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Zhu S, Luo Y, Li K, Mei C, Wang Y, Jiang L, Wang W, Zhang Q, Yang W, Lang W, Zhou X, Wang L, Ren Y, Ma L, Ye L, Huang X, Chen J, Sun J, Tong H. RIPK3 deficiency blocks R-2-hydroxyglutarate-induced necroptosis in IDH-mutated AML cells. SCIENCE ADVANCES 2024; 10:eadi1782. [PMID: 38630819 PMCID: PMC11023509 DOI: 10.1126/sciadv.adi1782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Mutant isocitrate dehydrogenases (IDHs) produce R-2-hydroxyglutarate (R-2HG), which inhibits the growth of most acute myeloid leukemia (AML) cells. Here, we showed that necroptosis, a form of programmed cell death, contributed to the antileukemia activity of R-2HG. Mechanistically, R-2HG competitively inhibited the activity of lysine demethylase 2B (KDM2B), an α-ketoglutarate-dependent dioxygenase. KDM2B inhibition increased histone 3 lysine 4 trimethylation levels and promoted the expression of receptor-interacting protein kinase 1 (RIPK1), which consequently caused necroptosis in AML cells. The expression of RIPK3 was silenced because of DNA methylation in IDH-mutant (mIDH) AML cells, resulting in R-2HG resistance. Decitabine up-regulated RIPK3 expression and repaired endogenous R-2HG-induced necroptosis pathway in mIDH AML cells. Together, R-2HG induced RIPK1-dependent necroptosis via KDM2B inhibition in AML cells. The loss of RIPK3 protected mIDH AML cells from necroptosis. Restoring RIPK3 expression to exert R-2HG's intrinsic antileukemia effect will be a potential therapeutic strategy in patients with AML.
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Affiliation(s)
- Shuanghong Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Yingwan Luo
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Kongfei Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Chen Mei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Yuxia Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Lingxu Jiang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Wei Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Qi Zhang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Wenli Yang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Wei Lang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Xinping Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Lu Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Yanling Ren
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Liya Ma
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Li Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Xin Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Gehr Family Center for Leukemia Research, City of Hope Medical Center and Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jie Sun
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, PR China
| | - Hongyan Tong
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, PR China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, PR China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, PR China
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Chellini L, Scarfò M, Bonvissuto D, Sette C, Paronetto MP. The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma. Oncogene 2024; 43:225-234. [PMID: 38017132 DOI: 10.1038/s41388-023-02894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Ewing sarcomas (ES) are aggressive paediatric tumours of bone and soft tissues. Resistance to chemotherapy and high propensity to metastasize remain the main causes of treatment failure. Thus, identifying novel targets for alternative therapeutic approaches is urgently needed. DNA/RNA helicases are emerging as crucial regulators of many cellular processes often deregulated in cancer. Among them, DHX9 is up-regulated in ES and collaborates with EWS-FLI1 in ES transformation. We report that DHX9 silencing profoundly impacts on the oncogenic properties of ES cells. Transcriptome profiling combined to bioinformatic analyses disclosed a gene signature commonly regulated by DHX9 and the Lysine Demethylase KDM2B, with the Hippo pathway regulator YAP1 as a prominent target. Mechanistically, we found that DHX9 enhances H3K9 chromatin demethylation by KDM2B and favours RNA Polymerase II recruitment, thus promoting YAP1 expression. Conversely, EWS-FLI1 binding to the promoter represses YAP1 expression. These findings identify the DHX9/KDM2B complex as a new druggable target to counteract ES malignancy.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy.
| | - Marzia Scarfò
- Plaisant Polo Tecnologico s.r.l, Castel Romano, Rome, Italy
| | - Davide Bonvissuto
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Claudio Sette
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- GSTeP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy.
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.
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Fatima N, Saif Ur Rahman M, Qasim M, Ali Ashfaq U, Ahmed U, Masoud MS. Transcriptional Factors Mediated Reprogramming to Pluripotency. Curr Stem Cell Res Ther 2024; 19:367-388. [PMID: 37073151 DOI: 10.2174/1574888x18666230417084518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 04/20/2023]
Abstract
A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.
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Affiliation(s)
- Nazira Fatima
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Muhammad Saif Ur Rahman
- Institute of Advanced Studies, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Uzair Ahmed
- EMBL Partnership Institute for Genome Editing Technologies, Vilnius University, Vilnius, 10257, Lithuania
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
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Šopin T, Liška F, Kučera T, Cmarko D, Vacík T. Lysine Demethylase KDM2A Promotes Proteasomal Degradation of TCF/LEF Transcription Factors in a Neddylation-Dependent Manner. Cells 2023; 12:2620. [PMID: 37998355 PMCID: PMC10670284 DOI: 10.3390/cells12222620] [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: 09/20/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Canonical Wnt signaling is essential for a plethora of biological processes ranging from early embryogenesis to aging. Malfunctions of this crucial signaling pathway are associated with various developmental defects and diseases, including cancer. Although TCF/LEF transcription factors (TCF/LEFs) are known to be essential for this pathway, the regulation of their intracellular levels is not completely understood. Here, we show that the lysine demethylase KDM2A promotes the proteasomal destabilization of TCF/LEFs independently of its demethylase domain. We found that the KDM2A-mediated destabilization of TCF/LEFs is dependent on the KDM2A zinc finger CXXC domain. Furthermore, we identified the C-terminal region of TCF7L2 and the CXXC domain of KDM2A as the domains responsible for the interaction between the two proteins. Our study is also the first to show that endogenous TCF/LEF proteins undergo KDM2A-mediated proteasomal degradation in a neddylation-dependent manner. Here, we reveal a completely new mechanism that affects canonical Wnt signaling by regulating the levels of TCF/LEF transcription factors through their KDM2A-promoted proteasomal degradation.
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Affiliation(s)
- Tijana Šopin
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 01 Prague, Czech Republic; (F.L.); (T.Š.); (D.C.)
| | - František Liška
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 01 Prague, Czech Republic; (F.L.); (T.Š.); (D.C.)
| | - Tomáš Kučera
- Institute of Histology and Embryology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 01 Prague, Czech Republic;
| | - Dušan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 01 Prague, Czech Republic; (F.L.); (T.Š.); (D.C.)
| | - Tomáš Vacík
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 01 Prague, Czech Republic; (F.L.); (T.Š.); (D.C.)
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5
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Xiong X, Huang X, Zhu Y, Hai Z, Fei X, Pan B, Yang Q, Xiong Y, Fu W, Lan D, Zhang X, Li J. Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis. Theriogenology 2023; 209:9-20. [PMID: 37354760 DOI: 10.1016/j.theriogenology.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/26/2023]
Abstract
Lysine-specific histone demethylase 2 (Kdm2a) is a regulatory factor of histone modifications that participates in gametogenesis and embryonic development. The mis-regulation of Kdm2a can lead to aberrant gene expression, thereby contributing to abnormal cell proliferation, differentiation, apoptosis, and tumorigenesis. However, due to the potential confounding effects that are secondary to the loss of Kdm2a function from the soma in existing whole-animal mutants, the in vivo function of Kdm2a in spermatogenesis for male fertility remains unknown. Herein, we focus on exploring the spatiotemporal expression profile and biological functions of Kdm2a in the spermatogenesis and fertility of male mice. A testis-specific knockout Kdm2a model (Kdm2a cKO) was established by using the Stra8-Cre/loxP recombinase system to explore the roles of Kdm2a in male fertility. Our results showed that Kdm2a was ubiquitously expressed and dynamically distributed in multiple tissues and cell types in the testis of mice. Surprisingly, Kdm2a-deficient adult males were completely fertile and comparable with their control (Kdm2aflox/flox) counterparts. Despite the significantly reduced total number of sperm and density of seminiferous tubules in Kdm2a cKO testis accompanied by the degeneration of spermatogenesis, the fertilization ability and embryonic developmental competence of the Kdm2a cKO were comparable with those of their control littermates, suggesting that Kdm2a disruption did not markedly affect male fertility, at least during younger ages. Furthermore, Kdm2a homozygous mutants exhibited a lower total number and motility of sperm than the control group and showed notably affected serum 17β-estradiol concentration. Interestingly, the transcriptome sequencing revealed that the loss of Kdm2a remarkably upregulated the expression level of Kdm2b. This effect, in turn, may induce compensative effects in the case of Kdm2a deficiency to maintain normal male reproduction. Together, our results reveal that Kdm2a shows spatiotemporal expression during testicular development and that its loss is insufficient to compromise the production of spermatozoa completely. The homologous Kdm2b gene might compensate for the loss of Kdm2a. Our work provides a novel Kdm2a cKO mouse allowing for the efficient deletion of Kdm2a in a testis-specific manner, and further investigated the biological function of Kdm2a and the compensatory effects of Kdm2b. Our study will advance our understanding of underlying mechanisms in spermatogenesis and male fertility.
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Affiliation(s)
- Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xiangyue Huang
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Yanjin Zhu
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Zhuo Hai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xixi Fei
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Bangting Pan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Qinhui Yang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Wei Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Daoliang Lan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xiaojian Zhang
- Center for Assisted Reproduction, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, 610072, PR China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China; Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China.
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6
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Spangler CJ, Skrajna A, Foley CA, Nguyen A, Budziszewski GR, Azzam DN, Arteaga EC, Simmons HC, Smith CB, Wesley NA, Wilkerson EM, McPherson JME, Kireev D, James LI, Frye SV, Goldfarb D, McGinty RK. Structural basis of paralog-specific KDM2A/B nucleosome recognition. Nat Chem Biol 2023; 19:624-632. [PMID: 36797403 PMCID: PMC10159993 DOI: 10.1038/s41589-023-01256-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/10/2023] [Indexed: 02/18/2023]
Abstract
The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic patch recognition proteome wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. Despite fundamental roles in transcriptional repression in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any related JumonjiC (JmjC) domain lysine demethylase, remain unclear. We used a covalent conjugate between H3K36 and a demethylase inhibitor to solve cryogenic electron microscopy structures of KDM2A and KDM2B trapped in action on a nucleosome substrate. Our structures show that KDM2-nucleosome binding is paralog specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.
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Affiliation(s)
- Cathy J Spangler
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Aleksandra Skrajna
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline A Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anh Nguyen
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gabrielle R Budziszewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dalal N Azzam
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eyla C Arteaga
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly C Simmons
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charlotte B Smith
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathaniel A Wesley
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily M Wilkerson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeanne-Marie E McPherson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert K McGinty
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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7
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Zuo Y, Zhan L, Wen H, Xue J, Tan Y, Sun W, Xu E. Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance. FASEB J 2023; 37:e22796. [PMID: 36723950 DOI: 10.1096/fj.202201657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/02/2023]
Abstract
Hypoxic postconditioning (HPC) with 8% oxygen increases nuclear accumulation of β-catenin through activating the classical Wnt pathway, thereby alleviating transient global cerebral ischemia (tGCI)-induced neuronal damage in the hippocampal CA1 subregion of adult rats. However, little is understood about the regulatory mechanism of nuclear β-catenin in HPC-mediated cerebral ischemic tolerance. Although lysine(K)-specific demethylase 2A (KDM2A) has been known as a crucial regulator of nuclear β-catenin destabilization, whether it plays an important role through modulating nuclear β-catenin in cerebral ischemic tolerance induced by HPC remains unknown. In this study, we explored the molecular mechanism of stabilizing nuclear β-catenin by inhibiting KDM2A-mediated demethylation in the HPC-offered neuroprotection against tGCI. In addition, we confirmed that nuclear methylated-β-catenin in CA1 decreased and nuclear β-catenin turnover increased after tGCI, which were reversed by HPC. The administration with methyltransferase inhibitor AdOx abrogated HPC-induced methylation and stabilization of nuclear β-catenin in CA1, as well as the neuroprotection against tGCI. Notably, HPC downregulated the expression of KDM2A in CA1 and reduced the interaction between KDM2A and β-catenin in the nucleus after tGCI. The knockdown of KDM2A with small-interfering RNA could upregulate nuclear methylated-β-catenin and stabilize β-catenin, thereby increasing survivin in CA1 and improving the cognitive function of rats after tGCI. Opposite results were observed by the administration of KDM2A-carried adenovirus vector. Furthermore, we demonstrated that KDM2A mediates the demethylation of nuclear β-catenin through jumonji C (JmjC) domain of KDM2A in HEK-293T and SH-SY5Y cells. Our data support that the inhibition of KDM2A-mediated demethylation of nuclear β-catenin contributes to HPC-induced neuroprotection against tGCI.
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Affiliation(s)
- Yunyan Zuo
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lixuan Zhan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Haixia Wen
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiahui Xue
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yafu Tan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weiwen Sun
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - En Xu
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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8
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Wang N, Ma T, Yu B. Targeting epigenetic regulators to overcome drug resistance in cancers. Signal Transduct Target Ther 2023; 8:69. [PMID: 36797239 PMCID: PMC9935618 DOI: 10.1038/s41392-023-01341-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/18/2023] Open
Abstract
Drug resistance is mainly responsible for cancer recurrence and poor prognosis. Epigenetic regulation is a heritable change in gene expressions independent of nucleotide sequence changes. As the common epigenetic regulation mechanisms, DNA methylation, histone modification, and non-coding RNA regulation have been well studied. Increasing evidence has shown that aberrant epigenetic regulations contribute to tumor resistance. Therefore, targeting epigenetic regulators represents an effective strategy to reverse drug resistance. In this review, we mainly summarize the roles of epigenetic regulation in tumor resistance. In addition, as the essential factors for epigenetic modifications, histone demethylases mediate the histone or genomic DNA modifications. Herein, we comprehensively describe the functions of the histone demethylase family including the lysine-specific demethylase family, the Jumonji C-domain-containing demethylase family, and the histone arginine demethylase family, and fully discuss their regulatory mechanisms related to cancer drug resistance. In addition, therapeutic strategies, including small-molecule inhibitors and small interfering RNA targeting histone demethylases to overcome drug resistance, are also described.
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Affiliation(s)
- Nan Wang
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ting Ma
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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9
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Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
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Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
- *Correspondence: Gilles Salbert,
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10
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Ai Y, Wu S, Zou C, Wei H. Circular RNA circFOXO3 regulates KDM2A by targeting miR-214 to promote tumor growth and metastasis in oral squamous cell carcinoma. J Cell Mol Med 2021; 26:1842-1852. [PMID: 34117688 PMCID: PMC8918406 DOI: 10.1111/jcmm.16533] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a pathological type of oral cancer, which accounts for over 90% of oral cancers. It has been widely shown that circRNA is involved in the regulation of multiple malignant oral diseases including OSCC. However, the mechanism underlying how circRNA regulates OSCC is still not clearly elucidated. In this article, we report circFOXO3 promotes tumor growth and invasion of OSCC by targeting miR‐214 which specifically degrades the lysine demethylase 2A (KDM2A). CircRNA sequencing was conducted in OSCC tumor and tumor‐side tissues, and the expression of circFOXO3 is found to be markedly increased in tumor tissues. CircFOXO3 is also highly expressed in several OSCC cell lines compared with human oral keratinocytes. Transwell assay and colony formation showed that knockdown of circFOXO3 prevents the invasion and proliferation of oral cancer cells. Via bioinformatic research, miR‐214 was found to be the target of circFOXO3 and correlate well with circFOXO3 both in vitro and in vivo. KDM2A was then validated by database analysis and luciferase assay to be the direct target of miR‐214. KDM2A helps to promote tumor invasiveness and proliferation of OSCC. Collectively, our results proved that circFOXO3 sponges miR‐214 to up‐regulate the expression of KDM2A, thus promotes tumor progression in OSCC.
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Affiliation(s)
- Yilong Ai
- School of Stomatology and Medicine, Foshan Stomatology Hospital, Foshan University, Foshan, China
| | - Siyuan Wu
- School of Stomatology and Medicine, Foshan Stomatology Hospital, Foshan University, Foshan, China
| | - Chen Zou
- School of Stomatology and Medicine, Foshan Stomatology Hospital, Foshan University, Foshan, China
| | - Haigang Wei
- School of Stomatology and Medicine, Foshan Stomatology Hospital, Foshan University, Foshan, China
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11
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Weiss RJ, Spahn PN, Chiang AW, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PL, Lewis NE, Esko JD. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol 2021; 17:684-692. [PMID: 33846619 PMCID: PMC8159865 DOI: 10.1038/s41589-021-00776-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/18/2021] [Indexed: 02/01/2023]
Abstract
Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Screening of A375 melanoma cells uncovered additional genes and pathways impacting HS formation. The top hit was the epigenetic factor KDM2B, a histone demethylase. KDM2B inactivation suppressed multiple HS sulfotransferases and upregulated the sulfatase SULF1. These changes differentially affected the interaction of HS-binding proteins. KDM2B-deficient cells displayed decreased growth rates, which was rescued by SULF1 inactivation. In addition, KDM2B deficiency altered the expression of many extracellular matrix genes. Thus, KDM2B controls proliferation of A375 cells through the regulation of HS structure and serves as a master regulator of the extracellular matrix.
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Affiliation(s)
- Ryan J. Weiss
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Philipp N. Spahn
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Qing Liu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Jing Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Kristina M. Hamill
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Sandra Rother
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Thomas M. Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Marten A. Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Bryce M. Timm
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Philip L.S.M. Gordts
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
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12
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Liu L, Liu J, Lin Q. Histone demethylase KDM2A: Biological functions and clinical values (Review). Exp Ther Med 2021; 22:723. [PMID: 34007332 DOI: 10.3892/etm.2021.10155] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
Histone lysine demethylation modification is a critical epigenetic modification. Lysine demethylase 2A (KDM2A), a Jumonji C domain-containing demethylase, demethylates the dimethylated H3 lysine 36 (H3K36) residue and exerts little or no activity on monomethylated and trimethylated H3K36 residues. KDM2A expression is regulated by several factors, such as microRNAs, and the phosphorylation of KDM2A also plays a vital role in its function. KDM2A mainly recognizes the unmethylated region of CpG islands and subsequently demethylates histone H3K36 residues. In addition, KDM2A recognizes and binds to phosphorylated proteins, and promotes their ubiquitination and degradation. KDM2A plays an important role in chromosome remodeling and gene transcription, and is involved in cell proliferation and differentiation, cell metabolism, heterochromosomal homeostasis and gene stability. Notably, KDM2A is crucial for tumorigenesis and progression. In the present review, the documented biological functions of KDM2A in physiological and pathological processes are comprehensively summarized.
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Affiliation(s)
- Lisheng Liu
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China.,Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Qinghai Lin
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
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13
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Di Nisio E, Lupo G, Licursi V, Negri R. The Role of Histone Lysine Methylation in the Response of Mammalian Cells to Ionizing Radiation. Front Genet 2021; 12:639602. [PMID: 33859667 PMCID: PMC8042281 DOI: 10.3389/fgene.2021.639602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic genomes are wrapped around nucleosomes and organized into different levels of chromatin structure. Chromatin organization has a crucial role in regulating all cellular processes involving DNA-protein interactions, such as DNA transcription, replication, recombination and repair. Histone post-translational modifications (HPTMs) have a prominent role in chromatin regulation, acting as a sophisticated molecular code, which is interpreted by HPTM-specific effectors. Here, we review the role of histone lysine methylation changes in regulating the response to radiation-induced genotoxic damage in mammalian cells. We also discuss the role of histone methyltransferases (HMTs) and histone demethylases (HDMs) and the effects of the modulation of their expression and/or the pharmacological inhibition of their activity on the radio-sensitivity of different cell lines. Finally, we provide a bioinformatic analysis of published datasets showing how the mRNA levels of known HMTs and HDMs are modulated in different cell lines by exposure to different irradiation conditions.
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Affiliation(s)
- Elena Di Nisio
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Counsil (IBPM-CNR), Rome, Italy
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14
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Abstract
The ubiquitin–proteasome system (UPS) is responsible for the rapid targeting of proteins for degradation at 26S proteasomes and requires the orchestrated action of E1, E2 and E3 enzymes in a well-defined cascade. F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases that determine which proteins are ubiquitinated. To date, around 70 FBPs have been identified in humans and can be subdivided into distinct families, based on the protein-recruiting domains they possess. The FBXL subfamily is defined by the presence of multiple leucine-rich repeat (LRR) protein-binding domains. But how the 22 FBPs of the FBXL family achieve their individual specificities, despite having highly similar structural domains to recruit their substrates, is not clear. Here, we review and explore the FBXL family members in detail highlighting their structural and functional similarities and differences and how they engage their substrates through their LRRs to adopt unique interactomes.
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Affiliation(s)
- Bethany Mason
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
| | - Heike Laman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
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15
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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16
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Alternative isoforms of KDM2A and KDM2B lysine demethylases negatively regulate canonical Wnt signaling. PLoS One 2020; 15:e0236612. [PMID: 33104714 PMCID: PMC7588095 DOI: 10.1371/journal.pone.0236612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
A precisely balanced activity of canonical Wnt signaling is essential for a number of biological processes and its perturbation leads to developmental defects or diseases. Here, we demonstrate that alternative isoforms of the KDM2A and KDM2B lysine demethylases have the ability to negatively regulate canonical Wnt signaling. These KDM2A and KDM2B isoforms (KDM2A-SF and KDM2B-SF) lack the N-terminal demethylase domain, but they still have the ability to bind to CpG islands in promoters and to interact with their protein partners via their other functional domains. We have observed that KDM2A-SF and KDM2B-SF bind to the promoters of axin 2 and cyclin D1, two canonical Wnt signaling target genes, and repress their activity. Moreover, KDM2A-SF and KDM2B-SF are both able to strongly repress a Wnt-responsive luciferase reporter. The transcriptional repression mediated by KDM2A-SF and KDM2B-SF, but also by KDM2A-LF, is dependent on their DNA binding domain, while the N-terminal demethylase domain is dispensable for this process. Surprisingly, KDM2B-LF is unable to repress both the endogenous promoters and the luciferase reporter. Finally, we show that both KDM2A-SF and KDM2B-SF are able to interact with TCF7L1, one of the transcriptional mediators of canonical Wnt signaling. KDM2A-SF and KDM2B-SF are thus likely to negatively affect the transcription of canonical Wnt signaling target genes by binding to their promoters and by interacting with TCF7L1 and other co-repressors.
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17
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Identification of Structural Elements of the Lysine Specific Demethylase 2B CxxC Domain Associated with Replicative Senescence Bypass in Primary Mouse Cells. Protein J 2020; 39:232-239. [DOI: 10.1007/s10930-020-09895-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Natesan R, Aras S, Effron SS, Asangani IA. Epigenetic Regulation of Chromatin in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:379-407. [PMID: 31900918 DOI: 10.1007/978-3-030-32656-2_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epigenetics refers to mitotically/meiotically heritable mechanisms that regulate gene transcription without a need for changes in the DNA code. Covalent modifications of DNA, in the form of methylation, and histone post-translational modifications, in the form of acetylation and methylation, constitute the epigenetic code of a cell. Both DNA and histone modifications are highly dynamic and often work in unison to define the epigenetic state of a cell. Most epigenetic mechanisms regulate gene transcription by affecting localized/genome-wide transitions between heterochromatin and euchromatin states, thereby altering the accessibility of the transcriptional machinery and in turn, reduce/increase transcriptional output. Altered chromatin structure is associated with cancer progression, and epigenetic plasticity primarily governs the resistance of cancer cells to therapeutic agents. In this chapter, we specifically focus on regulators of histone methylation and acetylation, the two well-studied chromatin post-translational modifications, in the context of prostate cancer.
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Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Aras
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Sander Effron
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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