scholarly journals Selective Inhibition of EZH2 and EZH1 Enzymatic Activity By a Small Molecule Suppresses MLL rearrangement-Induced Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3559-3559
Author(s):  
Gang Greg Wang

Enhancer of Zeste Homolog-2 (EZH2) and Related EZH1 Control Gene Expression and Promote Oncogenesis Via Methylating Histone H3 Lysine 27 (H3K27). These Methyltransferases Are Proposed to be Therapeutic Targets Due to Their Hyperactive Mutations and Overexpression Found in Cancer Including Various Hematological Malignancies. Here, We Characterized a Set of Small Molecules That Allow Pharmacological Manipulation of EZH2 and EZH1, Which Include UNC1999, a Highly Selective Inhibitor of Both Enzymes, and Its Di-Methylated Analog UNC2400, an Inactive Compound Useful to Assess Off-Target Effects. We Show That UNC1999 Suppresses H3K27 Tri- and Di-Methylation Globally and Inhibits Growth of MLL-Rearranged Leukemia Lines. Mechanistically, UNC1999 Preferentially Affects the Regulatory Elements Such As Enhancers and Distal Promoters, Leading to De-Repression of Many Known Polycomb Target Genes. Gene De-Repression Correlates with Decrease in H3K27me3 and Concurrent Gain in H3K27 Acetylation. UNC2400 Does Not Induce These Effects, Demonstrating UNC1999’s on-Target Inhibition. Oral Administration of UNC1999 Significantly Prolongs the Survival of a Well-Defined Murine Leukemia Model Generated By MLL-AF9. Thus, Our Studies Provide Detailed Profiling of a Set of Compounds for Studying EZH2 and EZH1 in Cancer and Establish Specific Inhibition of EZH2 and EZH1 Enzymatic Activities By Small Molecules As a Promising Therapeutics for MLL-Rearranged Leukemia. Disclosures No relevant conflicts of interest to declare.

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2501-2501
Author(s):  
Kyster Nanan ◽  
David P LeBrun

Abstract E2A-PBX1 (EP1) is a chimeric oncogenic transcription factor expressed consequent to the 1;19 chromosomal translocation in cases of acute lymphoblastic leukemia (ALL). EP1 can induce transcription of reporter genes and EP1-driven oncogenesis requires direct binding of EP1 with the transcriptional co-activator and histone acetyltransferase p300. Therefore, we hypothesized that EP1 recruits p300 and other co-activators to cis-acting regulatory elements throughout the genome thereby inducing or maintaining transcription of target genes some of which contribute to the neoplastic phenotype. Here we have used chromatin immunoprecipitation followed by next generation DNA sequencing (ChIP-seq) to identify and characterize EP1-bound sites across the genome of the t(1;19)-associated, ALL-derived cell line RCH-ACV. ChIP was performed with an anti-FLAG antibody using sheared chromatin prepared from RCH-ACV cells that stably expressed FLAG-tagged EP1; ChIP from parent RCH-ACV cells not expressing FLAG-EP1 served as a negative control for peak calling. Parallel immunoprecipitations were performed with antibodies for p300 and the chromatin marks H3K4me3, H3K4me1 and H3K27me3. Sequencing of DNA purified from the immunoprecipitated material and of total RNA (RNA-seq) was carried out commercially by BGI whereas bioinformatic analyses were performed in-house. Bioinformatic analysis of data from replicate samples identified 3166 EP1 binding peaks across the RCH-ACV genome (irreproducible discovery rate threshold <0.01). Most EP1 binding sites were located in intronic (1408 sites) or intergenic (1346 sites) regions. Binding site consensus analysis showed overrepresentation of binding motifs for REST, CTCF, MYC, PAX5 and other transcription factors suggesting indirect recruitment of EP1 to DNA mediated by protein-protein interactions. EP1-bound regions were enriched for p300 binding (Figure 1), consistent with the documented importance of p300 recruitment in EP1 oncogenesis. A particular association with H3K4me3 relative to H3K4me1 or H3K27me3 (Figure 2) suggested association with active promoters. Three hundred and forty-two genes had EP1 binding sites within 1000 bp of their transcriptional start sites and these genes were associated with differentially abundant transcription (Figure 3, P<0.001). Querying the online Mammalian Phenotype Ontology tool with genes associated with EP1 binding generated terms that were obviously rich in phenotypes pertaining to B-lymphopoiesis. In summary, our results suggest that EP1 recruits p300 and other co-activators to transcriptionally active chromatin in ALL cells. Results from studies currently underway to confirm the dependency of target gene expression and p300 recruitment upon binding of EP1 at specific binding sites will be presented. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 713-713
Author(s):  
Katharina Leonards ◽  
Marwa Almosailleakh ◽  
Samantha Tauchmann ◽  
Helene Mereau ◽  
Sabine Juge ◽  
...  

Abstract The nuclear receptor binding SET domain protein 1 (NSD1) histone (H3K36) methyltransferase is target of recurrent genetic alterations in human hematological malignancies and certain solid cancers. To study its role in normal hematopoiesis, we inactivated the Nsd1 gene in the blood forming system of the mouse. Vav1-iCre mediated cleavage of floxed exon 5 resulted in almost complete loss of Nsd1 expression at the mRNA and protein level. After a latency of 7-17 weeks, all Vav1-iCre;Nsd1fl/fl mice developed signs of disease, whereas heterozygous littermates expressed normal Nsd1 levels and remained healthy. Symptomatic mice presented anemia, reticulocytosis and thrombocytopenia with presence of erythroblasts on peripheral blood smears. Diseased mice had significant splenomegaly and infiltration of erythroblasts in spleen, liver and lung. Bone marrow (BM) transplantation from symptomatic mice was able to fully propagate the disease in wild type recipients, alone or in competition with normal cells. The majority of the BM and spleen cells of diseased mice expressed modest levels of the transferrin receptor (CD71dim) and variable amounts of c-Kit and FcγR-II/III, but no TER119, CD34, B220 or Sca-1. The cells formed abnormal BFU-like dense reddish and partially hemoglobinized colonies in erythropoietin (EPO) containing methylcellulose that could be replated up to 4 rounds. In Vav1-iCre;Nsd1fl/fl fetal livers, we also observed accumulation of abnormal erythroid progenitors, deficient for Nsd1, suggesting a prenatal origin of the phenotype. RNA sequencing of lineage marker-negative, Sca1+, c-Kit+ (LSK) cells revealed aberrant regulation of genes associated with/functioning in erythroid differentiation. Indeed, in vitro differentiation of Vav1-iCre;Nsd1fl/fl erythroblasts was significantly impaired. Retroviral expression of Nsd1 was able to partially rescue the erythroid differentiation block. Interestingly, Vav1-iCre;Nsd1fl/fl erythroblasts constitutively expressed significantly increased protein levels of the erythroid master transcriptional regulator GATA1 independent whether they were expanded as immature cells or induced for terminal maturation. Impaired terminal maturation of Vav1-iCre;Nsd1fl/fl erythroblasts was associated with reduced transactivation of GATA1 positively-regulated targets (HbbA, HbbB, Gpa, Bcl2l1, p21), while expression of GATA1-repressed target genes (Gata2, c-kit, Spi1) was not affected. Strikingly, exogenous expression of Gata1 was able to overcome the differentiation block of Vav1-iCre;Nsd1fl/fl erythroblasts depending on the integrity of the N- and C-zinc fingers, as seen in colony forming assays and liquid cultures. Chromatin immunoprecipitation (ChIP) revealed that binding of GATA1 to HbbA1 locus and to a lesser extent to regulatory elements in the Gata1 promoter region (G1-HE site) was impaired in Vav1-iCre;Nsd1fl/fl erythroblasts, but restored upon overexpression of exogenous Gata1 . However, we found no significant changes of global H3K36me1 and H3K36me2 marks in wild type and Vav1-iCre;Nsd1fl/fl erythroblasts. In addition, published ChIP-seq data revealed no enrichment for H3K36me1/2 marks near critical GATA1 binding sites in HbbA1 or Gata1 suggesting that NSD1 most likely regulates GATA1 activity by direct modification or by interfering with GATA1 interacting partners necessary for efficient transactivation of critical mediators of terminal erythroid maturation. Taken together, our work unraveled NSD1 as a critical regulator of terminal erythroid differentiation. Disclosures No relevant conflicts of interest to declare.


Author(s):  
Harri Makkonen ◽  
Jorma J. Palvimo

AbstractAndrogen receptor (AR) acts as a hormone-controlled transcription factor that conveys the messages of both natural and synthetic androgens to the level of genes and gene programs. Defective AR signaling leads to a wide array of androgen insensitivity disorders, and deregulated AR function, in particular overexpression of AR, is involved in the growth and progression of prostate cancer. Classic models of AR action view AR-binding sites as upstream regulatory elements in gene promoters or their proximity. However, recent wider genomic screens indicate that AR target genes are commonly activated through very distal chromatin-binding sites. This highlights the importance of long-range chromatin regulation of transcription by the AR, shifting the focus from the linear gene models to three-dimensional models of AR target genes and gene programs. The capability of AR to regulate promoters from long distances in the chromatin is particularly important when evaluating the role of AR in the regulation of genes in malignant prostate cells that frequently show striking genomic aberrations, especially gene fusions. Therefore, in addition to the mechanisms of DNA loop formation between the enhancer bound ARs and the transcription apparatus at the target core promoter, the mechanisms insulating distally bound ARs from promiscuously making contacts and activating other than their normal target gene promoters are critical for proper physiological regulation and thus currently under intense investigation. This review discusses the current knowledge about the AR action in the context of gene aberrations and the three-dimensional chromatin landscape of prostate cancer cells.


2007 ◽  
Vol 129 (25) ◽  
pp. 7752-7753 ◽  
Author(s):  
Justin S. Cisar ◽  
Julian A. Ferreras ◽  
Rajesh K. Soni ◽  
Luis E. N. Quadri ◽  
Derek S. Tan

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257265
Author(s):  
Seung-Soo Kim ◽  
Adam D. Hudgins ◽  
Jiping Yang ◽  
Yizhou Zhu ◽  
Zhidong Tu ◽  
...  

Type 1 diabetes (T1D) is an organ-specific autoimmune disease, whereby immune cell-mediated killing leads to loss of the insulin-producing β cells in the pancreas. Genome-wide association studies (GWAS) have identified over 200 genetic variants associated with risk for T1D. The majority of the GWAS risk variants reside in the non-coding regions of the genome, suggesting that gene regulatory changes substantially contribute to T1D. However, identification of causal regulatory variants associated with T1D risk and their affected genes is challenging due to incomplete knowledge of non-coding regulatory elements and the cellular states and processes in which they function. Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases, we conducted functional annotation analysis using genomic data from various public databases. These include 1) Roadmap Epigenomics, ENCODE, and RegulomeDB for epigenome data; 2) GTEx for tissue-specific gene expression and expression quantitative trait loci data; and 3) lncRNASNP2 for long non-coding RNA data. Our results indicated a prevalent enhancer-based immune dysregulation in T1D pathogenesis. We identified 26 high-probability causal enhancer SNPs associated with T1D, and 64 predicted target genes. The majority of the target genes play major roles in antigen presentation and immune response and are regulated through complex transcriptional regulatory circuits, including those in HLA (6p21) and non-HLA (16p11.2) loci. These candidate causal enhancer SNPs are supported by strong evidence and warrant functional follow-up studies.


2021 ◽  
pp. 1-13
Author(s):  
Francis Poulat

In vertebrates, gonadal sex determination is the process by which transcription factors drive the choice between the testicular and ovarian identity of undifferentiated somatic progenitors through activation of 2 different transcriptional programs. Studies in animal models suggest that sex determination always involves sex-specific transcription factors that activate or repress sex-specific genes. These transcription factors control their target genes by recognizing their regulatory elements in the non-coding genome and their binding motifs within their DNA sequence. In the last 20 years, the development of genomic approaches that allow identifying all the genomic targets of a transcription factor in eukaryotic cells gave the opportunity to globally understand the function of the nuclear proteins that control complex genetic programs. Here, the major transcription factors involved in male and female vertebrate sex determination and the genomic profiling data of mouse gonads that contributed to deciphering their transcriptional regulation role will be reviewed.


2020 ◽  
Author(s):  
SK Reilly ◽  
SJ Gosai ◽  
A Gutierrez ◽  
JC Ulirsch ◽  
M Kanai ◽  
...  

AbstractCRISPR screens for cis-regulatory elements (CREs) have shown unprecedented power to endogenously characterize the non-coding genome. To characterize CREs we developed HCR-FlowFISH (Hybridization Chain Reaction Fluorescent In-Situ Hybridization coupled with Flow Cytometry), which directly quantifies native transcripts within their endogenous loci following CRISPR perturbations of regulatory elements, eliminating the need for restrictive phenotypic assays such as growth or transcript-tagging. HCR-FlowFISH accurately quantifies gene expression across a wide range of transcript levels and cell types. We also developed CASA (CRISPR Activity Screen Analysis), a hierarchical Bayesian model to identify and quantify CRE activity. Using >270,000 perturbations, we identified CREs for GATA1, HDAC6, ERP29, LMO2, MEF2C, CD164, NMU, FEN1 and the FADS gene cluster. Our methods detect subtle gene expression changes and identify CREs regulating multiple genes, sometimes at different magnitudes and directions. We demonstrate the power of HCR-FlowFISH to parse genome-wide association signals by nominating causal variants and target genes.


2021 ◽  
Author(s):  
Vasiliki Theodorou ◽  
Aikaterini Stefanaki ◽  
Minas Drakos ◽  
Dafne Triantafyllou ◽  
Christos Delidakis

Background: ASC/ASCL proneural transcription factors are oncogenic and exhibit impressive reprogramming and pioneer activities. In both Drosophila and mammals, these factors are central in the early specification of the neural fate, where they act in opposition to Notch signalling. However, the role of ASC on the chromatin during CNS neural stem cells birth remains elusive. Results: We investigated the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and Zelda-independent, less accessible regions. Both classes cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in many biological processes necessary for neuroblast function. We identified an ASC-Notch regulated TF network that most likely act as the prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, lacking expression of many proneural targets and unable to divide. When they eventually start proliferating, they produce compromised progeny. Generation of lacZ reporter lines driven by proneural-bound elements display enhancer activity within neuroblasts and proneural dependency. Therefore, the partial neuroblast identity seen in the absence of ASC genes is driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild type embryos induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to establish the chromatin dynamics that promote neural specification. Conclusion: ASC factors bind a large number of enhancers to orchestrate the timely activation of the neural chromatin program during neuroectodermal to neuroblast transition. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4903-4903 ◽  
Author(s):  
Ibraheem H Motabi ◽  
Syed Ziauddin A. Zaidi ◽  
Mamoun Hassan Ibrahim ◽  
Imran K Tailor ◽  
Nawal Faiez Alshehry ◽  
...  

Abstract Introduction Respiratory viruses are an important cause of outbreaks of pneumonia in hematological malignancy patients. Recently, novel Middle East respiratory syndrome coronavirus (MERS-CoV) caused a cluster of life-threatening infections in Saudi Arabia (688 confirmed MERS-CoV infection cases with 282 deaths were reported to WHO by June 6, 2014 including 28% cases in HCW). Most patients had upper &/or lower respiratory tract symptoms but other features included abdominal pain, diarrhea, acute kidney injury & shock. Few hematology units were closed due to havoc. Here we report clinical features & outcome of 4 patients diagnosed at our unit during the peak period (mid-March through May 2015) including 2 who got chemotherapy (chemo) soon after recovery. Patient #1 A 62-yr-old male had free λ light chain multiple myeloma (MM) with spinal cord compression. After surgery & local radiation, he was sent to us with paraplegia & grade 4 infected sacral bedsore that needed inpatient care. He was started on CyBorD Cycle 2 on April 24, 2014. On May 2, he had a fever spike with shortness of breath (SOB) & cough. He was started on antibiotics. CXR revealed bilateral infiltrates & right sided pleural effusion. His O2 sat dropped & he needed CPAP. Oseltamivir was started & sputum was positive for MERS-CoV RT-PCR. He became afebrile with decreasing O2 requirement, CXR normalized & RT-PCR for MERS-CoV turned negative. Later he was able to receive 3rdcycle of CyBorD. Patient #2 A 65-yr-old lady came to us with B symptoms & huge organomegaly due to stage-IV DLBCL. On May 2, 2014 RCVP chemo was started. On day 6, she spiked fever with SOB, cough & was started on imipenem. CXR showed consolidation in right lower lobe. She needed 4L of O2/min. On May 10, 2014, she worsened with RR 32/min, O2 sat 79% on 15L O2/min & BP 79/47 mmHg. CXR revealed bilateral consolidation. She needed intubation & inotropic support in ICU. Vancomycin & oseltamivir were started & RT-PCR was positive for MERS-CoV on two nasopharyngeal swabs (NPS). LFT & RFT were normal but she continued to decline & died on May 13, 2014. Patient # 3 A 22-yr-old lady with past H/O AML t(8;21) was admitted on April 27, 2014 with 3 day H/O cough, fever & SOB. CXR had infiltrates in left lower lobe. She had severe pancytopenia & BMB confirmed relapsed AML. She had slightly raised LFT. Urine grew Ent. fecium. Antibiotics & voriconazole were used. She remained febrile over next 2 days. CT chest revealed extensive bilateral consolidation. She needed O2 up to 5L/Min for few days. RT-PCR for MERS-CoV was positive from NPS. She was initiated on oseltamivir. She became afebrile after 2 days & repeated RT-PCR for MERS-CoV was negative. Fludara, Ara-C (FA) chemo was started. She remained neutropenic for next 4 weeks but there was no recurrence of respiratory symptoms. BMB on day 28 of FA confirmed CR. CT chest revealed complete resolution of air space opacities. She was discharged with plan to undergo matched sibling donor Allo-HSCT. Patient #4 A 76-yr-old male with H/O HTN & CKD was diagnosed to have IgA κ MM. He was started on MPV chemo as inpatient due to logistic reasons. After 3 cycles of MPV, serum free κ chains decreased by 91% but remained on dialysis. On 21 April, 2014 he developed cough, SOB & fever. CXR revealed bilateral infiltrates & antibiotics were started. He worsened over next few days & CXR showed worsening bilateral consolidation. Eventually he needed intubation. He was treated with antimicrobials including voriconazole & oseltamir. RT-PCR for MERS-CoV was positive from NPS. Unfortunately he died few days later. Discussion: Patients with hematological malignancies are at increased risk of community & hospital-acquired infections. Recent outbreak of MERS-CoV infection has created a havoc among hematologists community. There is uncertainty about impact of MERS-CoV infection on continuation of chemo. We report 4 cases of hematological malignancies with MERS-CoV infection. Three of the 4 patients developed severe pneumonia & required intubation (2 died later) & one had milder form of pneumonia treated in isolation room. In addition to supportive care, all 4 received antimicrobials & oseltamivir. Chemo was safe soon after recovery from infection in the surviving 2 patients. We propose that during MERS-CoV epidemics, pneumonia can be treated with supportive care, antibiotics & oseltamivir. Chemo can be continued for the malignant disease soon after recovery. Further reports are needed to confirm our findings. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Author(s):  
Kyle A Cottrell ◽  
Luisangely Soto Torres ◽  
Jason D Weber

The RNA editing enzyme ADAR, is an attractive therapeutic target for multiple cancers. Through its deaminase activity, ADAR edits adenosine to inosine in dsRNAs. Loss of ADAR in some cancer cell lines causes activation of the type I interferon pathway and the PKR translational repressor, leading to inhibition of proliferation and stimulation of cell death. As such, inhibition of ADAR function is a viable therapeutic strategy for many cancers. However, there are no FDA approved inhibitors of ADAR. Two small molecules have been previously described as inhibitors of ADAR: 8-azaadenosine and 8-chloroadenosine. Here we show that neither molecule is a selective inhibitor of ADAR. Both 8-azaadenosine and 8-chloroadenosine show similar toxicity to ADAR-dependent and independent cancer cell lines. Furthermore, the toxicity of both small molecules is comparable between cell lines with knockdown of ADAR and cells with unperturbed ADAR expression. Treatment with neither molecule causes activation of PKR. Finally, treatment with either molecule has no effect on A-to-I editing of an ADAR substrate. Together these data show that 8-azaadenosine and 8-chloroadenosine are not suitable small molecules for therapies that require selective inhibition of ADAR, and neither should be used in preclinical studies as ADAR inhibitors.


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