosine phosphatase-like member b (PTPLB) may be a potential target of miR-1290. The 474-fold increase in miR-1290 in MVs from Nalm 6 cells, indicating that miR-1290 may participate in the modulation of leukemia by targeting PTPLB, a specific, negative regulator of p210 bcr-abl signal. In conclusion, we identified miRNAs and found that miRNA expression profiles were ALL subtype-specific. Altered miRNA expression levels may lead to an inappropriate expression of target oncoproteins or target tumor suppressors, thereby facilitating the development of leukemia. These findings expanded the potential diagnostic markers of leukemia and provided useful information to ALL pathogenesis. Disclosures: No relevant conflicts of interest to declare.

Mirnas and Gene Expression Profiles in CD34+ Cells Are Dependent On the Source of Progenitor Cells Employed in Transplantation.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3020-3020
Author(s):  
Alicia Báez ◽  
Beatriz Martin-Antonio ◽  
Concepción Prats-Martín ◽  
Isabel Álvarez-Laderas ◽  
María Victoria Barbado ◽  
...  
Keyword(s):  
Gene Expression ◽  
Conflicts Of Interest ◽  
Reference Group ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Cd34 Cells ◽  
Different Sources

Abstract Abstract 3020 Introduction: Hematopoietic progenitors cells (HPCs) used in allogenic transplantation (allo-HSCT) may have different biological properties depending on their source of origin: mobilized peripheral blood (PB), bone marrow (BM) or umbilical cord (UC), which may be reflected in miRNAs or gene expression. The identification of different patterns of expression could have clinical implications. The aim of this study was to determine differences in miRNAs and gene expression patterns in the different sources of HPCs used in allo-HSCT. Materials and Method: CD34 + cells were isolated by immunomagnetic separation and sorting from 5 healthy donors per type of source: UC, BM and PB mobilized with G-CSF. A pool of samples from PB not mobilized was used as reference group. We analyzed the expression of 375 miRNAs using TaqMan MicroRNA Arrays Human v2.0 (Applied Biosystems), and gene expression using Whole Human Genome Oligo microarray kit 4×44K (Agilent). The expression levels of genes and miRNAs were obtained by the 2-ΔΔCTmethod. From expression data hierarchical clustering was performed using the Euclidean distance. To identify genes and miRNAs differentially expressed between the different sources of HPCs statistical Kruskal Wallis test was applied. All analysis were performed using the Multiexperiment Viewer 4.7.1. The function of the miRNAs and genes of interest was determined from the various databases available online (TAM database, Gene Ontology and TargetScan Human). Results: Forty-two miRNAs differentially expressed between the different sources were identified. As compared to BM or UC, in mobilized PB most miRNAs were overexpressed, including the miRNA family of miR515, which is characteristic of embryonic stem cells. On the other hand, 47 genes differentially expressed between the different sources were identified. Interestingly, a similar pattern of expression was observed between movilized PB and UC as compared to BM. Interestingly, 13 of these genes are targets of the miRNAs also identified in this study, which suggests that their expression might be regulated by these miRNAs. Conclusion: There are significant differences in miRNAs and gene expression levels between the different sources of HPCs Disclosures: No relevant conflicts of interest to declare.

Absence of High-Dose Consolidation Courses and Low Numbers of Allogeneic HSCTs Did Not Affect Overall Optimistic Results in B-Cell Precursor Ph-Negative Adult ALL Patients Treated By Non-Intensive but Non-Interruptive ALL-2009 Protocol: Data of the Russian ALL Study Group

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2497-2497
Author(s):  
Elena N. Parovichnikova ◽  
Vera V. Troitskaya ◽  
Andrey Sokolov ◽  
Galina Kliasova ◽  
Larisa A. Kuzmina ◽  
...  
Keyword(s):  
Risk Factors ◽  
High Risk ◽  
Conflicts Of Interest ◽  
Univariate Analysis ◽  
Normal Karyotype ◽  
Risk Groups ◽  
High Dose ◽  
Late Response ◽  
Allogeneic Hsct ◽  
Blast Cells

Abstract Introduction It is postulated that the improvement in the overall treatment outcome in adult Ph-negative ALL came from the implementation of more aggressive pediatric-like protocols and higher portion of allogeneic HSCT. Here we report the results of the adult (15-55 yy) Ph-negative ALL protocol based on the opposite approaches: less intensive but non-interruptive treatment with low numbers of allo-HSCT. The study is registered on the ClinicalTrials.gov public site; NCT01193933. Patients and Methods The ALL-2009 is based on: (1) the replacement of prednisolone (Pdn) 60 mg/m2 with dexamethazone (Dexa) 10 mg/m2 if blast cells are >25% in b/m after prephase (7d); (2) de-intensified but non-interruptive 5 months induction/consolidation treatment (5 wks prd/dexa with 3 instead of 4 dauno/vncr pulses, 4 weeks of 6MP with 5 L-asp, 2 instead of 4 ARA-C blocks, 1 instead of 2 Cph injections during induction; induction-like 3 consolidations for 3wks, 2wks, 4wks-continuously without intervals), followed by (3) 2 late (at 6 mo) intensifications- with 1 day HD MTX and with 1 d HD ARA-C, both with L-asp and 3 ds dexa and (4) 2-yrs continuous 6MP/MTX maintenance with doses modification according to myelosuppression with monthly 3-days dexa/vncr/L-asp pulses (∑ L-asp = 590.000 IU/m2). The protocol was identical for all risk groups. Allo-HSCT was indicated only for extremely high-risk BCP-ALL (t(4;11),L>100). No central MRD monitoring was performed. Since Apr 2009 till June 2015 20 centers had recruited 168 BCP-Ph-negative ALL pts with a median age 28 years (15-54), 84f/84 m. Full cytogenetics was available in 67,3% (n=113), 43,4% of them (n=49) had normal karyotype (NK), 10% (n=9%) had no mitosis, 47,6% (n=54) - different abnormalities (hypoploid-1, hyperploid-12, t(11q23)/MLL-8, del11q23-2, t(1;19)-2, t(12;21)-1;others-28). 26,7% of pts (n=45) were in the standard risk (SR) group (WBC <30, EGIL BII-III, LDH < 2N; no late CR; t(4;11)-negative), 56,5% (n=95) - in the high risk (HR) group (WBC >30; EGIL BI, LDH > 2N; late CR; t(4;11)-positive), 28 patients (n=16,8%) were not qualified by the risk. The analysis was performed in June 2015. 158 pts were available for analysis. Results CR rate in 158 available for analysis pts was 87,7% (n=139), induction death occurred in 9,1% (n=14), resistance was registered in 3,2% (n=5). The majority of CR pts (87,8%) achieved it after prephase (12,2%, n=17) and the 1st phase of induction (75,6%, n=105). Late responders constituted 12,2% (n=17). Allogeneic BMT was performed only in 9 of 144 patients who survived induction (6,2%). Totally 31 pts (22,3%) had relapsed. At 60 mo OS for the whole group constituted - 50%, DFS - 51.3%. In a univariate analysis among various risk factors (age <> 30y, initial risk group, WBC, LDH, immunophenotype, late response >35d, PRD resistance) age (>30 y) became statistically significant for OS, DFS and relapse probability (RP) (pic.1), abnormal karyotype - for DFS (30% vs 68%, p=0,04) and RP (42% vs 19%, p= 0,04). In a multivariate analysis no common risk factors were significant. Conclusions Our data demonstrate that the proposed treatment approach is rather effective. We believe that constant non-interruptive treatment without intensive highly myelosuppressive consolidation courses and high portion of allogeneic HSCT may become an alternative and reproducible approach in adult Ph-negative ALL, though we have to stress that it should be very strict compliance of the pts to the protocol. All pts, mostly from the region hospitals who refused prolonged and constant treatment (~5%), relapsed. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

scholarly journals Role of miR-10b-5p in the prognosis of breast cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7728 ◽  
Author(s):  
Junmin Wang ◽  
Yanyun Yan ◽  
Zhiqi Zhang ◽  
Yali Li
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cancer Development ◽  
Clinicopathological Parameters ◽  
Aberrant Expression ◽  
Expression Levels ◽  
Ppi Networks

Breast cancer is the leading cause of cancer-related death in women worldwide. Aberrant expression levels of miR-10b-5p in breast cancer has been reported while the molecular mechanism of miR-10b-5p in tumorigenesis remains elusive. Therefore, this study was aimed to investigate the role of miR-10b-5p in breast cancer and the network of its target genes using bioinformatics analysis. In this study, the expression profiles and prognostic value of miR-10b-5p in breast cancer were analyzed from public databases. Association between miR-10b-5p and clinicopathological parameters were analyzed by non-parametric test. Moreover, the optimal target genes of miR-10b-5p were obtained and their expression patterns were examined using starBase and HPA database. Additionally, the role of these target genes in cancer development were explored via Cancer Hallmarks Analytics Tool (CHAT). The protein–protein interaction (PPI) networks were constructed to further investigate the interactive relationships among these genes. Furthermore, GO, KEGG pathway and Reactome pathway analyses were carried out to decipher functions of these target genes. Results demonstrated that miR-10b-5p was down-regulated in breast cancer and low expression of miR-10b-5p was significantly correlated to worse outcome. Five genes, BIRC5, E2F2, KIF2C, FOXM1, and MCM5, were considered as potential key target genes of miR-10b-5p. As expected, higher expression levels of these genes were observed in breast cancer tissues than in normal tissues. Moreover, analysis from CHAT revealed that these genes were mainly involved in sustaining proliferative signaling in cancer development. In addition, PPI networks analysis revealed strong interactions between target genes. GO, KEGG, and Reactome pathway analysis suggested that these target genes of miR-10b-5p in breast cancer were significantly involved in cell cycle. Predicted target genes were further validated by qRT-PCR analysis in human breast cancer cell line MDA-MB-231 transfected with miR-10b mimic or antisense inhibitors. Taken together, our data suggest that miR-10b-5p functions to impede breast carcinoma progression via regulation of its key target genes and hopefully serves as a potential diagnostic and prognostic marker for breast cancer.

scholarly journals Expression Profiling of a Panel of Apoptosis Related Micrornas in Patients with Acute Myeloid Leukemia

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4971-4971
Author(s):  
Eleftheria Hatzimichael ◽  
Aggeliki Dasoula ◽  
Maria Igglezou ◽  
Andreas Katsenos ◽  
Ioannis Sainis ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Mononuclear Cells ◽  
Conflicts Of Interest ◽  
Gradient Centrifugation ◽  
Target Prediction ◽  
Normal Karyotype ◽  
Membrane Transporters ◽  
Abnormal Karyotype ◽  
Altered Expression ◽  
Solute Carrier

Abstract Introduction: We evaluated the expression of a panel of apoptosis-associated microRNAs (miRNAs) in leukemic blasts isolated from AML patients and investigated their predicted targets. Patients and Methods: We used bone marrow or peripheral blood that were donated by nine AML patients (5 male, 4 female) at diagnosis. Mononuclear cells were isolated by Ficoll-Histopaque (Sigma Aldrich) density gradient centrifugation and were cryopreserved in liquid nitrogen at the Cancer Biobank Center of the University of Ioannina. MicroBeads technology (Miltenyl Biotec) was used for magnetic cell sorting of CD34+ cells of patients' samples, while mononuclear blood cells from healthy individuals were used as controls. Small RNA (< 200 b) was isolated using the NucleoSpin® miRNA kit (Macherey Nagel). Simultaneous quantification of 84 apoptosis- associated miRNAs was performed by using the miScript miRNA PCR Array Human Apoptosis (MIHS-114ZF, Qiagen) in a LightCycler® 480 instrument (Roche AG, Rotkreuz, Switzerland), and relative quantitation of expression was determined by the comparative CT method. For miRNA target prediction we used the RNA22 tool: https://cm.jefferson.edu/rna22 Results: We found 34 downregulated and 20 upregulated miRNAs compared to control. Among the downregulated miRNAs was the miR-29 family and among the upregulated was the miR-181 family, both of which have been previously implicated in AML. The top 10 downregulated miRNAs were miR-31-5p, miR-451a, miR-29b-3p, miR-409-3p, miR-144-3p, miR-9-5p, miR-192-5p, miR-542-3p, miR-134-5p, miR-29c-3p, whereas the top 10 upregulated miRNAs were miR-34a-5p, miR-181a-5p, miR-181c-5p, miR-181d-5p, miR-181b-5p, miR-222-3p, miR-125b-5p, miR-221-3p, Let-7c-5p, miR-186-3p. We used RNA22 to identify genes that are predicted to be simultaneously targeted by all of the 10 top downregulated miRNAs and also the genes that are predicted to be simultaneously targeted by all of the 10 top upregulated miRNAs. The predicted targets for all top 10 downregulated miRNAs include NSD1, MYST4 and SACS. NSD1 is an histone methyltransferase, whereas MYST4 is an histone acetyltransferase. The predicted targets of all top 10 upregulated miRNAs include 35 genes among which are zinc finger transcription factors with proapoptotic activity (ZNF704, ZNF268) and Solute Carrier (SLC) membrane transporters (SLC24A2, SLC24A4, SLC35E3) of undefined functions. When we compared miRNA expression in patients with abnormal karyotype versus patients with normal karyotype we found miR-125a-5p to be overexpressed in patients with abnormal karyotype. Overexpression of miR-125b has been previously reported in patients with myelodysplastic syndromes and APL and plays important roles in mitochondrial apoptosis. Conclusions: A variety of microRNAs are dysregylated in patients with AML. We confirm that the miR-29 family and the miR-181 family have altered expression in AML. We found miR-125a-5p to be overexpressed in patients with abnormal karyotype. Among predicted targets of the upregulated miRNAs are genes encoding proapoptotic zinc finger proteins and Solute Carrier membrane transporters, whereas among the predicted targets of the downregulated miRNAs are genes involved in chromatin remodeling, suggesting that altered function of epigenetic modifiers in AML may be due to dysregylation of miRNAs. Disclosures No relevant conflicts of interest to declare.

scholarly journals DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors

Life ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 59
Author(s):  
Joanna Boresowicz ◽  
Paulina Kober ◽  
Natalia Rusetska ◽  
Maria Maksymowicz ◽  
Agnieszka Paziewska ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mirna Expression ◽  
Target Genes ◽  
Expression Profiles ◽  
Pituitary Tumors ◽  
Target Prediction ◽  
Aberrant Methylation ◽  
Expression Levels ◽  
Putative Target ◽  
Encoding Genes

microRNAs are involved in pathogenesis of cancer. DNA methylation plays a role in transcription of miRNA-encoding genes and may contribute to changed miRNA expression in tumors. This issue was not investigated in pituitary neuroendocrine tumors (PitNETs) previously. DNA methylation patterns, assessed with HumanMethylation450K arrays in 34 PitNETs and five normal pituitaries, were used to determine differentially methylated CpGs located at miRNA genes. It showed aberrant methylation in regions encoding for 131 miRNAs. DNA methylation data and matched miRNA expression profiles, determined with next-generation sequencing (NGS) of small RNAs, were correlated in 15 PitNETs. This showed relationship between methylation and expression levels for 12 miRNAs. DNA methylation and expression levels of three of them (MIR145, MIR21, and MIR184) were determined in the independent group of 80 tumors with pyrosequencing and qRT-PCR and results confirmed both aberrant methylation in PitNETs and correlation between methylation and expression. Additionally, in silico target prediction was combined with analysis of established miRNA profiles and matched mRNA expression pattern, assessed with amplicon-based NGS to indicate putative target genes of epigenetically deregulated miRNAs. This study reveals aberrant DNA methylation in miRNA-encoding genes in gonadotroph PitNETs. Methylation changes affect expression level of miRNAs that regulate putative target genes with tumorigenesis-relevant functions.

The Level of Histone Deacetylase 7 in Pediatric ALL and Its Effect on Survival

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5099-5099
Author(s):  
Bei Hou ◽  
Huyong Zheng
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Histone Deacetylase ◽  
Conflicts Of Interest ◽  
Risk Group ◽  
Lymphoblastic Leukemia ◽  
Intermediate Risk ◽  
Newly Diagnosed ◽  
Altered Expression ◽  
Expression Levels ◽  
Pediatric All

Abstract Background Leukemia is the most common pediatric malignancy and a major cause of mortality and morbidity in children. Nearly 15,000 children are newly diagnosed with leukemia in China each year and among them, acute lymphoblastic leukemia (ALL) accounts for more than 75%. Altered expression of histone deacetylases (HDACs) is a common feature in several human malignancies and may represent an interesting target for cancer treatment . With increasing focus on precision medicine, HDACs have emerged as promising therapeutic target in pediatric ALL. Methods We detect the histone deacetylase 7(HDAC7) expression in the bone marrow samples of 254 children with newly diagnosed acute lymphoblastic leukemia (ALL) at Hematology Oncology Center of Beijing Children`s Hospital from January 2010 to the end of 2012 via qRT-PCR using the TaqMan gene expression probes. 3 patients that have been completely remission for 3 years are used as normal control. We find out that the expression levels of HDAC7 are associated with the unfavorable events (such as induction failure, relapse and/or death due to any cause ) occurence rates and 5-EFS. Results Here we find that the HDAC7 expression levels are associated with the unfavorable events occurence rates and 5-EFS. We find that in the intermediate risk group of 157 patients, the patients who have lower level of HDAC7 expression have higher unfavorable event occurence rates than the higher expression of HDAC7 group (p=0.001). The group of higher HDAC7 expression have higher 5-EFS than the lower group in both the intermediate risk group(p=0.001) and the T-ALL group(n=18). Conclusion We conclude that HDAC7 has a potent anti-oncogenic effect on specific pediatric B-cell leukemia, indicating that its deregulation may contribute to the pathogenesis of the disease. Disclosures No relevant conflicts of interest to declare.

scholarly journals Expression Profiling Identifies TWIST2 Target Genes in Setleis Syndrome Patient Fibroblast and Lymphoblast Cells

2021 ◽  
Vol 18 (4) ◽  
pp. 1997
Author(s):  
Noe E. Crespo ◽  
Alexandra Torres-Bracero ◽  
Jessicca Y. Renta ◽  
Robert J. Desnick ◽  
Carmen L. Cadilla
Keyword(s):  
Expression Profiling ◽  
Target Genes ◽  
Expression Profiles ◽  
Gene Activation ◽  
Gene Expression Profiles ◽  
Autosomal Recessive Disorder ◽  
Cell Types ◽  
Skin Lesions ◽  
Altered Expression ◽  
Facial Development

Background: Setleis syndrome (SS) is a focal facial dermal dysplasia presenting with bilateral temporal skin lesions, eyelash abnormalities and absent meibomian glands. SS is a rare autosomal recessive disorder caused by mutations in the TWIST2 gene, which codes for a transcription factor of the bHLH family known to be involved in skin and facial development. Methods: We obtained gene expression profiles by microarray analyses from control and SS patient primary skin fibroblast and lymphoblastoid cell lines. Results: Out of 983 differentially regulated genes in fibroblasts (fold change ≥ 2.0), 479 were down-regulated and 509 were up-regulated, while in lymphoblasts, 1248 genes were down-regulated and 73 up-regulated. RT-PCR reactions confirmed altered expression of selected genes. Conclusions: TWIST2 is described as a repressor, but expression profiling suggests an important role in gene activation as well, as evidenced by the number of genes that are down-regulated, with a much higher proportion of down-regulated genes found in lymphoblastoid cells from an SS patient. As expected, both types of cell types showed dysregulation of cytokine genes. These results identify potential TWIST2 target genes in two important cell types relevant to rare disorders caused by mutations in this bHLH gene.

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