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Chatzilygeroudi T, Chondrou V, Boers R, Siamoglou S, Athanasopoulou K, Verigou E, Gribnau J, Alexis S, Labropoulou V, Kourakli A, Patrinos GP, Sgourou A, Symeonidis A. Fetal hemoglobin induction in azacytidine responders enlightens methylation patterns related to blast clearance in higher-risk MDS and CMML. Clin Epigenetics 2024; 16:79. [PMID: 38879530 PMCID: PMC11180405 DOI: 10.1186/s13148-024-01687-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND As new treatment options for patients with higher-risk myelodysplastic syndromes are emerging, identification of prognostic markers for hypomethylating agent (HMA) treatment and understanding mechanisms of their delayed and short-term responses are essential. Early fetal hemoglobin (HbF) induction has been suggested as a prognostic indicator for decitabine-treated patients. Although epigenetic mechanisms are assumed, responding patients' epigenomes have not been thoroughly examined. We aimed to clarify HbF kinetics and prognostic value for azacytidine treated patients, as well as the epigenetic landscape that might influence HbF re-expression and its clinical relevance. RESULTS Serial HbF measurements by high-performance liquid chromatography (n = 20) showed induction of HbF only among responders (p = 0.030). Moreover, HbF increase immediately after the first azacytidine cycle demonstrated prognostic value for progression-free survival (PFS) (p = 0.032, HR = 0.19, CI 0.24-1.63). Changes in methylation patterns were revealed with methylated DNA genome-wide sequencing analysis (n = 7) for FOG-1, RCOR-1, ZBTB7A and genes of the NuRD-complex components. Targeted pyrosequencing methodology (n = 28) revealed a strong inverse correlation between the degree of γ-globin gene (HBG2) promoter methylation and baseline HbF levels (p = 0.003, rs = - 0.663). A potential epigenetic mechanism of HbF re-expression in azacytidine responders was enlightened by targeted methylation analysis, through hypomethylation of site -53 of HBG2 promoter (p = 0.039, rs = - 0.504), which corresponds to MBD2-NuRD binding site, and to hypermethylation of the CpG326 island of ZBTB7A (p = 0.05, rs = 0.482), a known HbF repressor. These changes were associated to blast cell clearance (pHBG2 = 0.011, rs = 0.480/pZBTB7A = 0.026, rs = 0.427) and showed prognostic value for PFS (pZBTB7A = 0.037, HR = 1.14, CI 0.34-3.8). CONCLUSIONS Early HbF induction is featured as an accessible prognostic indicator for HMA treatment and the proposed potential epigenetic mechanism of HbF re-expression in azacytidine responders includes hypomethylation of the γ-globin gene promoter region and hypermethylation of the CpG326 island of ZBTB7A. The association of these methylation patterns with blast clearance and their prognostic value for PFS paves the way to discuss in-depth azacytidine epigenetic mechanism of action.
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Affiliation(s)
- Theodora Chatzilygeroudi
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Ruben Boers
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rio, Patras, Greece
| | - Katerina Athanasopoulou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Evgenia Verigou
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Joost Gribnau
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Spyridon Alexis
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Vassiliki Labropoulou
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Alexandra Kourakli
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - George P Patrinos
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rio, Patras, Greece
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Argiris Symeonidis
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece.
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Pokharel B, Ravikumar Y, Rathinavel L, Chewonarin T, Pongpom M, Tipsuwan W, Koonyosying P, Srichairatanakool S. The Discovery of Selective Protein Arginine Methyltransferase 5 Inhibitors in the Management of β-Thalassemia through Computational Methods. Molecules 2024; 29:2662. [PMID: 38893537 PMCID: PMC11173459 DOI: 10.3390/molecules29112662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 06/21/2024] Open
Abstract
β-Thalassemia is an inherited genetic disorder associated with β-globin chain synthesis, which ultimately becomes anemia. Adenosine-2,3-dialdehyde, by inhibiting arginine methyl transferase 5 (PRMT5), can induce fetal hemoglobin (HbF) levels. Hence, the materialization of PRMT5 inhibitors is considered a promising therapy in the management of β-thalassemia. This study conducted a virtual screening of certain compounds similar to 5'-deoxy-5'methyladenosine (3XV) using the PubChem database. The top 10 compounds were chosen based on the best docking scores, while their interactions with the PRMT5 active site were analyzed. Further, the top two compounds demonstrating the lowest binding energy were subjected to drug-likeness analysis and pharmacokinetic property predictions, followed by molecular dynamics simulation studies. Based on the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) score and molecular interactions, (3R,4S)-2-(6-aminopurin-9-yl)-5-[(4-ethylcyclohexyl)sulfanylmethyl]oxolane-3,4-diol (TOP1) and 2-(6-Aminopurin-9-yl)-5-[(6-aminopurin-9-yl)methylsulfanylmethyl]oxolane-3,4-diol (TOP2) were identified as potential hit compounds, while TOP1 exhibited higher binding affinity and stabler binding capabilities than TOP2 during molecular dynamics simulation (MDS) analysis. Taken together, the outcomes of our study could aid researchers in identifying promising PRMT5 inhibitors. Moreover, further investigations through in vivo and in vitro experiments would unquestionably confirm that this compound could be employed as a therapeutic drug in the management of β-thalassemia.
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Affiliation(s)
- Bishant Pokharel
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (B.P.); (Y.R.); (T.C.); (P.K.)
| | - Yuvaraj Ravikumar
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (B.P.); (Y.R.); (T.C.); (P.K.)
| | | | - Teera Chewonarin
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (B.P.); (Y.R.); (T.C.); (P.K.)
| | - Monsicha Pongpom
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Wachiraporn Tipsuwan
- Division of Biochemistry, School of Medical Science, University of Phayao, Phayao 5600, Thailand;
| | - Pimpisid Koonyosying
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (B.P.); (Y.R.); (T.C.); (P.K.)
| | - Somdet Srichairatanakool
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (B.P.); (Y.R.); (T.C.); (P.K.)
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Nakhaee S, Rezayee M, Mansouri B, Hadianfar A, Zadeh AA, Zardast M, Sefat MP, Mehrpour O. Comparison of Thyroid Function in Lead-Poisoned Patients and Healthy Individuals in Eastern Iran. Biol Trace Elem Res 2022; 200:3097-3102. [PMID: 34599429 DOI: 10.1007/s12011-021-02935-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022]
Abstract
Lead (Pb) is a prevalent environmental toxic metal that may harmfully affect the function of the thyroid gland. Our information about the effects of lead on thyroid function in lead poisoning is limited. The present study aimed to evaluate thyroid function in lead-poisoned patients compared with the healthy group. In this study, two groups of lead poisoning subjects (lead concentrations ≥ 25 μg/dL) (n = 56) (HBLC group) and randomly selected age and gender-matched healthy individuals with lower blood lead concentrations (BLC < 10 μg/dL) (n = 58) (LBLC group) were included. Thyroid function tests, including thyroxine (T4), triiodothyronine (T3), and thyroid-stimulating hormone (TSH) concentration, were measured for each patient in both groups (for the HBLC group, it was taken on admission). The linear regression model was used to investigate the effects of lead poisoning on thyroid function tests. A p-value of less than 0.05 was considered significant. Our study showed no significant difference between the two groups in terms of age and gender. The mean concentration of T3 and TSH in the HBLC group was significantly lower than the LBLC group, but the mean levels of T4 were significantly higher in the HBLC group (p < 0.05). Based on the linear regression model results, the T3 and TSH levels in the LBLC group were significantly higher by 13.86 and 0.43 units than the HBLC group, respectively. The current study results showed that lead poisoning affects thyroid function, reduces TSH, and increases T4.
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Affiliation(s)
- Samaneh Nakhaee
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Maryam Rezayee
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Borhan Mansouri
- Substance Abuse Prevention Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Hadianfar
- Department of Epidemiology and Biostatistics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Amirabadi Zadeh
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Mahmoud Zardast
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Malihe Parsa Sefat
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Omid Mehrpour
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran.
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA.
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Starlard-Davenport A, Fitzgerald A, Pace BS. Exploring epigenetic and microRNA approaches for γ-globin gene regulation. Exp Biol Med (Maywood) 2021; 246:2347-2357. [PMID: 34292080 DOI: 10.1177/15353702211028195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Therapeutic interventions aimed at inducing fetal hemoglobin and reducing the concentration of sickle hemoglobin is an effective approach to ameliorating acute and chronic complications of sickle cell disease, exemplified by the long-term use of hydroxyurea. However, there remains an unmet need for the development of additional safe and effective drugs for single agent or combination therapy for individuals with β-hemoglobinopathies. Regulation of the γ-globin to β-globin switch is achieved by chromatin remodeling at the HBB locus on chromosome 11 and interactions of major DNA binding proteins, such as KLF1 and BCL11A in the proximal promoters of the globin genes. Experimental evidence also supports a role of epigenetic modifications including DNA methylation, histone acetylation/methylation, and microRNA expression in γ-globin gene silencing during development. In this review, we will critically evaluate the role of epigenetic mechanisms in γ-globin gene regulation and discuss data generated in tissue culture, pre-clinical animal models, and clinical trials to support drug development to date. The question remains whether modulation of epigenetic pathways will produce sufficient efficacy and specificity for fetal hemoglobin induction and to what extent targeting these pathways form the basis of prospects for clinical therapy.
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Affiliation(s)
- Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ashley Fitzgerald
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Betty S Pace
- Department of Pediatrics, Division of Hematology/Oncology, Augusta University, Augusta, GA 30912, USA
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Bao X, Zhang X, Wang L, Wang Z, Huang J, Zhang Q, Ye Y, Liu Y, Chen D, Zuo Y, Liu Q, Xu P, Huang B, Fang J, Lao J, Feng X, Li Y, Kurita R, Nakamura Y, Yu W, Ju C, Huang C, Mohandas N, Li D, Zhao C, Xu X. Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia. Am J Hum Genet 2021; 108:709-721. [PMID: 33735615 DOI: 10.1016/j.ajhg.2021.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022] Open
Abstract
The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic implications for treatment of β-thalassemia and sickle cell anemia, two major global health problems. Although significant progress has been made in our understanding of the molecular mechanism of the fetal-to-adult hemoglobin switch, the mechanism of epigenetic regulation of HbF silencing remains to be fully defined. Here, we performed whole-genome bisulfite sequencing and RNA sequencing analysis of the bone marrow-derived GYPA+ erythroid cells from β-thalassemia-affected individuals with widely varying levels of HbF groups (HbF ≥ 95th percentile or HbF ≤ 5th percentile) to screen epigenetic modulators of HbF and phenotypic diversity of β-thalassemia. We identified an ETS2 repressor factor encoded by ERF, whose promoter hypermethylation and mRNA downregulation are associated with high HbF levels in β-thalassemia. We further observed that hypermethylation of the ERF promoter mediated by enrichment of DNMT3A leads to demethylation of γ-globin genes and attenuation of binding of ERF on the HBG promoter and eventually re-activation of HbF in β-thalassemia. We demonstrated that ERF depletion markedly increased HbF production in human CD34+ erythroid progenitor cells, HUDEP-2 cell lines, and transplanted NCG-Kit-V831M mice. ERF represses γ-globin expression by directly binding to two consensus motifs regulating γ-globin gene expression. Importantly, ERF depletion did not affect maturation of erythroid cells. Identification of alterations in DNA methylation of ERF as a modulator of HbF synthesis opens up therapeutic targets for β-hemoglobinopathies.
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Roy K, Mahendru S, Kukreti R, Kukreti S. Unusual stability exhibited by (AT) XN 12(AT) Y motif associated with high fetal hemoglobin levels. J Biomol Struct Dyn 2019; 37:3848-3857. [PMID: 30295130 DOI: 10.1080/07391102.2018.1532320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Quasi-palindromic sequences (AT)XN12(AT)Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults arise due to pathological conditions such as sickle cell disease and β-thalassemia. However, elevated levels of HbF are also associated with a reducing morbidity and mortality in patients with β-thalassemia and thus ameliorate the severity of the disease. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, and circular dichroism (CD) techniques, we demonstrated that it exhibits a hairpin-duplex equilibrium. Intramolecular species (hairpin) were observed in both low and high salt concentrations in gel assay studies displaying the unusual stability of intramolecular species even at the high counter-ion concentration. The unusual stability of hairpin secondary structures was also demonstrated by the monophasic nature of the melting profiles for the oligonucleotides which persisted at low as well as high salt and oligomer concentrations. Change in CD spectra as a function of oligomer concentration indicates that the bimolecular duplex formation is selectively favored over monomolecular hairpin formation at and above 9 µM oligomer concentration. Thus, we hypothesize that imperfect inverted repeat sequence (AT)XN12(AT)Y of HS2 of β-globin gene LCR forms the unusually stable hairpins which may result in the formation of a cruciform structure that may be recruited for binding by various nuclear proteins that could result in elevated HbF levels. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kapil Roy
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
| | - Swati Mahendru
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
| | - Ritushree Kukreti
- b Genomics and Molecular Medicine Unit , Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research , Delhi , India
| | - Shrikant Kukreti
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
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