scholarly journals Epigenetic Drug Combination Alters Methylation Patterns in Patient-Derived Xenograft Models of KMT2A-Rearranged Pediatric AML Treated In Vivo

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2376-2376
Author(s):  
Anilkumar Gopalakrishnapillai ◽  
Erin Lynn Crowgey ◽  
Adam Marsh ◽  
E. Anders Kolb ◽  
Sonali P. Barwe
Keyword(s):  
Combination Treatment ◽  
Drug Combination ◽  
Cpg Sites ◽  
Cpg Site ◽  
Patient Derived Xenograft ◽  
Epigenetic Drug ◽  
Xenograft Models ◽  
Pediatric Aml ◽  
Methylation Patterns

Abstract Pediatric acute myeloid leukemia (AML) patients possessing rearrangement of the KMT2A (previously known as MLL) gene on 11q23 constitute a subclass with a particularly poor prognosis. The five-year survival rate for these patients is only about 44% due to poor response to conventional chemotherapy and frequent early relapse. Aberrant epigenetic modifications play an important role in leukemogenesis in KMT2A-rearranged leukemia. Accordingly, several epigenome modifying drugs have been tested in preclinical studies of KMT2A-rearranged leukemia. Acknowledging the co-regulatory effects of DNA methylation and histone modifications in determining chromatin structure and governing gene expression, we combined DNA hypomethylating agent azacitidine with histone deacetylase inhibitor panobinostat in the hopes of achieving greater efficacy. We showed that this epigenetic drug combination was more efficacious than single agents using cell line derived xenograft models of pediatric AML (Gopalakrishnapillai et al., Leuk Res, 2017). We evaluated the efficacy of this epigenetic drug combination in patient-derived xenograft models of KMT2A rearranged pediatric AML and observed that similar to MV4;11 model, this combination induced complete remission in NTPL-146 model with KMT2A-MLLT1 fusion (Fig. 1A, P<0.001). We analyzed the methylome of AML cells harvested from xenografted mice treated with control, azacitidine, panobinostat, or a combination of the two. Methylation sensitive restriction endonucleases were utilized to fragment genomic DNA prior to library construction for next generation sequencing. GenPro software platform designed for highly quantitative, sensitive, and low error-rate detection of methylation at individual CpG sites was used. Methylation patterns between treatment groups were discriminated using an ordinate analysis technique of non-metric multidimensional scaling (NMDS) (Fig. 1B). CpG methylation profiles were compared among the four groups analyzed to isolate patterns conserved within groups while also differing between groups. The first two component axes were plotted to locate the individual sample points in a 2D plane. Samples from distinct PDX models undergoing similar treatment clustered together. The panobinostat-treated samples showed minimal differences compared to the control, while the azacitidine-treated samples clustered away. Interestingly, the samples treated with the combination, did not overlap with either treatment, indicating that although panobinostat alone showed minimal impact on methylation patterns, panobinostat together with azacitidine produced a distinct methylation pattern. Venn intersection sets of statistically significant differentially methylated CpG sites in the 3-way analyses derived from the control group comparisons showed 2086 CpG sites exclusively altered in the combination treatment (Fig. 1C). In order to determine the effect of the combination treatment on global methylation, the differences in methylation load (dML) per each CpG site between control and the combination treatment were summed across 1MB genome intervals and the distribution of these dML was plotted (Fig. 1D). There was a strong shift in methylation signal, with the majority of the intervals being hypomethylated in the treatment group compared to the control. Although global hypomethylation was observed in combination treatment, the most statistically significant CpG sites were hypermethylated in the combination treatment compared to the control as seen in the volcano plot in which log fold-change was plotted against the p-value (Fig. 1E). Circular ideogram presented with a mean subtraction of CpG methylation scores to calculate a summation methylation load score across chromosomal domains (Fig. 1F). The correlative association between top CpG sites is shown as arcs tracking the highest correlation for each CpG site. Gene labels indicate the positions of the top 60 CpG sites, with green and red indicating higher methylation in control and in combination treatment respectively. In conclusion, we have identified differential methylation patterns following in vivo treatment of KMT2A rearranged pediatric AML xenograft models with azacitidine and panobinostat combination compared to azacitidine alone. These methylation changes are likely to influence the increased survival seen in mice receiving combination treatment. Figure 1 Figure 1. Disclosures Gopalakrishnapillai: Geron: Research Funding. Marsh: Genome Profiling LLC: Current Employment. Barwe: Prelude Therapeutics: Research Funding.

scholarly journals Imetelstat Significantly Reduces Leukemia Stem Cells in Patient-Derived Xenograft Models of Pediatric AML

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3352-3352
Author(s):  
Sonali P. Barwe ◽  
Fei Huang ◽  
E. Anders Kolb ◽  
Anilkumar Gopalakrishnapillai
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Research Funding ◽  
Annexin V ◽  
Telomerase Activity ◽  
Leukemia Stem Cells ◽  
Patient Derived Xenograft ◽  
Pediatric Aml ◽  
Pdx Models

Abstract Introduction Acute myeloid leukemia (AML) is the deadliest malignancy in children. Despite the use of maximally intensive therapy, 20% of patients experience recurrent disease. These patients are also burdened with significant treatment-related toxicities. To improve survival in pediatric AML, novel targeted therapies that are more effective and less toxic are needed. Telomerase inhibition has been shown to be effective in reducing leukemic burden and eradicating leukemia stem cells (LSCs) in syngeneic mouse models of AML and in patient-derived xenograft (PDX) models of adult AML (Bruedigam et al., 2014). Recent transcriptome analyses demonstrate that the genomic landscape of pediatric AML is distinct from adult AML (Bolouri et al., 2018). In fact, mutations in the telomerase complex components are infrequent in pediatric AML unlike adult AML patients (Aalbers et al., 2013). However, similar to what is seen in adult patients, Aalbers et al. identified that telomere lengths in pediatric AML cells were shortened compared to normal leukocytes, and pediatric AML patients with the shortest telomere length tend to have shorter overall survival. Furthermore, the 5-year survival rate was 88% for pediatric AML patients who had lower telomerase activity, and 43% for those patients with higher telomerase activity, suggesting telomerase activity could be an important prognostic factor in pediatric AML patients (Verstovsek et al., 2003). Imetelstat is an oligonucleotide that specifically binds with high affinity to the RNA template of telomerase and is a potent, competitive inhibitor of telomerase enzymatic activity (Asai et al., 2003; Herbert et al., 2005). In this study, we evaluated if imetelstat has anti-leukemia activity in pediatric AML PDX models. Results The PDX lines tested in this study were derived using samples from pediatric AML patients who were 1-14 years old, representing different FAB subtypes. Mouse passaged pediatric AML PDX lines (n=6) were treated ex vivo with imetelstat or mismatch oligo control and the viability of LSC (CD34+CD38low population) was determined at 48 or 96 h by staining with BV785-human CD45, APC-human CD34, Pacific blue-human CD38, FITC conjugated annexin V and propidium iodide (PI). Imetelstat treatment significantly increased apoptosis/death (PI+/annexin V+) of the LSC population in a dose-dependent manner in all PDX lines evaluated (Fig. 1A, B), while it had limited activity on LSCs in normal pediatric bone marrow samples (n=4). The efficacy of imetelstat either alone or in combination with chemotherapy or azacitidine was evaluated in two distinct PDX models of pediatric AML in vivo. Mice engrafted with both NTPL-377 and DF-2 lived longer when treated with imetelstat than the untreated mice (Fig. 1C, D, n=5 each, P<0.05). Mice receiving standard chemotherapy consisting of cytarabine and daunorubicin or azacitidine showed prolonged survival compared to the untreated mice. Interestingly, sequential administration of imetelstat following chemotherapy treatment provided additional benefit over chemotherapy alone (P<0.01). Concurrent treatment of azacitidine and imetelstat further extended survival of these mice compared to azacitidine alone (P<0.05). At the end of the in vivo studies, the percentage of LSC population was evaluated in the bone marrow of mice post euthanasia. There was a significant reduction of LSC population in mice treated with imetelstat compared to those treated with the mismatch oligo (Fig. 1E, F, P<0.05). Neither chemotherapy nor azacitidine alone affected LSC population compared to untreated mice. However, imetelstat significantly reduced the LSC population when combined with chemotherapy or azacitidine compared to single agent (P<0.05). These results were confirmed by secondary transplantation in mice, which showed delayed engraftment of cells isolated from imetelstat treated mice (Fig. 1G, H). Conclusions Imetelstat treatment of pediatric AML PDX samples showed significant dose- and time-dependent effects on the viability of the LSCs to induce cell apoptosis/death. These results were corroborated in vivo in two distinct PDX models which showed reduced LSC population and increased median survival in mice with imetelstat treatment. Combining imetelstat with chemotherapy or azacitidine further enhanced activity against LSCs, suggesting imetelstat could represent an effective therapeutic strategy for pediatric AML. Figure 1 Figure 1. Disclosures Barwe: Prelude Therapeutics: Research Funding. Huang: Geron Corp: Current Employment, Current equity holder in publicly-traded company. Gopalakrishnapillai: Geron: Research Funding.

scholarly journals Epigenetic Drug Combination Chemo-Sensitizes Pediatric AML By Reducing Cell Adhesion and Dislodging AML Cells from the Bone Marrow

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2637-2637
Author(s):  
Samantha Weber ◽  
Anilkumar Gopalakrisnapillai ◽  
E. Anders Kolb ◽  
Sonali Barwe
Keyword(s):  
Bone Marrow ◽  
Peripheral Blood ◽  
Drug Combination ◽  
Epigenetic Therapy ◽  
Cell Contact ◽  
Advisory Committees ◽  
Epigenetic Drugs ◽  
Epigenetic Drug ◽  
Direct Cell ◽  
Pediatric Aml

Abstract Background We showed earlier that prolonged treatment with a combination of azacitidine (DNMT1 inhibitor) and panobinostat (HDAC inhibitor) induced complete remission in a disseminated xenograft model of KMT2A rearranged AML (Gopalakrishnapillai et al., 2017, Leuk Res). Pretreatment with epigenetic drugs has been shown to induce chemo-sensitivity in some malignancies. However, studies on the use of epigenetic drugs in overcoming chemoresistance mediated by the bone marrow microenvironment are limited. The aim of this study was to determine the merit of incorporating epigenetic therapy with chemotherapy in AML treatment regimen and to identify the mechanism by which epigenetic drugs can chemosensitize AML. Methods AML cell lines and PDX lines were co-cultured with HS5 bone marrow stromal cells. Cell viability following drug treatment was assessed by flow cytometry. For determination of cell adhesion, violet proliferation dye stained AML cells were co-cultured with HS5 cells. Following treatment, non-adherent cells were removed by washes with phosphate buffered saline. The number of adherent AML cells was determined by flow cytometry. NSG-B2m mice were engrafted with MV4;11 cells and bled regularly to evaluate disease progression. Once engraftment was confirmed mice were assigned to treatment groups. Epigenetic therapy constituted azacitidine and panobinostat (2.5 mg/Kg each; Qd5). Chemotherapy constituted cytarabine (50 mg/Kg; Qd5) and daunorubicin (1.5 mg/Kg; Qd3). Mice were euthanized when they reached predetermined experimental endpoints. All animal studies were approved by the Institutional Animal Care and Use Committee. Results AML cells in co-culture with HS5 bone marrow stromal cells were less sensitive to chemotherapeutics cytarabine and daunorubicin compared to AML cells in monoculture. This chemoprotection was not achieved when AML cells were cultured in HS5 conditioned media or in Transwell inserts suspended over HS5 monolayers, suggesting that direct cell-to-cell contact was required. MV4;11 cells exposed to epigenetic drugs or cytarabine alone retained 70% viability. Pre-treatment with the epigenetic drug combination of azacitidine and panobinostat prior to cytarabine exposure greatly reduced cell viability in MV4;11 cells harboring KMT2A fusion (Fig. 1A). Similar chemo-sensitization was observed when four distinct KMT2A rearranged PDX lines were used ex vivo. This sensitization was accompanied by reduced binding of AML cells to HS5 cells following treatment with epigenetic drugs (Fig. 1B). We evaluated the efficacy of the epigenetic therapy and chemotherapy combination in disseminated xenograft models of pediatric AML. NSG-B2m mice transplanted with MV4;11 cells via the tail vein were randomly assigned to four groups - 1) vehicle, 2) epigenetic therapy 3) chemotherapy (cytarabine + daunorubicin), and 4) epigenetic therapy followed by chemotherapy. The mice receiving the epigenetic therapy and chemotherapy combination survived significantly longer than mice treated with any other condition (Fig. 1C). To assess the leukemic cell distribution in peripheral blood, bone marrow and spleen following treatment, a cohort of mice receiving epigenetic therapy alone or chemotherapy alone were euthanized a day after treatment concluded. The percentage of leukemic cells in bone marrow and spleen was lower in mice treated with epigenetic therapy than those treated with chemotherapy, consistent with the survival data. Surprisingly, the peripheral blood counts were significantly higher in mice receiving epigenetic drug combination. These results together with our in vitro data indicate that epigenetic therapy induces mobilization of AML cells to the blood stream. This increased availability of AML cells may promote enhanced sensitivity to chemotherapy. Conclusion Our data suggest that direct cell-to-cell contact plays a major role in mediating chemoprotective effects of the bone marrow microenvironment. These chemoprotective effects can be overcome by pretreatment with epigenetic drug combination azacitidine and panobinostat. Epigenetic drugs interfere with AML cell interactions with the microenvironment and dislodge AML cells from their protective niche. Thus, mobilization of AML cells to peripheral blood is a potential mechanism of chemo-sensitization mediated by epigenetic drugs. Disclosures Kolb: Servier: Membership on an entity's Board of Directors or advisory committees; Roche- Genentech: Membership on an entity's Board of Directors or advisory committees.

scholarly journals The Molecular Subtype of Adult Acute Lymphoblastic Leukemia Samples Determines the Engraftment Site and Proliferation Kinetics in Patient-Derived Xenograft Models

Cells ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 150
Author(s):  
Anna Richter ◽  
Catrin Roolf ◽  
Anett Sekora ◽  
Gudrun Knuebel ◽  
Saskia Krohn ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Molecular Subtype ◽  
Lymphoblastic Leukemia ◽  
Clonal Diversity ◽  
Model Systems ◽  
Leukemic Cells ◽  
Patient Derived Xenograft ◽  
Molecular Stability ◽  
Xenograft Models

In acute lymphoblastic leukemia (ALL), conventional cell lines do not recapitulate the clonal diversity and microenvironment. Orthotopic patient-derived xenograft models (PDX) overcome these limitations and mimic the clinical situation, but molecular stability and engraftment patterns have not yet been thoroughly assessed. We herein describe and characterize the PDX generation in NSG mice. In vivo tumor cell proliferation, engraftment and location were monitored by flow cytometry and bioluminescence imaging. Leukemic cells were retransplanted for up to four passages, and comparative analyses of engraftment pattern, cellular morphology and genomic hotspot mutations were conducted. Ninety-four percent of all samples were successfully engrafted, and the xenograft velocity was dependent on the molecular subtype, outcome of the patient and transplantation passage. While BCR::ABL1 blasts were located in the spleen, KMT2A-positive cases had higher frequencies in the bone marrow. Molecular changes appeared in most model systems, with low allele frequency variants lost during primary engraftment. After the initial xenografting, however, the PDX models demonstrated high molecular stability. This protocol for reliable ALL engraftment demonstrates variability in the location and molecular signatures during serial transplantation. Thorough characterization of experimentally used PDX systems is indispensable for the correct analysis and valid data interpretation of preclinical PDX studies.

scholarly journals Murine De Novo Methyltransferase Dnmt3a Demonstrates Strand Asymmetry and Site Preference in the Methylation of DNA In Vitro

2002 ◽  
Vol 22 (3) ◽  
pp. 704-723 ◽  
Author(s):  
Iping G. Lin ◽  
Li Han ◽  
Alexander Taghva ◽  
Laura E. O’Brien ◽  
Chih-Lin Hsieh
Keyword(s):  
Dna Methyltransferase ◽  
De Novo ◽  
Dna Methyltransferases ◽  
Site Preference ◽  
Cpg Sites ◽  
Methylation Of Dna ◽  
Wide Range ◽  
Methylation Patterns

ABSTRACT CpG methylation is involved in a wide range of biological processes in vertebrates as well as in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA methyltransferase activity in mouse and human. It has been proposed that de novo methylation observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b methyltransferases, while Dntm1 is believed to be responsible for maintaining the established methylation patterns upon replication. Analysis of the sites methylated in vivo using the bisulfite genomic sequencing method confirms the previous finding that some regions of the plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However, the preferred targets of the enzyme cannot be determined due to the presence of other methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed. These analyses revealed that the two cDNA strands have distinctly different methylation patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most likely methylates one strand of DNA without concurrent methylation of the CpG site on the complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites more frequently than others, depending on the sequence context. Methylation of each DNA strand independently and with possible sequence preference is a novel feature among the known DNA methyltransferases.

scholarly journals Combination Treatment with the GSK-3 Inhibitor 9-ING-41 and CCNU Cures Orthotopic Chemoresistant Glioblastoma in Patient-Derived Xenograft Models

2017 ◽  
Vol 10 (4) ◽  
pp. 669-678 ◽  
Author(s):  
Andrey Ugolkov ◽  
Wenan Qiang ◽  
Gennadiy Bondarenko ◽  
Daniel Procissi ◽  
Irina Gaisina ◽  
...  
Keyword(s):  
Combination Treatment ◽  
Patient Derived Xenograft ◽  
Xenograft Models

Head-to-head comparison of various antipsychotic agents on genome-wide methylation in schizophrenia

2021 ◽  
Author(s):  
Christopher Adanty ◽  
Ahmad Shakeri ◽  
John Strauss ◽  
Ariel Graff ◽  
Vincenzo De Luca
Keyword(s):  
Smoking Status ◽  
Antipsychotic Agents ◽  
Differentially Methylated Region ◽  
Clinical Effects ◽  
Healthy Controls ◽  
Cpg Sites ◽  
Cpg Site ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Genome Wide Significance

Aim: To explore possible differences in genome-wide methylation between schizophrenia patients who consume various antipsychotics. Methods: We compared DNA methylation in leukocytes between the following cohorts: clozapine (n = 19) versus risperidone (n = 19), clozapine (n = 12) versus olanzapine (n = 12), clozapine (n = 9) versus quetiapine (n = 9) and clozapine (n = 33) versus healthy controls (n = 33). Subjects were matched for age, sex, ethnicity, smoking status and leukocyte proportions. Results: No single CpG site reached genome-wide significance for clozapine versus risperidone/olanzapine/quetiapine. For clozapine versus quetiapine, one significantly differentially methylated region was found – ch5: 176797920–176798049 (fwer = 0.075). Clozapine versus healthy controls yielded thousands of significantly differentially methylated CpG sites. Conclusions: Establishing antipsychotic induced genome-wide methylation patterns will further elucidate the biological and clinical effects of antipsychotic administration.

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