scholarly journals Epigenetic Heterogeneity in Friedreich Ataxia Underlies Variable FXN Reactivation

2021 ◽  
Vol 15 ◽  
Author(s):  
Layne N. Rodden ◽  
Kaitlyn M. Gilliam ◽  
Christina Lam ◽  
David R. Lynch ◽  
Sanjay I. Bidichandani

Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat in intron 1 of the FXN gene. The expanded repeat induces repressive histone changes and DNA hypermethylation, which result in epigenetic silencing and FXN transcriptional deficiency. A class I histone deacetylase inhibitor (HDACi-109) reactivates the silenced FXN gene, although with considerable inter-individual variability, which remains etiologically unexplained. Because HDAC inhibitors work by reversing epigenetic silencing, we reasoned that epigenetic heterogeneity among patients may help to explain this inter-individual variability. As a surrogate measure for epigenetic heterogeneity, a highly quantitative measurement of DNA hypermethylation via bisulfite deep sequencing, with single molecule resolution, was used to assess the prevalence of unmethylated, partially methylated, and fully methylated somatic FXN molecules in PBMCs from a prospective cohort of 50 FRDA patients. Treatment of the same PBMCs from this cohort with HDACi-109 significantly increased FXN transcript to levels seen in asymptomatic heterozygous carriers, albeit with the expected inter-individual variability. Response to HDACi-109 correlated significantly with the prevalence of unmethylated and partially methylated FXN molecules, supporting the model that FXN reactivation involves a proportion of genes that are amenable to correction in non-dividing somatic cells, and that heavily methylated FXN molecules are relatively resistant to reactivation. FXN reactivation is a promising therapeutic strategy in FRDA, and inter-individual variability is explained, at least in part, by somatic epigenetic heterogeneity.

PLoS ONE ◽  
2008 ◽  
Vol 3 (4) ◽  
pp. e1958 ◽  
Author(s):  
Myriam Rai ◽  
Elisabetta Soragni ◽  
Kai Jenssen ◽  
Ryan Burnett ◽  
David Herman ◽  
...  

2005 ◽  
Vol 25 (13) ◽  
pp. 5429-5444 ◽  
Author(s):  
Yun Dai ◽  
Mohamed Rahmani ◽  
Paul Dent ◽  
Steven Grant

ABSTRACT NF-κB activation is reciprocally regulated by RelA/p65 acetylation and deacetylation, which are mediated by histone acetyltransferases (HATs) and deacetylases (HDACs). Here we demonstrate that in leukemia cells, NF-κB activation by the HDAC inhibitors (HDACIs) MS-275 and suberoylanilide hydroxamic acid was associated with hyperacetylation and nuclear translocation of RelA/p65. The latter events, as well as the association of RelA/p65 with IκBα, were strikingly diminished by either coadministration of the IκBα phosphorylation inhibitor Bay 11-7082 (Bay) or transfection with an IκBα superrepressor. Inhibition of NF-κB by pharmacological inhibitors or genetic strategies markedly potentiated apoptosis induced by HDACIs, and this was accompanied by enhanced reactive oxygen species (ROS) generation, downregulation of Mn-superoxide dismutase and XIAP, and c-Jun N-terminal kinase 1 (JNK1) activation. Conversely, N-acetyl l-cysteine blocked apoptosis induced by Bay/HDACIs by abrogating ROS generation. Inhibition of JNK1 activation attenuated Bay/HDACI lethality without affecting NF-κB inactivation and ROS generation. Finally, XIAP overexpression dramatically protected cells against the Bay/HDACI regimen but failed to prevent ROS production and JNK1 activation. Together, these data suggest that HDACIs promote the accumulation of acetylated RelA/p65 in the nucleus, leading to NF-κB activation. Moreover, interference with these events by either pharmacological or genetic means leads to a dramatic increase in HDACI-mediated lethality through enhanced oxidative damage, downregulation of NF-κB-dependent antiapoptotic proteins, and stress-related JNK1 activation.


2011 ◽  
Vol 16 (10) ◽  
pp. 1247-1253 ◽  
Author(s):  
Bryan D. Marks ◽  
Stephen A. Fakhoury ◽  
William J. Frazee ◽  
Hildegard C. Eliason ◽  
Steven M. Riddle

Developing molecularly targeted therapeutics with minimal off-target effects is facilitated by an understanding of compound selectivity. However, for HDAC inhibitors, a clear understanding of specificity has been challenging. In particular, it has been suggested that use of nonspecific substrates and the presence of multiple HDAC activities in enzyme preparations may complicate interpretation of inhibitor experiments. To overcome these and other potential limitations of activity-based HDAC assays, the authors have developed an assay format based on measurement of the binding affinity of inhibitors rather than measurement of enzyme activity. One advantage of this format is that it does not require use of a substrate and thus ameliorates concerns about lack of specificity of existing substrates. This assay is based on an Alexa Fluor® 647-labeled HDAC inhibitor or “tracer,” which binds with a high affinity to Class I and Class IIb HDACs. Unlike activity assays, which can be affected by the presence of residual untagged endogenous HDACs from the host expression system, the signal in this format is dependent on the presence of an epitope tag on the specific HDAC of interest. The authors demonstrate the utility of this method by determining the potencies of commonly used inhibitors for six human HDACs.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 264-264 ◽  
Author(s):  
Olatoyosi M. Odenike ◽  
Serhan Alkan ◽  
Dorie Sher ◽  
John E. Godwin ◽  
Dezheng Huo ◽  
...  

Abstract Recruitment of histone deacetylases and DNA hypermethylation of promoter regions of specific genes are two mechanisms of transcriptional repression and gene silencing which have been linked, and are implicated in differentiation block in AML. We hypothesized that the histone deacetylase inhibitor (HDI) depsipeptide could result in transcriptional de-repression, upregulation of specific target genes and differentiation of the leukemic clone in AML. Eighteen patients (pts), median age 60 years (range 25–77) with relapsed or refractory AML were enrolled on a multicenter Phase II study of depsipeptide in AML. Patients were stratified into 2 groups on study entry: Group A (n=14) included patients without specific chromosomal abnormalities known to recruit histone deacetylases. Group B (n=4) included patients with chromosomal aberrations such as the t(8;21), inv 16 and t(15;17) known to recruit histone deacetylases. Depsipeptide was administered intravenously at a dose of 18mg/m2/d on days 1, 8 and 15 of a 28 day cycle. Peripheral blood mononuclear cells were obtained prior to (hour 0), and after 4 (hr 4) and 24 hrs (hr 24), on days 1 and 8 of the first cycle of therapy for evaluation of histone acetylation by flow cytometry, and gene re-expression by REAL-time RT-PCR. Target genes of interest include MDR1, a target of HDI mediated upregulation, and p15INK4B (p15), a target of DNA hypermethylation in AML. MDR1 and p15 copy numbers are expressed as a normalized quotient of MDR1 and p15, respectively, to the housekeeping gene ABL. The drug has been well tolerated. The most common adverse effects noted included grade 1/2 nausea, vomiting and fatigue. No objective evidence of response (CR or PR) or other evidence of antileukemic activity has been seen in group A. In contrast, 2 of 4 pts (50%) in Group B, have had a disappearance of bone marrow blasts (blast percentage < 5%) in the setting of a normocellular marrow, with concomitant recovery of near-normal hematopoiesis following 1 and 2 cycles of therapy respectively. This anti-leukemic effect was short-lived, with both pts developing an increase in bone marrow blasts within 30 days of the initial response. Both of these patients also had translocations involving the AML1 gene {1 had t(8;21) and the other had a novel translocation t(4;21)}. Interestingly both of these responding pts and one other pt (75%) in cohort B demonstrated an increase in H3 acetylation at 4 and/or 24 hrs, in contrast to 4 of 14 pts (28%) in cohort A. There was an overall mean increase of 41% in MDR1 expression at hr 4 on days 1 and 8 (p=0.04). p15 expression was also upregulated at hr 4 on days 1 and 8 (91% mean increase, p=0.01). We conclude that the HDI, depsipeptide, may have anti-leukemic activity in specific cytogenetic subsets of AML known to recruit histone deacetylases, and this is associated with a concomitant increase in histone acetylation. In addition, upregulation of specific target genes occurred in patient derived mononuclear cells, following depsipeptide treatment. The study remains open to accrual for pts with specific chromosomal abnormalities known to recruit histone deacetylases.


2009 ◽  
Vol 89 (7) ◽  
pp. 791-799 ◽  
Author(s):  
Tetsuo Kondo ◽  
Tadao Nakazawa ◽  
Defu Ma ◽  
Dongfeng Niu ◽  
Kunio Mochizuki ◽  
...  

MedChemComm ◽  
2016 ◽  
Vol 7 (3) ◽  
pp. 464-470 ◽  
Author(s):  
Andreas S. Madsen ◽  
Christian A. Olsen

Kinetic evaluation of HDAC inhibitors containing different zinc-binding chemotypes demonstrates that trifluoromethyl ketone-containing compounds can inhibit individual HDAC isozymes via differential mechanisms.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 960-960
Author(s):  
Katharine Rose Press ◽  
Jeffrey Keefer ◽  
Steven D. Gore ◽  
Hetty E. Carraway ◽  
Sarah Sakoian ◽  
...  

Fetal hemoglobin induction with hydroxyurea (HU) is a mainstay of therapy for β-hemoglobinopathies, especially sickle cell disease (SCD). A high level of fetal hemoglobin (HbF) has a direct relationship with acute clinical status in SCD patients including pain crises, acute chest syndrome, and death. However, not all patients benefit from HU, and more effective HbF induction strategies are needed. DNA methyl transferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors have been shown in vitro to induce HbF production through epigenetic modification of the β-globin gene cluster. Azacitidine (AZA) is a DNMT already used in some SCD patients resistant to HbF modulation with HU. Entinostat (MS-275) is an orally available histone deacetylase inhibitor with a long half-life and established antitumor activity in preclinical models. Recent studies suggest that drugs, which act with different molecular and epigenetic mechanisms, have synergistic effects on induction of fetal hemoglobin (Fard et al. IJHOSCR 2013). In this study, we evaluated the effects of a combination of AZA and MS-275 on HbF levels. This was preformed as a correlative study of a phase I clinical trial (J0443 trial) of these drugs in patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). We sequentially measured the level of HbF the peripheral blood in 33 patients receiving different doses of AZA (range: 30mg/m2 to 50mg/m2 per day for 10 doses) and MS-275 (range: 2 to 8 mg/m2 orally on days 3 and 10). Patients completed a minimum of four 28-day cycles of combined therapy. HbF levels were measured in peripheral blood at baseline, at day 15 or 16 and day 29 or 30 of cycle 1, and after cycles 2, 4, and if applicable 6. Azacitidine dose positively correlated with HbF fold increase (mean of 1.1, 2.3, and 2.1 for doses of 30, 40, and 50 mg respectively, p=0.07) while MS-275 dose had a slightly negative correlation with HbF level (mean of 3.0, 1.8, and 1.3 for doses of 2, 4, and 6mg respectively, p=0.13). There was no correlation between baseline HbF and HbF fold increase after exposure to treatment (p=NS) and no correlation between baseline HbF levels and clinical disease response (p=0.19). Interestingly, we demonstrated a correlation between HbF fold increase and clinical disease response: median fold increase of 3.5 for patients achieving hematologic normalization (complete response, partial response, or trilineage hematological improvement) versus 1.4 in non-responders (p=0.006). The positive correlation between AZA dose and HbF increase is consistent with prior work showing that this drug induces HbF production. The correlation between clinical response and HbF induction could reflect a greater susceptibility to AZA potentially related to differing methylomes. Alternatively, it may also represent a known increase in HbF in the setting of stress erythropoiesis. The slight inverse correlation between MS-275 and HbF level was surprising, as other HDAC inhibitors are known to induce HbF in vitro. However, these results are in line with the methylation data found in the more recent randomized phase 2 trial of AZA +/- MS-275 (E1905 trial) that showed a potential pharmacodynamic antagonism of the combination (Prebet et al. J Clin Oncol. 2014). Overall, this work supports the use of AZA as a clinical inducer of HbF. It also shows the importance of trialing various combinations of HbF inducers, as not all drugs work synergistically and some may even be antagonistic in combination. Disclosures Off Label Use: Azacitidine (AZA) is a DNA methyl transferase (DNMT) inhibitor. Entinostat (MS-275) is an orally available histone deacetylase inhibitor. Both drugs were used in a phase I clinical trial (J0443 trial) of these drugs in patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). . Keefer:MAST therapeutics: Employment. Gore:Celgene: Consultancy, Honoraria, Research Funding. Prebet:CELGENE: Research Funding.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4463-4463
Author(s):  
Ilan Bernstein ◽  
Francis Giles ◽  
Susan O’Brien ◽  
Elizabeth Sullivan ◽  
Norbert Vey ◽  
...  

Abstract Laromustine (Cloretazine®) (1,2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[(methylamino)carbonyl] hydrazine), a sulfonylhydrazine prodrug producing chlorethylating and carbamoylating subspecies, has demonstrated clinical activity in patients with hematologic disorders (Giles et al., J Clin Oncol, 2007). The effect of laromustine is modulated primarily through the formation of hard chloroethylating electrophiles with preferential alkylating activity for the O6 position of guanine, ultimately resulting in the formation of interstrand cross-links which prevent DNA replication and transcription, leading to cell death. The DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) plays a major role in repairing O6-chloroethylguanine alkylations, critical to the formation of interstrand crosslinks. Epigenetic silencing of the MGMT encoding gene related to DNA hypermethylation has been shown to participate in the pathogenesis of neoplastic disease (Hegi et al., NEJM 2005). Since the alkylating properties of laromustine target DNA sites normally repaired by MGMT, the absence of the enzyme may represent a unique cellular environment for specific susceptibility to laromustine (Ishiguro et al., Mol Cancer Ther, 2005). In vitro findings have supported the hypothesis that cellular content of MGMT may predict response. In vivo correlation between clinical response in patients treated with laromustine and the cellular evidence of epigenetic silencing of the encoding MGMT gene has yet to be demonstrated (Giles et al., Clin Cacner Res, 2004). Our research aimed to determine the DNA methylation status of MGMT isolated from the peripheral blood or bone marrow of patients with AML or high-risk MDS enrolled to a phase II, single-agent study of laromustine (600 mg/m2 IV over 30 minutes) (Giles et al. J Clin Oncol, 2007). We also aimed to establish a correlation between hypermethylation of MGMT and clinical response to laromustine. Combined bisulfite restriction analysis (COBRA) was used to determine the MGMT gene methylation status of patients treated with laromustine. Bone marrow or peripheral blood leukocyte samples from 76 patients enrolled in a phase II, single agent study of laromustine were coded and blinded to investigators. DNA from each sample was extracted and bisulfite treated. PCR was used to amplify the MGMT CpG Island promoter region (REF/NT_008818.15/Hs10_8975) from 58 patients, prior to methylation specific restriction enzyme digestion. Results were correlated with clinical data of response to laromustine. The DNA methylation status of MGMT was determined in 58 of the enrolled patients. DNA hypermethylation was found in 3 of the 58 patients (5%). Two of these 3 patients achieved a complete response (CR) (66%), compared to 11 of the 55 patients who achieved a CR, CR with platelet recovery < 100,000/mm3 (CRp) or a partial response (PR) and did not exhibit MGMT hypermethylation (20%). Hypermethylation of the MGMT gene promoter is a rare event in AML (5%), however, epigenetic inactivation of MGMT may predict a subgroup of patients with a higher likelihood of response to laromustine (Odds Ratio=8). Clinical investigation of laromustine in patients with AML, high-risk MDS and other cancers, specifically those with a higher methylation frequency of the MGMT encoding gene is warranted.


Sign in / Sign up

Export Citation Format

Share Document