scholarly journals Gene Expression Profiles Identify Biomarkers of Resistance to Decitabine in Myelodysplastic Syndromes

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3494
Author(s):  
Seungyoun Kim ◽  
Dong-Yeop Shin ◽  
Dayeon Kim ◽  
Somi Oh ◽  
Junshik Hong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Leukemia Cell ◽  
Treatment Strategies ◽  
Myeloid Cell ◽  
Leukemia Cell Line ◽  
Immune Checkpoints ◽  
Hematopoietic Stem

Myelodysplastic syndrome (MDS) is a clonal hematopoietic stem cell disease characterized by inefficient hematopoiesis and the potential development of acute leukemia. Among the most notable advances in the treatment of MDS is the hypomethylating agent, decitabine (5-aza-2′deoxycytidine). Although decitabine is well known as an effective method for treating MDS patients, only a subset of patients respond and a tolerance often develops, leading to treatment failure. Moreover, decitabine treatment is costly and causes unnecessary toxicity. Therefore, clarifying the mechanism of decitabine resistance is important for improving its therapeutic efficacy. To this end, we established a decitabine-resistant F-36P cell line from the parental F-36P leukemia cell line, and applied a genetic approach employing next-generation sequencing, various experimental techniques, and bioinformatics tools to determine differences in gene expression and relationships among genes. Thirty-eight candidate genes encoding proteins involved in decitabine-resistant-related pathways, including immune checkpoints, the regulation of myeloid cell differentiation, and PI3K-Akt signaling, were identified. Interestingly, two of the candidate genes, AKT3 and FOS, were overexpressed in MDS patients with poor prognoses. On the basis of these results, we are pursuing development of a gene chip for diagnosing decitabine resistance in MDS patients, with the goal of ultimately improving the power to predict treatment strategies and the prognosis of MDS patients.

scholarly journals A Gene Depleted DNA Methylation Canyon Maintains Hematopoietic Stem Cell Self-Renewal and NPM1c+ Leukemia By Regulating the Gene Expression of HOXA Cluster

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 649-649
Author(s):  
Xiaotian Zhang ◽  
Margaret Goodell ◽  
Mira Jeong ◽  
Haley Gore ◽  
Wanding Zhou
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Stem Cell ◽  
Cell Line ◽  
Long Range ◽  
Leukemia Cell ◽  
Leukemia Cell Line ◽  
Hoxa Cluster ◽  
Self Renewal ◽  
Hematopoietic Stem

Abstract DNA methylation Canyons (DMC in short, also referred to as DNA methylation Valleys) are long unmethylated regions (UMR) over 3.5kb, in the mammalian genome. DMCs are associated with homeotic genes and can be classified into active DMCs marked by H3K4me3 and repressive DMCs marked by H3K27me3. We performed high resolution in situ HiC on human hematopoietic stem and progenitor cells (HSPC) and differentiated red blood cell (RBC) progenitors derived from HSPC. We found that DMCs over 7.3kb form significant 3D micro-compartment interactions with each other. These interactions are extremely long range and can occur between two loci separated by 60Mb. Thus, we name these DMCs over 7.3kb as Grand DNA methylation Canyon (GDMC). GDMCs are repressive DMCs and bear the highest level of H3K27me3 in the HSPC compared with the remaining UMRs under 7.3kb. Additionally, we found that the interacting GDMCs is organized by Polycomb mediated long range interaction but not cohesion loop extrusion. We also found GDMC interactions disappear in differentiated RBC progenitors derived from HSPC. This suggests a function of GDMC interactions in stem cell maintenance. We thus set out to test the function of GDMC interactions in stem cell self-renewal by deleting GDMC loci. We found one GDMC that lacks genes and transcription activity and enhancer activity marked by H3K4me3 and H3K27ac, is interacting with a repressive part (covered by H3K27me3) of the HOXA cluster only in HSPC. This GDMC is thus named "Geneless Canyon"- GLC in short. By deleting GLC, we found that HSPC self-renewal is impaired significantly. Moreover, expression of active HOXA9 and HOXA10 gene adjacent to the repressive part of HOXA cluster also decreased after deletion. When we checked the 3D genomic interactions around the HOXA region after deletion, we found the long range interactions with GLC disappear, and the enhancer interactions with active HOXA cluster gene promoters are also weakened. This suggests that GDMC interactions can act as the scaffold for the enhancer-promoter interactions to maintain active gene expression.In the detailed examination of regulatory elements in GLC, we found that CTCF binding sites are at the boundary of neighboring Lamin associated domain (LAD) and GLC (Figure 1A). The CTCFs are forming cohesion extrusion loops to include the whole LAD region. Deletion of the CTCF sites also result in the loss of HOXA9 and HOXA10 expression as well as the compromise of self-renewal. Since HOXA9-10 genes are important transcriptional factors for leukemias carrying NPM1c+ and MLL-X mutations. We thus performed CTCF deletions in cell lines with OCI-AML3 and MV4:11 as leukemia cell line models carrying NPM1c+ and MLL-X mutations. We surprisingly found the NPM1c+ cell leukemia cell line display the growth arrest with CTCF deletion, while the MLL-X cell line MV4:11 don't display such effect (Figure 1B). We perform in situ HiC on OCI-AML3 and MV4:11 and found in OCI-AML3 cells GLC forms interaction with HOXA9-HOTTIP regions, while in MV4:11 cells there is no such interaction (Figure 1C).Further examination on epigenomic profiles identified that GLC is activated as super enhancer in OCI-AML3 cells with the loss of Polycomb binding. This indicates that NPM1c+ leukemia may utilize the GLC region as enhancer to boost active gene expression in from HOXA9 to Hottip, with a different mechanism than HSPC. Gene expression analysis after the CTCF deletion further validates that after the CTCF deletion the expression of HOXA9, HOXA10 and HOXA11 is decreased. Interestingly, GLC is also hypermethylated in the OCI_AML3 cells. Thus, we have discovered an important DNA methylation Canyon that regulates the hematopoietic stem cell self-renewal via the structural organization of HOXA region that act as the scaffold for the enhancer-promoter interaction. This Canyon can also act as a super enhancer to activate the HOXA expression in the NPM1c+ leukemia. This suggests the versatile roles of Polycomb targeted Canyon in normal hematopoiesis and leukemia development. Figure. 1 Figure. 1. Disclosures No relevant conflicts of interest to declare.

scholarly journals Differing responses of globin and glycophorin gene expression to hemin in the human leukemia cell line K562

Blood ◽  
1982 ◽  
Vol 59 (4) ◽  
pp. 738-746 ◽  
Author(s):  
BL Tonkonow ◽  
R Hoffman ◽  
D Burger ◽  
JT Elder ◽  
EM Mazur ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Globin Gene ◽  
Leukemia Cell ◽  
K562 Cells ◽  
Leukemia Cell Line ◽  
Human Leukemia ◽  
Globin Mrna ◽  
Human Leukemia Cell Line ◽  
Globin Gene Expression

Abstract The human leukemia cell line, K562, produces embryonic and fetal hemoglobins and glycophorin A, proteins normally associated only with erythroid cells. Hemoglobin accumulation is enhanced by exposure of the cells to 0.05 mM hemin. We have examined K562 cells before and after exposure to hemin to determine whether expression of these erythroid proteins was shared by all cells or confined to specific subpopulations. Globin gene expression was examined by quantitation of globin mRNA sequences, using a 3H-globin cDNA molecular hybridization probe. Constitutive cells produced globin mRNA, the content of which was increased 3–4-fold by hemin. Cell-to-cell distribution of globin mRNA was determined by in situ hybridization of 3H-globin cDNA to constitutive and hemin-treated K562 cells. Virtually all cells in the culture exhibited grain counts above background, indicating globin gene expression by all cells, rather than a confined subpopulation. Virtually all hemin-treated cells had 3–5-fold higher grain counts, indicating uniformly increased globin gene expression. The glycophorin content of K562 cells was estimated by fluorescence-activated cell sorting (FACS) of cells labeled with fluorescein-labeled antiglycophorin antiserum. The vast majority of constitutive cells contained glycophorin, but exhibited to apparent increase in glycophorin accumulation after hemin exposure. Thus, glycophorin and globin genes exhibited differential responses to hemin. These differences could reflect normal differences in the patterns of specialized gene expression in stem cells. Alternatively, different aberrations of gene expression could be occurring in response to the determinants of the neoplastic properties of K562.

2′,5′-Oligoadenylate-Antisense Chimeras Cause RNase L to Selectively Degrade bcr/abl mRNA in Chronic Myelogenous Leukemia Cells

Blood ◽  
1998 ◽  
Vol 92 (11) ◽  
pp. 4336-4343 ◽  
Author(s):  
Avudaiappan Maran ◽  
Cornelius F. Waller ◽  
Jayashree M. Paranjape ◽  
Guiying Li ◽  
Wei Xiao ◽  
...  
Keyword(s):  
Cell Growth ◽  
Cell Line ◽  
Chronic Myelogenous Leukemia ◽  
Leukemia Cell ◽  
Myelogenous Leukemia ◽  
Leukemia Cell Line ◽  
Leukemia Cells ◽  
Mrna Levels ◽  
Rnase L ◽  
Hematopoietic Stem

We report an RNA targeting strategy, which selectively degrades bcr/abl mRNA in chronic myelogenous leukemia (CML) cells. A 2′,5′-tetraadenylate activator (2-5A) of RNase L was chemically linked to oligonucleotide antisense directed against either the fusion site or against the translation start sequence in bcr/abl mRNA. Selective degradation of the targeted RNA sequences was demonstrated in assays with purified RNase L and decreases of p210bcr/abl kinase activity levels were obtained in the CML cell line, K562. Furthermore, the 2-5A-antisense chimeras suppressed growth of K562, while having substantially reduced effects on the promyelocytic leukemia cell line, HL60. Findings were extended to primary CML cells isolated from bone marrow of patients. The 2-5A-antisense treatments both suppressed proliferation of the leukemia cells and selectively depleted levels of bcr/abl mRNA without affecting levels of β-actin mRNA, determined by reverse transcriptase-polymerase chain reaction (RT-PCR). The specificity of this approach was further shown with control oligonucleotides, such as chimeras containing an inactive dimeric form of 2-5A, antisense lacking 2-5A, or chimeras with altered sequences including several mismatched nucleotides. The control oligonucleotides had either reduced or no effect on CML cell growth and bcr/abl mRNA levels. These findings show that CML cell growth can be selectively suppressed by targeting bcr/abl mRNA with 2-5A-antisense for decay by RNase L and suggest that these compounds should be further explored for their potential as ex vivo purging agents of autologous hematopoietic stem cell transplants from CML patients.

scholarly journals Pheno-RNA, a method to identify genes linked to a specific phenotype: application to cellular transformation

2020 ◽  
Author(s):  
Rabih Darwiche ◽  
Kevin Struhl
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Candidate Genes ◽  
Expression Profile ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Cellular Transformation ◽  
Breast Cell Line ◽  
Highly Correlated

ABSTRACTCellular transformation is associated with dramatic changes in gene expression, but it is difficult to determine which regulated genes are oncogenically relevant. Here, we describe Pheno-RNA, a general approach to identify candidate genes associated with a specific phenotype. Specifically, we generate a “phenotypic series” by treating a non-transformed breast cell line with a wide variety of molecules that induce cellular transformation to various extents. By performing transcriptional profiling across this phenotypic series, the expression profile of every gene can be correlated with the transformed phenotype. We identify ~200 genes whose expression profiles are very highly correlated with the transformation phenotype, strongly suggesting their importance in transformation. Within biological categories linked to cancer, some genes show high correlations with the transformed phenotype, but others do not. Many genes whose expression profiles are highly correlated with transformation have never been linked to cancer, suggesting the involvement of heretofore unknown genes in cancer.

scholarly journals The effect of Kagocel® on gene expression of Toll-like receptors of innate immunity in THP-1 human monocytes with different levels of differentiation

2021 ◽  
Vol 21 (2) ◽  
pp. 116-121
Author(s):  
T. M. Sokolova ◽  
V. V. Poloskov
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Active Ingredient ◽  
Viral Infections ◽  
Leukemia Cell ◽  
Leukemia Cell Line ◽  
Acute Monocytic Leukemia ◽  
Toll Like Receptors ◽  
Monocytic Leukemia ◽  
Different Levels

Kagocel® is used in Russia for the treatment of viral infections. In terms of its chemical structure, Kagocel® active ingredient is a copolymer of gossypol polyphenol and carboxymethylcellulose. The study investigated antiviral and cytokine-inducing activity of Kagocel®, as well as its toxic effects. The aim of the study was to investigate the effect of Kagoce ® active ingredient on the induction of expression of the innate immune system receptor genes (Toll-like receptors, TLR) in the THP-1 human acute monocytic leukemia cell line with different levels of differentiation. Materials and methods: the effect of Kagocel active ingredient was investigated at the concentrations of 0.2 and 2 mg/mL in the THP-1 human acute monocytic leukemia cell line with different levels of differentiation: non-differentiated monocytes, and monocytes differentiated into macrophage-like cells. Comparative analysis of the activity of TLR 2, 3, 4, 7, 8, 9 genes was carried out by quantitative RT-PCR. The study determined standard deviations of the levels of gene expression in the experimental cells (2deltaCq ± SD) relative to the expression in the control cells. Results: Kagocel active ingredient at the concentration of 0.2 mg/mL induced activation of TLR2 expression in THP-1 monocytes by 3.5 times, TLR3 by 2 times, TLR4 by 1.6 times, and at the concentration of 2 mg/mL also induced activation of TLR7 and TLR8 by 1.4 times, and TLR9 by 2 times. The levels of TLR2, TLR3, TLR9 induction were significantly higher in THP-1 monocytes partially differentiated into macrophage-like cells, and the highest stimulation level was observed for TLR2 (8 times). Conclusions: the results obtained characterise Kagocel® as a stimulator of TLR genes in the THP-1 cell line. The number of TLR genes induced in THP-1 monocytes was shown to increase with the increase in the product concentration. THP-1 monocyte differentiation into macrophage-like cells enhances susceptibility to Kagocel®. The positive regulation of TLR genes activity may account for antiviral and interferon-inducing properties of Kagocel®, and also suggests the possibility of expanding the use of the product for various immune-associated diseases.

Analysis of the Role of Wnt Signaling for the Interaction between Leukemia Cells and Stroma.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4314-4314
Author(s):  
Akihiro Abe ◽  
Yosuke Niwa ◽  
Jinglan Xu ◽  
Momoko Suzuki ◽  
Fumihiko Hayakawa ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Cell Line ◽  
Leukemia Cell ◽  
Specific Inhibitor ◽  
Canonical Pathway ◽  
Leukemia Cell Line ◽  
Human Leukemia ◽  
Self Renewal ◽  
Hematopoietic Stem

Abstract Wnt signaling plays an important role in hematopoietic stem cell self-renewal and proliferation. Recent results also revealed that an aberrant activation of Wnt signaling has been related with hematological malignancies. We have previously reported a stroma-dependent human leukemia cell line, TRL-01, which could not be maintained by any cytokines without stroma or on fibronectin-coated plate although they periodically stimulated the proliferation. We here analyzed the role of Wnt signaling on the cell-adhesion, proliferation and survival of this cell line. TRL-01 was maintained on human bone marrow stroma cell line, hTERT. The apoptosis of TRL-01 on hTERT was suppressed by Wnt-receptor competitor, secreted Frizzled related protein (sFRP)-1, or Rho kinase inhibitor, Y29632 but not by specific inhibitor of canonical pathway, DKK-1. However, the apoptosis of TRL-01 without hTERT was not affected by sFRP-1, Y29632 or DKK-1. These results suggest that survival of TRL-01 on stroma was regulated by non-canonical pathway of Wnt signaling. Next, the effects of Wnt3A, 5A and 10B on TRL-01 were analyzed by establishing hTERT transduced with Wnt3A, 5A or 10B genes. Wnt3A is known as an important factor for the stimulation of self-renewal and proliferation of hematopoietic stem cells, and Wnt5A and 10B were reported to be expressed in B-ALL. When TRL-01 was cocultured with hTERT/Wnt3A or 10B, adhesion was reduced and β-catenin was significantly increased. The condition medium from hTERT/Wnt3A or 10B also stimulates the accumulation of β-catenin but inhibited the survival and proliferation of TRL-01. Wnt5A did not have any significant effects. These results suggest that Wnt3A and 10B stimulate canonical pathway with accumulation of β-catenin but negatively regulate the survival and proliferation of TRL-01. Comparing the expression pattern of Wnt transcripts of TRL-01 and hTERT by RT-PCR, Wnt5A, 5B and 14 were found to be dominantly expressed in hTERT. The role of Wnt5B and 14 for the interaction between TRL-01 and hTERT remains to be elucidated.

To Study the Proliferative Inhibition of Anticancer Drug in Two Kinds of Ph (+) Leukemia Cell Lines.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4110-4110
Author(s):  
Yuping Gong ◽  
Xi Yang ◽  
Ting Niu
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
Cell Line ◽  
Cell Lines ◽  
K562 Cell ◽  
Lymphoblastic Leukemia ◽  
Leukemia Cell ◽  
Myelogenous Leukemia ◽  
Leukemia Cell Line ◽  
Leukemia Cell Lines

Abstract Abstract 4110 Objective To study the proliferative inhibition of imatinib, daunorubicin and bortezomib in two kinds of Ph(+) leukemia cell lines: chronic myelogenous leukemia cell line K562 expressing P210 protein and acute lymphoblastic leukemia cell line SUP-B15 expressing P190 protein. Methods (1) Cell proliferation with imatinib, daunorubicin and bortezomib for 72 hours was analyzed by the MTT assay and displayed by growth curve and IC50 value. (2) The change of bcr-abl gene mRNA levels after the 48 hours' intervention of imatinib (final concentration at 0μM, 0.35μM, 1 μM) was detected by reverse transcription polymerase chain reaction (RT-PCR). Results (1) The IC50 values of K562 and SUP-B15 cells inhibited by imatinib, daunorubicin and bortezomib for 72 hours was respectively 0.286±0.06 (μmol/L), 0.303±0.009 (μmol/L), 22.127±3.592 (nmol/L) and 1.387±0.180(μmol/L), 0.117±0.017 (μmol/L), 12.350±0.740 (nmol/L), which indicated that the K562 cell line was the more sensitive to imatinib than SUP-B15 cell line, whereas the SUP-B15 cell line had the more sensitivity to daunorubicin and bortezomib. (2) There was no change of bcr-abl gene expression after the 48 hours' intervention of imatinib in both cell lines. Conclusion (1) Imatinib, daunorubicin and bortezomib had good anti-cancer effect to Ph+ leukemia cells in vitro. What's more, the K562 cell was the more sensitive to imatinib and only imatinib will have good effect on chronic myelogenous leukemia. Whereas the SUP-B15 cell had the more sensitivity to daunorubicin and bortezomib and combining imatinib with daunorubicin or bortezomib, the effect will be better on Ph(+) acute lymphoblastic leukemia. (2) The short time intervention of imatinib had no effect on the bcr-abl gene expression and imatinib could need long time to show curative effect for the Ph+ leukemia. Disclosures: No relevant conflicts of interest to declare.

Leukemia Cell-Derived Exosomes Targeted Dendritic Cells Can Induce More Strong Anti-Leukemia Response Than Exosomes Alone

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4278-4278
Author(s):  
Chang Sheng ◽  
Jing Sun ◽  
Chun Wang ◽  
Siguo Hao
Keyword(s):  
Cell Line ◽  
K562 Cell ◽  
Conflicts Of Interest ◽  
Leukemia Cell ◽  
Disease Free Survival ◽  
Membrane Vesicles ◽  
Biological Properties ◽  
Leukemia Cell Line ◽  
Leukemia Cells ◽  
Hematopoietic Stem

Abstract Abstract 4278 Exosomes are the newest family number of ‘bioactive vesicles’ that play important roles in antigen presentation. Recent clinical trials about exosomes have shown minor clinical benefit. However, exosomes derived from leukemia cell lines were less studied, In this study, we investigated the biological properties and anti-leukemia immunity of leukemia cell-derived exosomes (LEX). The results showed that like other tumor cells, similarly, leukemia cells can release exosomes too. Transmission electron microscopy showed that exosomes derived from NB4 cell, a promyloblastic leukemia cell line and K562 cell, a chronic myeloid leukemia cell line were membrane vesicles with diameter about 50–100μ m, and loading their specific moleculars such as RAR-α and ABL and adherent moleculars such as ICAM-1. Similarly, our data also demonstrated the presence of Hsp70 in these two leukemia cell-derived exosomes. The data from two-dimensional electrophoresis of K562 cell-derived exosomes showed that most of molecules expressing on leukemia cells were detected on their exosomes, indicating that LEX load most of proteins expressed on their original leukemia cells. Out data also demonstrated that LEX can induce anti-leukemia CTL response and LEX-targeted DC can induce more efficient anti-leukemia immunity compared with LEX alone. In conclusion, exosome-based therapies could be considered as a promising strategy to prolong disease-free survival in patients with leukemia after consolidation or hematopoietic stem cell transplantation. Disclosures: No relevant conflicts of interest to declare.

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