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Zhu Y, He J, Li Z, Yang W. Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia. BMC Bioinformatics 2023; 24:37. [PMID: 36737692 PMCID: PMC9896718 DOI: 10.1186/s12859-023-05148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been reported to have a crucial impact on the pathogenesis of acute myeloid leukemia (AML). Cuproptosis, a copper-triggered modality of mitochondrial cell death, might serve as a promising therapeutic target for cancer treatment and clinical outcome prediction. Nevertheless, the role of cuproptosis-related lncRNAs in AML is not fully understood. METHODS The RNA sequencing data and demographic characteristics of AML patients were downloaded from The Cancer Genome Atlas database. Pearson correlation analysis, the least absolute shrinkage and selection operator algorithm, and univariable and multivariable Cox regression analyses were applied to identify the cuproptosis-related lncRNA signature and determine its feasibility for AML prognosis prediction. The performance of the proposed signature was evaluated via Kaplan-Meier survival analysis, receiver operating characteristic curves, and principal component analysis. Functional analysis was implemented to uncover the potential prognostic mechanisms. Additionally, quantitative real-time PCR (qRT-PCR) was employed to validate the expression of the prognostic lncRNAs in AML samples. RESULTS A signature consisting of seven cuproptosis-related lncRNAs (namely NFE4, LINC00989, LINC02062, AC006460.2, AL353796.1, PSMB8-AS1, and AC000120.1) was proposed. Multivariable cox regression analysis revealed that the proposed signature was an independent prognostic factor for AML. Notably, the nomogram based on this signature showed excellent accuracy in predicting the 1-, 3-, and 5-year survival (area under curve = 0.846, 0.801, and 0.895, respectively). Functional analysis results suggested the existence of a significant association between the prognostic signature and immune-related pathways. The expression pattern of the lncRNAs was validated in AML samples. CONCLUSION Collectively, we constructed a prediction model based on seven cuproptosis-related lncRNAs for AML prognosis. The obtained risk score may reveal the immunotherapy response in patients with this disease.
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Affiliation(s)
- Yidong Zhu
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Jun He
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China ,grid.412538.90000 0004 0527 0050Department of Hematology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Zihua Li
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China ,grid.412538.90000 0004 0527 0050Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Wenzhong Yang
- Department of Hematology, Shanghai Punan Hosptial of Pudong New District, Shanghai, 200125, China.
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Li X, Chen M, Liu B, Lu P, Lv X, Zhao X, Cui S, Xu P, Nakamura Y, Kurita R, Chen B, Huang DCS, Liu DP, Liu M, Zhao Q. Transcriptional silencing of fetal hemoglobin expression by NonO. Nucleic Acids Res 2021; 49:9711-9723. [PMID: 34379783 PMCID: PMC8464040 DOI: 10.1093/nar/gkab671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
Human fetal globin (γ-globin) genes are developmentally silenced after birth, and reactivation of γ-globin expression in adulthood ameliorates symptoms of hemoglobin disorders, such as sickle cell disease (SCD) and β-thalassemia. However, the mechanisms by which γ-globin expression is precisely regulated are still incompletely understood. Here, we found that NonO (non-POU domain-containing octamer-binding protein) interacted directly with SOX6, and repressed the expression of γ-globin gene in human erythroid cells. We showed that NonO bound to the octamer binding motif, ATGCAAAT, of the γ-globin proximal promoter, resulting in inhibition of γ-globin transcription. Depletion of NonO resulted in significant activation of γ-globin expression in K562, HUDEP-2, and primary human erythroid progenitor cells. To confirm the role of NonO in vivo, we further generated a conditional knockout of NonO by using IFN-inducible Mx1-Cre transgenic mice. We found that induced NonO deletion reactivated murine embryonic globin and human γ-globin gene expression in adult β-YAC mice, suggesting a conserved role for NonO during mammalian evolution. Thus, our data indicate that NonO acts as a novel transcriptional repressor of γ-globin gene expression through direct promoter binding, and is essential for γ-globin gene silencing.
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Affiliation(s)
- Xinyu Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mengxia Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Biru Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Peifen Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiang Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuaiying Cui
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Peipei Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
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3
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Ali G, Tariq MA, Shahid K, Ahmad FJ, Akram J. Advances in genome editing: the technology of choice for precise and efficient β-thalassemia treatment. Gene Ther 2020; 28:6-15. [PMID: 32355226 DOI: 10.1038/s41434-020-0153-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 04/16/2020] [Indexed: 11/09/2022]
Abstract
Beta (β)-thalassemia is one of the most significant hemoglobinopathy worldwide. The high prevalence of the β-thalassemia carriers aggravates the disease burden for patients and national economies in the developing world. The survival of β-thalassemia patients solely relies on repeated transfusions, which eventually results into multi-organ damage. The fetal γ-globin genes are ordinarily silenced at birth and replaced by the adult β-globin genes. However, mutations that cause lifelong persistence of fetal γ-globin, ameliorate the debilitating effects of β-globin mutations. Therefore, therapeutically reactivating the fetal γ-globin gene is a prime focus of researchers. CRISPR/Cas9 is the most common approach to correct disease causative mutations or to enhance or disrupt the expression of proteins to mitigate the effects of the disease. CRISPR/cas9 and prime gene editing to correct mutations in hematopoietic stem cells of β-thalassemia patients has been considered a novel therapeutic approach for effective hemoglobin production. However, genome-editing technologies, along with all advantages, have shown some disadvantages due to either random insertions or deletions at the target site of edition or non-specific targeting in genome. Therefore, the focus of this review is to compare pros and cons of these editing technologies and to elaborate the retrospective scope of gene therapy for β-thalassemia patients.
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Affiliation(s)
- Gibran Ali
- Institute of Regenerative Medicine, Physiology and Cell Biology Department, University of Health Sciences Lahore, Khyaban-e-Jamia Punjab, Lahore, 54600, Pakistan.
| | - Muhammad Akram Tariq
- Institute of Regenerative Medicine, Physiology and Cell Biology Department, University of Health Sciences Lahore, Khyaban-e-Jamia Punjab, Lahore, 54600, Pakistan
| | - Kamran Shahid
- Department of Oncology Medicine, University of Texas Health Science Center at Tyler, 11937 US HWY 271, Tyler, 75708, TX, USA
| | - Fridoon Jawad Ahmad
- Institute of Regenerative Medicine, Physiology and Cell Biology Department, University of Health Sciences Lahore, Khyaban-e-Jamia Punjab, Lahore, 54600, Pakistan.
| | - Javed Akram
- University of Health Sciences Lahore, Khyaban-e-Jamia Punjab, Lahore, 54600, Pakistan
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Pan Q, Wang L, Zhang H, Liang C, Li B. Identification of a 5-Gene Signature Predicting Progression and Prognosis of Clear Cell Renal Cell Carcinoma. Med Sci Monit 2019; 25:4401-4413. [PMID: 31194719 PMCID: PMC6587650 DOI: 10.12659/msm.917399] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Although the mortality rates of clear cell renal cell carcinoma (ccRCC) have decreased in recent years, the clinical outcome remains highly dependent on the individual patient. Therefore, identifying novel biomarkers for ccRCC patients is crucial. Material/Methods In this study, we obtained RNA sequencing data and clinical information from the TCGA database. Subsequently, we performed integrated bioinformatic analysis that includes differently expressed genes analysis, gene ontology and KEGG pathway analysis, protein-protein interaction analysis, and survival analysis. Moreover, univariate and multivariate Cox proportional hazards regression models were constructed. Results As a result, we identified a total of 263 dysregulated genes that may participate in the metastasis of ccRCC, and established a predictive signature relying on the expression of OTX1, MATN4, PI3, ERVV-2, and NFE4, which could serve as significant progressive and prognostic biomarkers for ccRCC. Conclusions We identified differentially expressed genes that may be involved in the metastasis of ccRCC. Moreover, a predictive signature based on the expression of OTX1, MATN4, PI3, ERVV-2, and NFE4 could be an independent prognostic factor for ccRCC.
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Affiliation(s)
- Qiufeng Pan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Longwang Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Hao Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Chaoqi Liang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Bing Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
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Adelvand P, Hamid M, Sardari S. The intrinsic genetic and epigenetic regulator factors as therapeutic targets, and the effect on fetal globin gene expression. Expert Rev Hematol 2017; 11:71-81. [DOI: 10.1080/17474086.2018.1406795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pegah Adelvand
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammed Hamid
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Basak A, Sankaran VG. Regulation of the fetal hemoglobin silencing factor BCL11A. Ann N Y Acad Sci 2016; 1368:25-30. [PMID: 26963603 DOI: 10.1111/nyas.13024] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/16/2022]
Abstract
The clinical severity of sickle cell disease and β-thalassemia, the major disorders of β-globin, can be ameliorated by increased production of fetal hemoglobin (HbF). Here, we provide a brief overview of the fetal-to-adult hemoglobin switch that occurs in humans shortly after birth and review our current understanding of one of the most potent known regulators of this switching process, the multiple zinc finger-containing transcription factor BCL11A. Originally identified in genome-wide association studies, multiple orthogonal lines of evidence have validated BCL11A as a key regulator of hemoglobin switching and as a promising therapeutic target for HbF induction. We discuss recent studies that have highlighted its importance in silencing the HbF-encoding genes and discuss opportunities that exist to further understand the regulation of BCL11A and its mechanism of action, which could provide new insight into opportunities to induce HbF for therapeutic purposes.
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Affiliation(s)
- Anindita Basak
- Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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7
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Wang IK, Sun KT, Tsai TH, Chen CW, Chang SS, Yu TM, Yen TH, Lin FY, Huang CC, Li CY. MiR-20a-5p mediates hypoxia-induced autophagy by targeting ATG16L1 in ischemic kidney injury. Life Sci 2015; 136:133-41. [PMID: 26165754 DOI: 10.1016/j.lfs.2015.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 06/04/2015] [Accepted: 07/06/2015] [Indexed: 12/14/2022]
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Induction of human fetal hemoglobin expression by adenosine-2',3'-dialdehyde. J Transl Med 2013; 11:14. [PMID: 23316703 PMCID: PMC3599103 DOI: 10.1186/1479-5876-11-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 01/09/2013] [Indexed: 12/15/2022] Open
Abstract
Background Pharmacologic reactivation of fetal hemoglobin expression is a promising strategy for treatment of sickle cell disease and β-thalassemia. The objective of this study was to investigate the effect of the methyl transferase inhibitor adenosine-2’,3’-dialdehyde (Adox) on induction of human fetal hemoglobin (HbF) in K562 cells and human hematopoietic progenitor cells. Methods Expression levels of human fetal hemoglobin were assessed by northern blot analysis and Real-time PCR. HbF and adult hemoglobin (HbA) content were analyzed using high-performance liquid chromatography (HPLC). DNA methylation levels on human gamma-globin gene promoters were determined using Bisulfite sequence analysis. Enrichment of histone marks on genes was assessed by chromosome immunoprecipitation (ChIP). Results Adox induced γ-globin gene expression in both K562 cells and in human bone marrow erythroid progenitor cells through a mechanism potentially involving inhibition of protein arginine methyltransferase 5 (PRMT5). Conclusions The ability of methyl transferase inhibitors such as Adox to efficiently reactivate fetal hemoglobin expression suggests that these agents may provide a means of reactivating fetal globin expression as a therapeutic option for treating sickle cell disease and β-thalassemia.
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Abstract
The fetal-to-adult hemoglobin switch and silencing of fetal hemoglobin (HbF) have been areas of long-standing interest among hematologists, given the fact that clinical induction of HbF production holds tremendous promise to ameliorate the clinical symptoms of sickle cell disease (SCD) and β-thalassemia. In this article, we discuss historic attempts to induce HbF that have resulted in some therapeutic approaches to manage SCD and β-thalassemia. We then go on to discuss how more recent molecular studies that have identified regulators, including BCL11A, MYB, and KLF1, hold great promise to develop targeted and more effective approaches for HbF induction. We go on to discuss strategies by which such approaches may be developed. Older studies in this field can provide important lessons for future studies aimed at developing more effective strategies for HbF induction, and we therefore chronologically cover the work accomplished as this field has evolved over the course of the past four decades.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA.
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10
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Xu Z, He Y, Ju J, Rank G, Cerruti L, Ma C, Simpson RJ, Moritz RL, Jane SM, Zhao Q. The role of WDR5 in silencing human fetal globin gene expression. Haematologica 2012; 97:1632-40. [PMID: 22689669 DOI: 10.3324/haematol.2012.061937] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Histone H3 lysine 4 (K4) methylation has been linked with transcriptional activity in mammalian cells. The WD40-repeat protein, WDR5, is an essential component of the MLL complex that induces histone H3 K4 methylation, but the role of WDR5 in human globin gene regulation has not yet been established. DESIGN AND METHODS To study the role of WDR5 in human globin gene regulation, we performed knockdown experiments in both K562 cells and primary human bone marrow erythroid progenitor cells (BMC). The effects of WDR5 knockdown on γ-globin gene expression were determined. Biochemical approaches were also employed to investigate WDR5 interaction molecules. Chromosomal marks in the globin locus were analyzed by ChIP. RESULTS We found that WDR5 interacted with protein arginine methyltransferase 5 (PRMT5), a known repressor of γ-globin gene expression, and was essential for generating tri-methylated H3K4 (H3K4me3) at the γ-globin promoter in K562 cells. Enforced expression of WDR5 in K562 cells reduced γ-globin gene expression, whereas knockdown of WDR5 increased γ-globin gene expression in both K562 cells and primary human bone marrow erythroid progenitor cells. Consistent with this, both histone H3 and H4 acetylation at the γ-globin promoter were increased, while histone H4R3 and H3K9 methylation were decreased, in WDR5 knockdown cells compared to controls. We found that WDR5 interacted with HDAC1 and a PHD domaincontaining protein, ING2 (inhibitor of growth), an H3K4me3 mark reader, to enhance γ-globin gene transcriptional repression. In human BMC, levels of WDR5 were highly enriched on the γ-promoter relative to levels on other globin promoters and compared to the γ-promoter in cord blood erythroid progenitors, suggesting that WDR5 is important in the developmental globin gene expression program. CONCLUSIONS Our data are consistent with a model in which WDR5 binds the γ-globin promoter in a PRMT5-dependent manner; H3K4me3 induced at the γ-globin promoter by WDR5 may result in the recruitment of the ING2-associated HDAC1 component and consequent silencing of γ-globin gene expression.
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Affiliation(s)
- Zhen Xu
- Molecular Immunology and Cancer Research Center, The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
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11
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Xu Z, Gao X, He Y, Ju J, Zhang M, Liu R, Wu Y, Ma C, Ma C, Lin Z, Huang X, Zhao Q. Synergistic effect of SRY and its direct target, WDR5, on Sox9 expression. PLoS One 2012; 7:e34327. [PMID: 22523547 PMCID: PMC3327683 DOI: 10.1371/journal.pone.0034327] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 02/25/2012] [Indexed: 11/18/2022] Open
Abstract
SRY is a sex-determining gene that encodes a transcription factor, which triggers male development in most mammals. The molecular mechanism of SRY action in testis determination is, however, poorly understood. In this study, we demonstrate that WDR5, which encodes a WD-40 repeat protein, is a direct target of SRY. EMSA experiments and ChIP assays showed that SRY could bind to the WDR5 gene promoter directly. Overexpression of SRY in LNCaP cells significantly increased WDR5 expression concurrent with histone H3K4 methylation on the WDR5 promoter. To specifically address whether SRY contributes to WDR5 regulation, we introduced a 4-hydroxy-tamoxifen-inducible SRY allele into LNCaP cells. Conditional SRY expression triggered enrichment of SRY on the WDR5 promoter resulting in induction of WDR5 transcription. We found that WDR5 was self regulating through a positive feedback loop. WDR5 and SRY interacted and were colocalized in cells. In addition, the interaction of WDR5 with SRY resulted in activation of Sox9 while repressing the expression of β-catenin. These results suggest that, in conjunction with SRY, WDR5 plays an important role in sex determination.
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Affiliation(s)
- Zhen Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinxing Gao
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yinghong He
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
- School of Basic Medicine, Dali University, Yunnan, China
| | - Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Miaomiao Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ronghua Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yupeng Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chunyan Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chi Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhaoyu Lin
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Xingxu Huang
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
- * E-mail:
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Identification of a PRMT5-dependent repressor complex linked to silencing of human fetal globin gene expression. Blood 2010; 116:1585-92. [PMID: 20495075 DOI: 10.1182/blood-2009-10-251116] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Defining the molecular mechanisms underpinning fetal (gamma) globin gene silencing may provide strategies for reactivation of gamma-gene expression, a major therapeutic objective in patients with beta-thalassemia and sickle cell disease (SCD). We have previously demonstrated that symmetric methylation of histone H4 Arginine 3 (H4R3me2s) by the protein arginine methyltransferase PRMT5 is required for recruitment of the DNA methyltransferase DNMT3A to the gamma-promoter, and subsequent DNA methylation and gene silencing. Here we show in an erythroid cell line, and in primary adult erythroid progenitors that PRMT5 induces additional repressive epigenetic marks at the gamma-promoter through the assembly of a multiprotein repressor complex containing the histone modifying enzymes SUV4-20h1, casein kinase 2alpha (CK2alpha), and components of the nucleosome remodeling and histone deacetylation complex. Expression of a mutant form of PRMT5 lacking methyltransferase activity or shRNA-mediated knockdown of SUV4-20h1 resulted in loss of complex binding to the gamma-promoter, reversal of both histone and DNA repressive epigenetic marks, and increased gamma-gene expression. The repressive H4K20me3 mark induced by SUV4-20h1 is enriched on the gamma-promoter in erythroid progenitors from adult bone marrow compared with cord blood, suggesting developmental specificity. These studies define coordinated epigenetic events linked to fetal globin gene silencing, and provide potential therapeutic targets for the treatment of beta-thalassemia and SCD.
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A zinc-finger transcriptional activator designed to interact with the gamma-globin gene promoters enhances fetal hemoglobin production in primary human adult erythroblasts. Blood 2010; 115:3033-41. [PMID: 20190190 DOI: 10.1182/blood-2009-08-240556] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Fetal hemoglobin (HbF) is a potent genetic modifier of the severity of beta-thalassemia and sickle cell anemia. We used an in vitro culture model of human erythropoiesis in which late-stage erythroblasts are derived directly from human CD34(+) hematopoietic cells to evaluate HbF production. This system recapitulates expression of globin genes according to the developmental stage of the originating cell source. When cytokine-mobilized peripheral blood CD34(+) cells from adults were cultured, background levels of HbF were 2% or less. Cultured cells were readily transduced with lentiviral vectors when exposed to vector particles between 48 and 72 hours. Among the genetic elements that may enhance fetal hemoglobin production is an artificial zinc-finger transcription factor, GG1-VP64, designed to interact with the proximal gamma-globin gene promoters. Our data show that lentiviral-mediated, enforced expression of GG1-VP64 under the control of relatively weak erythroid-specific promoters induced significant amounts of HbF (up to 20%) in erythroblasts derived from adult CD34(+) cells without altering their capacity for erythroid maturation and only modestly reducing the total numbers of cells that accumulate in culture after transduction. These observations demonstrate the potential for sequence-specific enhancement of HbF in patients with beta-thalassemia or sickle cell anemia.
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Chen RL, Chou YC, Lan YJ, Huang TS, Shen CKJ. Developmental silencing of human zeta-globin gene expression is mediated by the transcriptional repressor RREB1. J Biol Chem 2010; 285:10189-97. [PMID: 20133935 DOI: 10.1074/jbc.m109.049130] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian embryonic zeta-globin genes, including that of humans, are expressed at the early embryonic stage and then switched off during erythroid development. This autonomous silencing of the zeta-globin gene transcription is probably regulated by the cooperative work of various protein-DNA and protein-protein complexes formed at the zeta-globin promoter and its upstream enhancer (HS-40). We present data here indicating that a protein-binding motif, ZF2, contributes to the repression of the HS-40-regulated human zeta-promoter activity in erythroid cell lines and in transgenic mice. Combined site-directed mutagenesis and EMSA suggest that repression of the human zeta-globin promoter is mediated through binding of the zinc finger factor RREB1 to ZF2. This model is further supported by the observation that human zeta-globin gene transcription is elevated in the human erythroid K562 cell line or the primary erythroid culture upon RNA interference (RNAi)(2) knockdown of RREB1 expression. These data together suggest that RREB1 is a putative repressor for the silencing of the mammalian zeta-globin genes during erythroid development. Because zeta-globin is a powerful inhibitor of HbS polymerization, our experiments have provided a foundation for therapeutic up-regulation of zeta-globin gene expression in patients with severe hemoglobinopathies.
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Affiliation(s)
- Ruei-Lin Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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15
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Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ, Cerruti L, Curtis DJ, Patel DJ, Allis CD, Cunningham JM, Jane SM. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 2009; 16:304-311. [PMID: 19234465 PMCID: PMC5120857 DOI: 10.1038/nsmb.1568] [Citation(s) in RCA: 380] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 01/27/2009] [Indexed: 12/12/2022]
Abstract
Mammalian gene silencing is established through methylation of histones and DNA, although the order in which these modifications occur remains contentious. Using the human beta-globin locus as a model, we demonstrate that symmetric methylation of histone H4 arginine 3 (H4R3me2s) by the protein arginine methyltransferase PRMT5 is required for subsequent DNA methylation. H4R3me2s serves as a direct binding target for the DNA methyltransferase DNMT3A, which interacts through the ADD domain containing the PHD motif. Loss of the H4R3me2s mark through short hairpin RNA-mediated knockdown of PRMT5 leads to reduced DNMT3A binding, loss of DNA methylation and gene activation. In primary erythroid progenitors from adult bone marrow, H4R3me2s marks the inactive methylated globin genes coincident with localization of PRMT5. Our findings define DNMT3A as both a reader and a writer of repressive epigenetic marks, thereby directly linking histone and DNA methylation in gene silencing.
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Affiliation(s)
- Quan Zhao
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia.,Molecular Immunology and Cancer Research Center, The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Gerhard Rank
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia
| | - Yuen T Tan
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia
| | - Haitao Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Robert L Moritz
- Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
| | - Richard J Simpson
- Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
| | - Loretta Cerruti
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia
| | - David J Curtis
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
| | - John M Cunningham
- Department of Pediatrics and Institute of Molecular Pediatric Sciences, University of Chicago, 5839 South Maryland Avenue, Chicago, Illinois 60637, USA
| | - Stephen M Jane
- Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, VIC 3050, Australia.,Department of Medicine, University of Melbourne, Grattan Street, Parkville, VIC 3050, Australia
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16
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Fetal hemoglobin chemical inducers for treatment of hemoglobinopathies. Ann Hematol 2008; 88:505-28. [PMID: 19011856 DOI: 10.1007/s00277-008-0637-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 10/27/2008] [Indexed: 12/29/2022]
Abstract
The switch from fetal ((G)gamma and (A)gamma) to adult (beta and delta) globin gene expression occurs at birth, leading to the gradual replacement of HbF with HbA. Genetic regulation of this switch has been studied for decades, and the molecular mechanisms underlying this developmental change in gene expression have been in part elucidated. The understanding of the developmental regulation of gamma-globin gene expression was paralleled by the identification of a series of chemical compounds able to reactivate HbF synthesis in vitro and in vivo in adult erythroid cells. Reactivation of HbF expression is an important therapeutic option in patients with hemoglobin disorders, such as sickle cell anemia and beta-thalassemia. These HbF inducers can be grouped in several classes based on their chemical structures and mechanisms of action. Clinical studies with some of these agents have shown that they were effective, in a part of patients, in ameliorating the clinical condition. The increase in HbF in response to these drugs varies among patients with beta-thalassemia and sickle cell disease due to individual genetic determinants.
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Silencing of Agamma-globin gene expression during adult definitive erythropoiesis mediated by GATA-1-FOG-1-Mi2 complex binding at the -566 GATA site. Mol Cell Biol 2008; 28:3101-13. [PMID: 18347053 DOI: 10.1128/mcb.01858-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Autonomous silencing of gamma-globin transcription is an important developmental regulatory mechanism controlling globin gene switching. An adult stage-specific silencer of the (A)gamma-globin gene was identified between -730 and -378 relative to the mRNA start site. A marked copy of the (A)gamma-globin gene inserted between locus control region 5' DNase I-hypersensitive site 1 and the epsilon-globin gene was transcriptionally silenced in adult beta-globin locus yeast artificial chromosome (beta-YAC) transgenic mice, but deletion of the 352-bp region restored expression. This fragment reduced reporter gene expression in K562 cells, and GATA-1 was shown to bind within this sequence at the -566 GATA site. Further, the Mi2 protein, a component of the NuRD complex, was observed in erythroid cells with low gamma-globin levels, whereas only a weak signal was detected when gamma-globin was expressed. Chromatin immunoprecipitation of fetal liver tissue from beta-YAC transgenic mice demonstrated that GATA-1, FOG-1, and Mi2 were recruited to the (A)gamma-globin -566 or (G)gamma-globin -567 GATA site when gamma-globin expression was low (day 18) but not when gamma-globin was expressed (day 12). These data suggest that during definitive erythropoiesis, gamma-globin gene expression is silenced, in part, by binding a protein complex containing GATA-1, FOG-1, and Mi2 at the -566/-567 GATA sites of the proximal gamma-globin promoters.
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Abstract
The developmental changes in expression of the beta like genes from embryonic to adult stages of human life are controlled at least partially at the level of the promoter sequences of these genes and their binding factors, and competition for promoter specific interactions with the locus control region (LCR). In recent years, the control of beta globin genes has also been investigated at the level of chromatin structure involving the chemical modification of histones and their remodelling by DNA dependent ATPases (SMARCA) containing protein complexes. The role of intergenic RNA is also being investigated with renewed interest. Although a wealth of information on the structure/function relationship of the LCR and globin promoters has been gathered over more than two decades, the fundamental nature of the control of these genes at the molecular level is still not completely understood. In the following pages, we intend to briefly describe the progress made in the field and discuss future directions.
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Affiliation(s)
- Milind C Mahajan
- Department of Human Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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Mankidy R, Faller DV, Mabaera R, Lowrey CH, Boosalis MS, White GL, Castaneda SA, Perrine SP. Short-chain fatty acids induce gamma-globin gene expression by displacement of a HDAC3-NCoR repressor complex. Blood 2006; 108:3179-86. [PMID: 16849648 PMCID: PMC1895523 DOI: 10.1182/blood-2005-12-010934] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-level induction of fetal (gamma) globin gene expression for therapy of beta-hemoglobinopathies likely requires local chromatin modification and dissociation of repressor complexes for gamma-globin promoter activation. A novel gamma-globin-inducing short-chain fatty acid derivative (SCFAD), RB7, which was identified through computational modeling, produced a 6-fold induction in a reporter assay that detects only strong inducers of the gamma-globin gene promoter and in cultured human erythroid progenitors. To elucidate the molecular mechanisms used by high-potency SCFADs, chromatin immunoprecipitation (ChIP) assays performed at the human gamma- and beta-globin gene promoters in GM979 cells and in erythroid progenitors demonstrate that RB7 and butyrate induce dissociation of HDAC3 (but not HDAC1 or HDAC2) and its adaptor protein NCoR, specifically from the gamma-globin gene promoter. A coincident and proportional recruitment of RNA polymerase II to the gamma-globin gene promoter was observed with exposure to these gamma-globin inducers. Knockdown of HDAC3 by siRNA induced transcription of the gamma-globin gene promoter, demonstrating that displacement of HDAC3 from the gamma-globin gene promoter by the SCFAD is sufficient to induce gamma-globin gene expression. These studies demonstrate new dynamic alterations in transcriptional regulatory complexes associated with SCFAD-induced activation of the gamma-globin gene and provide a specific molecular target for potential therapeutic intervention.
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