1
|
Deogharia M, Venegas-Zamora L, Agrawal A, Shi M, Jain AK, McHugh KJ, Altamirano F, Marian AJ, Gurha P. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization. Cardiovasc Res 2024; 120:630-643. [PMID: 38230606 PMCID: PMC11074792 DOI: 10.1093/cvr/cvae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 01/18/2024] Open
Abstract
AIMS Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation. METHODS AND RESULTS KDM5A, B, and C proteins were mainly expressed in the early post-natal stages, and their expressions were progressively downregulated in the post-natal CMs and were absent in adult hearts and CMs. In contrast, KDM5 proteins were persistently expressed in the iPSC-CMs up to 60 days after the induction of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor, induced differential expression of 2372 genes, including upregulation of genes involved in fatty acid oxidation (FAO), OXPHOS, and myogenesis in the iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the cleavage under targets and release using nuclease assay showed enriched of the H3K4me3 peaks at the promoter regions of genes encoding FAO, OXPHOS, and sarcomere proteins. Consistent with the chromatin and gene expression data, KDM5 inhibition increased the expression of multiple sarcomere proteins and enhanced myofibrillar organization. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene and increased its RNA and protein levels. Knockdown of ESRRA in KDM5-C70-treated iPSC-CM suppressed expression of a subset of the KDM5 targets. In conjunction with changes in gene expression, KDM5 inhibition increased oxygen consumption rate and contractility in iPSC-CMs. CONCLUSION KDM5 inhibition enhances maturation of iPSC-CMs by epigenetically upregulating the expressions of OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
Collapse
Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
| | - Leslye Venegas-Zamora
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
| | - Akanksha Agrawal
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
| | - Miusi Shi
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Kevin J McHugh
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
- Department of Chemistry, Rice University, Houston, 6500 Main Street, Houston, TX 77030, USA
| | - Francisco Altamirano
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University, Ithaca, NY, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
| |
Collapse
|
2
|
Chen YC, Gowda K, Amin S, Schell TD, Sharma AK, Robertson GP. Pharmacological agents targeting drug-tolerant persister cells in cancer. Pharmacol Res 2024; 203:107163. [PMID: 38569982 DOI: 10.1016/j.phrs.2024.107163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/05/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Current cancer therapy can be effective, but the development of drug resistant disease is the usual outcome. These drugs can eliminate most of the tumor burden but often fail to eliminate the rare, "Drug Tolerant Persister" (DTP) cell subpopulations in residual tumors, which can be referred to as "Persister" cells. Therefore, novel therapeutic agents specifically targeting or preventing the development of drug-resistant tumors mediated by the remaining persister cells subpopulations are needed. Since approximately ninety percent of cancer-related deaths occur because of the eventual development of drug resistance, identifying, and dissecting the biology of the persister cells is essential for the creation of drugs to target them. While there remains uncertainty surrounding all the markers identifying DTP cells in the literature, this review summarizes the drugs and therapeutic approaches that are available to target the persister cell subpopulations expressing the cellular markers ATP-binding cassette sub-family B member 5 (ABCB5), CD133, CD271, Lysine-specific histone demethylase 5 (KDM5), and aldehyde dehydrogenase (ALDH). Persister cells expressing these markers were selected as the focus of this review because they have been found on cells surviving following drug treatments that promote recurrent drug resistant cancer and are associated with stem cell-like properties, including self-renewal, differentiation, and resistance to therapy. The limitations and obstacles facing the development of agents targeting these DTP cell subpopulations are detailed, with discussion of potential solutions and current research areas needing further exploration.
Collapse
Affiliation(s)
- Yu-Chi Chen
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Krishne Gowda
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Shantu Amin
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Todd D Schell
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Arun K Sharma
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Gavin P Robertson
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Dermatology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA, USA; The Pennsylvania State University Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Penn State Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
| |
Collapse
|
3
|
San TT, Kim J, Kim HJ. Histone Lysine Demethylase KDM5 Inhibitor CPI-455 Induces Astrocytogenesis in Neural Stem Cells. ACS Chem Neurosci 2024; 15:1570-1580. [PMID: 38501572 DOI: 10.1021/acschemneuro.4c00003] [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] [Indexed: 03/20/2024] Open
Abstract
Lysine-specific histone demethylase 5A (KDM5A) is known to facilitate proliferation in cancer cells and maintain stemness to repress the astrocytic differentiation of neural stem cells (NSCs). In the study presented here, we investigated the effect of a KDM5 inhibitor, CPI-455, on NSC fate control. CPI-455 induced astrocytogenesis in NSCs during differentiation. Kdm5a, but not Kdm5c, knockdown induced glial fibrillary acidic protein (Gfap) transcription. CPI-455 induced signal transducer and activator of transcription 3, increased bone morphogenetic protein 2 expression, and enhanced mothers against decapentaplegic homolog 1/5/9 phosphorylation. The treatment of CPI-455 enhanced the methylation of histone H3 lysine 4 in the Gfap promoter when compared to that of the dimethyl sulfoxide control. In addition, CPI-455 treatment significantly reduced the recruitment of KDM5A to the Gfap promoter. Our data suggest that the KDM5 inhibitor CPI-455 effectively controls NSC cell fate via KDM5A inhibition and induces astrocytogenesis.
Collapse
Affiliation(s)
- Thin Thin San
- Neuropharmacology and Stem Cell Lab, College of Pharmacy, Chung-Ang University, 06974 Seoul, Republic of Korea
| | - Junhyung Kim
- Neuropharmacology and Stem Cell Lab, College of Pharmacy, Chung-Ang University, 06974 Seoul, Republic of Korea
| | - Hyun-Jung Kim
- Neuropharmacology and Stem Cell Lab, College of Pharmacy, Chung-Ang University, 06974 Seoul, Republic of Korea
| |
Collapse
|
4
|
Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG. Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening. RSC Chem Biol 2024; 5:209-215. [PMID: 38456036 PMCID: PMC10915964 DOI: 10.1039/d3cb00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
PHD fingers are a type of chromatin reader that primarily recognize chromatin as a function of lysine methylation state. Dysregulated PHD fingers are implicated in various human diseases, including acute myeloid leukemia. Targeting PHD fingers with small molecules is considered challenging as their histone tail binding pockets are often shallow and surface-exposed. The KDM5A PHD1 finger regulates the catalytic activity of KDM5A, an epigenetic enzyme often misregulated in cancers. To identify ligands that disrupt the PHD1-histone peptide interaction, we conducted a high-throughput screen and validated hits by orthogonal methods. We further elucidated structure-activity relationships in two classes of compounds to identify features important for binding. Our investigation offers a starting point for further optimization of small molecule PHD1 ligands.
Collapse
Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Sophia L Qin
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Gregory M Lee
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Michelle R Arkin
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| |
Collapse
|
5
|
Vergnes L, Wiese CB, Zore T, Riestenberg C, Avetisyan R, Reue K. Gene Regulation and Mitochondrial Activity During White and Brown Adipogenesis Are Modulated by KDM5 Histone Demethylase. J Endocr Soc 2024; 8:bvae029. [PMID: 38425435 PMCID: PMC10904225 DOI: 10.1210/jendso/bvae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 03/02/2024] Open
Abstract
Body fat accumulation differs between males and females and is influenced by both gonadal sex (ovaries vs testes) and chromosomal sex (XX vs XY). We previously showed that an X chromosome gene, Kdm5c, is expressed at higher levels in females compared to males and correlates with adiposity in mice and humans. Kdm5c encodes a KDM5 histone demethylase that regulates gene expression by modulating histone methylation at gene promoters and enhancers. Here, we use chemical inhibition and genetic knockdown to identify a role for KDM5 activity during early stages of white and brown preadipocyte differentiation, with specific effects on white adipocyte clonal expansion, and white and brown adipocyte gene expression and mitochondrial activity. In white adipogenesis, KDM5 activity modulates H3K4 histone methylation at the Dlk1 gene promoter to repress gene expression and promote progression from preadipocytes to mature adipocytes. In brown adipogenesis, KDM5 activity modulates H3K4 methylation and gene expression of Ucp1, which is required for thermogenesis. Unbiased transcriptome analysis revealed that KDM5 activity regulates genes associated with cell cycle regulation and mitochondrial function, and this was confirmed by functional analyses of cell proliferation and cellular bioenergetics. Using genetic knockdown, we demonstrate that KDM5C is the likely KDM5 family member that is responsible for regulation of white and brown preadipocyte programming. Given that KDM5C levels are higher in females compared to males, our findings suggest that sex differences in white and brown preadipocyte gene regulation may contribute to sex differences in adipose tissue function.
Collapse
Affiliation(s)
- Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Temeka Zore
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie Riestenberg
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
6
|
Terao M, Yamashita Y, Takada Y, Itoh Y, Suzuki T. Structural optimization of a lysine demethylase 5 inhibitor for improvement of its cellular activity. Bioorg Med Chem 2024; 98:117579. [PMID: 38168630 DOI: 10.1016/j.bmc.2023.117579] [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: 12/07/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024]
Abstract
Lysine demethylase 5 (KDM5) subfamily proteins are important in epigenetic gene regulation. They are involved in the growth and drug resistance of cancer cells. Therefore, KDM5s are potential cancer therapeutic targets, and their inhibitors hold promise as anti-cancer drugs. Several KDM5 inhibitors, including KDM5-C49 (2a), have exhibited potent KDM5-inhibitory activities in in vitro enzyme assays. However, they do not show enough cellular activity despite being converted to their prodrugs. We hypothesized that their poor lipophilicity should prevent them from sufficiently penetrating the cell membrane, and introducing more lipophilic groups should improve cellular activities. In this study, we investigated 2a and KDM5-C70 (3a), a prodrug of 2a, and attempted to improve its cellular activity by replacing the N,N-dimethyl amino group of 3a with more lipophilic groups. N-Butyl, N-methyl amino compound 2e exhibited potent and selective KDM5-inhibitory activity equal to that of 2a. Furthermore, the cell membrane permeability of 3e, an ethyl ester prodrug of 2e, was six times higher than that of 3a in a parallel artificial membrane permeation assay. In addition, western blot analysis indicated that treating human lung cancer A549 cells with 3e increased histone methylation levels more strongly than that with 3a. Thus, we identified compound 3e as a more cell-active KDM5 inhibitor that has sufficient cell membrane permeability.
Collapse
Affiliation(s)
- Mitsuhiro Terao
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yasunobu Yamashita
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| |
Collapse
|
7
|
Sarah L, Fujimori DG. Recent developments in catalysis and inhibition of the Jumonji histone demethylases. Curr Opin Struct Biol 2023; 83:102707. [PMID: 37832177 PMCID: PMC10769511 DOI: 10.1016/j.sbi.2023.102707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 10/15/2023]
Abstract
Histone methylation, one of the most common histone modifications, has fundamental roles in regulating chromatin-based processes. Jumonji histone lysine demethylases (JMJC KDMs) influence regulation of gene transcription through both their demethylation and chromatin scaffolding functions. It has recently been demonstrated that dysregulation of JMJC KDMs contributes to pathogenesis and progression of several diseases, including cancer. These observations have led to an increased interest in modulation of enzymes that regulate lysine methylation. Here, we highlight recent progress in understanding catalysis of JMJC KDMs. Specifically, we focus on recent research advances on elucidation of JMJC KDM substrate recognition and interactomes. We also highlight recently reported JMJC KDM inhibitors and describe their therapeutic potentials and challenges. Finally, we discuss alternative strategies to target these enzymes, which rely on targeting JMJC KDMs accessory domains as well as utilization of the targeted protein degradation strategy.
Collapse
Affiliation(s)
- Letitia Sarah
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco; San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco; San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco; San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco; San Francisco, CA 94158, USA.
| |
Collapse
|
8
|
Deogharia M, Agrawal A, Shi M, Jain AK, McHugh KJ, Altamirano F, Marian AJ, Gurha P. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.535169. [PMID: 37090524 PMCID: PMC10120725 DOI: 10.1101/2023.04.11.535169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Rationale Human pluripotent stem cell-derived CMs (iPSC-CMs) are a valuable tool for disease modeling, cell therapy and to reconstruct the CM maturation process and identify, characterize factors that regulate maturation. The transition from immature fetal to adult CM entails coordinated regulation of the mature gene programming, which is characterized by the induction of myofilament and OXPHOS gene expression among others. Recent studies in Drosophila , C. elegans, and C2C12 myoblast cell lines have implicated the histone H3K4me3 demethylase KDM5 and its homologs, as a potential regulator of developmental gene program and mitochondrial function. We speculated that KDM5 may potentiate the maturation of iPSC-CMs by targeting a conserved epigenetic program that encompass mitochondrial OXPHOS and other CM specific maturation genes. Objectives The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation. Methods and Results Immunoblot analysis revealed that KDM5A, B, and C expression was progressively downregulated in postnatal cardiomyocytes and absent in adult hearts and CMs. Additionally, KDM5 proteins were found to be persistently expressed in iPSC-CMs up to 60 days after the onset of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor-resulted in differential regulation of 2,372 genes including upregulation of Fatty acid oxidation (FAO), OXPHOS, and myogenic gene programs in iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the CUT&RUN assay revealed enriched H3K4me3 peaks at the promoter regions of FAO, OXPHOS, and sarcomere genes. Consistent with the chromatin and gene expression data, KDM5 inhibition led to increased expression of multiple sarcomere proteins, enhanced myofibrillar organization and improved calcium handling. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene, which is known to regulate OXPHOS and cardiomyocyte maturation, and resulted in its increased RNA and protein levels. Finally, KDM5 inhibition increased baseline, peak, and spare oxygen consumption rates in iPSC-CMs. Conclusions KDM5 regulates the maturation of iPSC-CMs by epigenetically regulating the expression of ESRRA, OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
Collapse
|
9
|
Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
Collapse
Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
| |
Collapse
|
10
|
Hoekstra M, Ridgeway NH, Biggar KK. Characterization of KDM5 lysine demethylase family substrate preference and identification of novel substrates. J Biochem 2022; 173:31-42. [PMID: 36205465 DOI: 10.1093/jb/mvac081] [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: 06/17/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 12/29/2022] Open
Abstract
The KDM5/JARID1 sub-family are 2-oxoglutarate and Fe(II)-dependent lysine-specific histone demethylases that are characterized by their Jumonji catalytic domains. The KDM5 family is known to remove tri-/di-methyl modifications from lysine-4 of histone H3 (i.e. H3-K4me2/3), a mark associated with active gene expression. As a result, studies to date have revolved around the influence of KDM5 on disease through their ability to regulate H3-K4me2/3. Recent evidence demonstrates that KDM5 may influence disease beyond H3-K4 demethylation, making it critical to further investigate KDM5-mediated demethylation of non-histone proteins. To help identify potential non-histone substrates for the KDM5 family, we developed a library of 180 permutated peptide substrates, with sequences that are systematically altered from the wild-type H3-K4me3 substrate. From this library, we characterized recombinant KDM5A/B/C/D substrate preference and developed recognition motifs for each KDM5 demethylase. The recognition motifs developed were used to predict potential substrates for KDM5A/B/C/D and profiled to generate a list of high-ranking and medium/low-ranking substrates for further in vitro validation. Through this approach, we identified 66 high-ranking substrates in which KDM5 demethylases displayed significant in vitro activity towards.
Collapse
Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Nashira H Ridgeway
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| |
Collapse
|
11
|
Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5. Sci Rep 2022; 12:20680. [PMID: 36450832 PMCID: PMC9712658 DOI: 10.1038/s41598-022-24154-0] [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: 08/18/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
JmjC (Jumonji-C) domain-containing 5 (JMJD5) plays important roles in circadian regulation in plants and humans and is involved in embryonic development and cell proliferation. JMJD5 is a 2-oxoglutarate (2OG) and Fe(II) dependent oxygenase of the JmjC subfamily, which includes histone Nε-methyl lysine-demethylases (KDMs) and hydroxylases catalysing formation of stable alcohol products. JMJD5 is reported to have KDM activity, but has been shown to catalyse C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6) in vitro. We report crystallographic analyses of human JMJD5 complexed with 2OG analogues, including the widely used hypoxia mimic pyridine-2,4-dicarboxylate, both D- and L-enantiomers of the oncometabolite 2-hydroxyglutarate, and a cyclic N-hydroxyimide. The results support the assignment of JMJD5 as a protein hydroxylase and reveal JMJD5 has an unusually compact 2OG binding pocket suitable for exploitation in development of selective inhibitors. They will be useful in the development of chemical probes to investigate the physiologically relevant roles of JMJD5 in circadian rhythm and development and explore its potential as a medicinal chemistry target.
Collapse
|
12
|
Tang K, Jiao LM, Qi YR, Wang TC, Li YL, Xu JL, Wang ZW, Yu B, Liu HM, Zhao W. Discovery of Novel Pyrazole-Based KDM5B Inhibitor TK- 129 and Its Protective Effects on Myocardial Remodeling and Fibrosis. J Med Chem 2022; 65:12979-13000. [DOI: 10.1021/acs.jmedchem.2c00797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kai Tang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Le-Min Jiao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Yu-Ruo Qi
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Tian-Ci Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Ya-Lan Li
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Jia-Le Xu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Zi-Wei Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Bin Yu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Wen Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| |
Collapse
|
13
|
JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
Collapse
|
14
|
Liu H, Lin J, Zhou W, Moses R, Dai Z, Kossenkov AV, Drapkin R, Bitler BG, Karakashev S, Zhang R. KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer. Cancer Immunol Res 2022; 10:1028-1038. [PMID: 35726891 PMCID: PMC9357105 DOI: 10.1158/2326-6066.cir-22-0088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/31/2022] [Accepted: 05/26/2022] [Indexed: 02/05/2023]
Abstract
The extent to which effector CD8+ T cells infiltrate into tumors is one of the major predictors of clinical outcome for patients with epithelial ovarian cancer (EOC). Immune cell infiltration into EOC is a complex process that could be affected by the epigenetic makeup of the tumor. Here, we have demonstrated that a lysine 4 histone H3 (H3K4) demethylase, (lysine-specific demethylase 5A; KDM5A) impairs EOC infiltration by immune cells and inhibits antitumor immune responses. Mechanistically, we found that KDM5A silenced genes involved in the antigen processing and presentation pathway. KDM5A inhibition restored the expression of genes involved in the antigen-presentation pathway in vitro and promoted antitumor immune responses mediated by CD8+ T cells in vivo in a syngeneic EOC mouse model. A negative correlation between expression of KDM5A and genes involved in the antigen processing and presentation pathway such as HLA-A and HLA-B was observed in the majority of cancer types. In summary, our results establish KDM5A as a regulator of CD8+ T-cell infiltration of tumors and demonstrate that KDM5A inhibition may provide a novel therapeutic strategy to boost antitumor immune responses.
Collapse
Affiliation(s)
- Heng Liu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Jianhuang Lin
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Wei Zhou
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Renyta Moses
- Cell and Molecular Biology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhongping Dai
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Andrew V. Kossenkov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO 13001, USA
| | - Sergey Karakashev
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA,Corresponding authors: Rugang Zhang, Ph.D., 3601 Spruce Street, Philadelphia, PA 19104; Phone: 215-495-6840;.; Sergey Karakashev, Ph.D., 3601 Spruce Street, Philadelphia, PA 19104; Phone: 215-707-8901;
| | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA,Corresponding authors: Rugang Zhang, Ph.D., 3601 Spruce Street, Philadelphia, PA 19104; Phone: 215-495-6840;.; Sergey Karakashev, Ph.D., 3601 Spruce Street, Philadelphia, PA 19104; Phone: 215-707-8901;
| |
Collapse
|
15
|
Xi JY, Zhang RY, Chen K, Yao L, Li MQ, Jiang R, Li XY, Fan L. Advances and perspectives of proteolysis targeting chimeras (PROTACs) in drug discovery. Bioorg Chem 2022; 125:105848. [DOI: 10.1016/j.bioorg.2022.105848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
|
16
|
Farghaly TA, Al-Hasani WA, Ibrahim MH, Abdellattif MH, Abdallah ZA. Design, Synthesis, Anticancer Activity and Docking Studies of Thiazole Linked Phenylsulfone Moiety as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Thoraya A. Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Wedian A. Al-Hasani
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona H. Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Zeinab A. Abdallah
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| |
Collapse
|
17
|
Singh S, Abu-Zaid A, Jin H, Fang J, Wu Q, Wang T, Feng H, Quarni W, Shao Y, Maxham L, Abdolvahabi A, Yun MK, Vaithiyalingam S, Tan H, Bowling J, Honnell V, Young B, Guo Y, Bajpai R, Pruett-Miller SM, Grosveld GC, Hatley M, Xu B, Fan Y, Wu G, Chen EY, Chen T, Lewis PW, Rankovic Z, Li Y, Murphy AJ, Easton J, Peng J, Chen X, Wang R, White SW, Davidoff AM, Yang J. Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma. Sci Transl Med 2022; 14:eabq2096. [PMID: 35857643 PMCID: PMC9548378 DOI: 10.1126/scitranslmed.abq2096] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3-Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1-governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1+ RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1-related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.
Collapse
Affiliation(s)
- Shivendra Singh
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jie Fang
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Tingting Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Helin Feng
- Department of Orthopedics, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Waise Quarni
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Shao
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lily Maxham
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Alireza Abdolvahabi
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Protein Technologies Center, Molecular Interaction Analysis, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Haiyan Tan
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Center for Proteomics and Metabolomics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Bowling
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Victoria Honnell
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yian Guo
- Department of Biostatistics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richa Bajpai
- Center for Advanced Genome Engineering, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gerard C Grosveld
- Department of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mark Hatley
- Department of Oncology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Eleanor Y. Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yimei Li
- Department of Biostatistics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew J. Murphy
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Center for Proteomics and Metabolomics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Stephen W. White
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew M. Davidoff
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
| |
Collapse
|
18
|
Schonfeld M, Averilla J, Gunewardena S, Weinman SA, Tikhanovich I. Male-Specific Activation of Lysine Demethylases 5B and 5C Mediates Alcohol-Induced Liver Injury and Hepatocyte Dedifferentiation. Hepatol Commun 2022; 6:1373-1391. [PMID: 35084807 PMCID: PMC9134811 DOI: 10.1002/hep4.1895] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Alcohol-associated liver disease (ALD) is a major cause of alcohol-related mortality. Sex differences in sensitivity to ALD are well described, but these are often disregarded in studies of ALD development. We aimed to define sex-specific pathways in liver exposed to alcohol. Mice were fed the Lieber-DeCarli alcohol liquid diet or a combination of a high-fat diet with alcohol in water. Single-cell RNA sequencing (scRNA-Seq) was performed on liver cells from male and female mice. Mice were treated with adeno-associated virus (AAV)-short hairpin (sh)Control or AAV-sh lysine demethylase 5b (shKdm5b) and/or AAV-shKdm5c vectors. Changes after Kdm5b/5c knockdown were assessed by RNA-Seq and histone H3 lysine K4 (H3K4)me3 chromatin immunoprecipitation-Seq analysis. Using scRNA-Seq analysis, we found several sex-specific pathways induced by alcohol, including pathways related to lipid metabolism and hepatocyte differentiation. Bioinformatic analysis suggested that two epigenetic regulators, H3K4-specific lysine demethylases KDM5B and KDM5C, contribute to sex differences in alcohol effects. We found that in alcohol-fed male mice, KDM5B and KDM5C are involved in hepatocyte nuclear factor 4 alpha (Hnf4a) down-regulation, hepatocyte dedifferentiation, and an increase in fatty acid synthesis. This effect is mediated by alcohol-induced KDM5B and KDM5C recruitment to Hnf4a and other gene promoters in male but not in female mice. Kdm5b and Kdm5c knockdown or KDM5-inhibitor treatment prevented alcohol-induced lipid accumulation and restored levels of Hnf4a and other hepatocyte differentiation genes in male mice. In addition, Kdm5b knockdown prevented hepatocellular carcinoma development in male mice by up-regulating Hnf4a and decreasing tumor cell proliferation. Conclusion: Alcohol specifically activates KDM5 demethylases in male mice to promote alcohol-induced hepatocyte dedifferentiation and tumor development.
Collapse
Affiliation(s)
- Michael Schonfeld
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Janice Averilla
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Sumedha Gunewardena
- Department of Molecular and Integrative PhysiologyUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Steven A. Weinman
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
- Liver CenterUniversity of Kansas Medical CenterKansas CityKSUSA
- Kansas City VA Medical CenterKansas CityMOUSA
| | - Irina Tikhanovich
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| |
Collapse
|
19
|
Epigenetic Factors as Etiological Agents, Diagnostic Markers, and Therapeutic Targets for Luminal Breast Cancer. Biomedicines 2022; 10:biomedicines10040748. [PMID: 35453496 PMCID: PMC9031900 DOI: 10.3390/biomedicines10040748] [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: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Luminal breast cancer, an etiologically heterogeneous disease, is characterized by high steroid hormone receptor activity and aberrant gene expression profiles. Endocrine therapy and chemotherapy are promising therapeutic approaches to mitigate breast cancer proliferation and recurrence. However, the treatment of therapy-resistant breast cancer is a major challenge. Recent studies on breast cancer etiology have revealed the critical roles of epigenetic factors in luminal breast cancer tumorigenesis and drug resistance. Tumorigenic epigenetic factor-induced aberrant chromatin dynamics dysregulate the onset of gene expression and consequently promote tumorigenesis and metastasis. Epigenetic dysregulation, a type of somatic mutation, is a high-risk factor for breast cancer progression and therapy resistance. Therefore, epigenetic modulators alone or in combination with other therapies are potential therapeutic agents for breast cancer. Several clinical trials have analyzed the therapeutic efficacy of potential epi-drugs for breast cancer and reported beneficial clinical outcomes, including inhibition of tumor cell adhesion and invasiveness and mitigation of endocrine therapy resistance. This review focuses on recent findings on the mechanisms of epigenetic factors in the progression of luminal breast cancer. Additionally, recent findings on the potential of epigenetic factors as diagnostic biomarkers and therapeutic targets for breast cancer are discussed.
Collapse
|
20
|
Eze CC, Ezeokonkwo AM, Ugwu ID, Eze UF, Onyeyilim EL, Attah IS, Okonkwo IV. Azole-pyrimidine Hybrid Anticancer Agents: A Review of Molecular Structure, Structure Activity Relationship and Molecular Docking. Anticancer Agents Med Chem 2022; 22:2822-2851. [PMID: 35306990 DOI: 10.2174/1871520622666220318090147] [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: 09/02/2021] [Revised: 12/07/2021] [Accepted: 01/18/2022] [Indexed: 11/22/2022]
Abstract
Cancer has emerged as one of the leading causes of deaths globally partly due to the steady rise in anticancer drug resistance. Pyrimidine and pyrimidine-fused heterocycles are some of the privileged scaffolds in medicine, as they possess diverse biological properties. Pyrimidines containing azole nucleus possesses inestimable anticancer potency and has enormous potential to conduct the regulation of cellular pathways for selective anticancer activity. The present review outlines the molecular structure of pyrimidine-fused azoles with significant anticancer activity. The structure activity relationship and molecular docking studies have also been discussed. The current review is the first complete compilation of significant literature on the proposed topic from 2016 to 2020. The information contained in this review offers a useful insight to chemists in the design of new and potent anticancer azole-pyrimidine analogues.
Collapse
Affiliation(s)
- Chinweike Cosmas Eze
- Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | | | - Izuchukwu David Ugwu
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Uchenna Florence Eze
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Ebuka Leonard Onyeyilim
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Izuchi Solomon Attah
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Ifeoma Vivian Okonkwo
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| |
Collapse
|
21
|
Yang GJ, Wu J, Miao L, Zhu MH, Zhou QJ, Lu XJ, Lu JF, Leung CH, Ma DL, Chen J. Pharmacological inhibition of KDM5A for cancer treatment. Eur J Med Chem 2021; 226:113855. [PMID: 34555614 DOI: 10.1016/j.ejmech.2021.113855] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Abstract
Lysine-specific demethylase 5A (KDM5A, also named RBP2 or JARID1A) is a demethylase that can remove methyl groups from histones H3K4me1/2/3. It is aberrantly expressed in many cancers, where it impedes differentiation and contributes to cancer cell proliferation, cell metastasis and invasiveness, drug resistance, and is associated with poor prognosis. Pharmacological inhibition of KDM5A has been reported to significantly attenuate tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. This review will present the structural aspects of KDM5A, its role in carcinogenesis, a comparison of currently available approaches for screening KDM5A inhibitors, a classification of KDM5A inhibitors, and its potential as a drug target in cancer therapy.
Collapse
Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China
| | - Liang Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Qian-Jin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
22
|
Hoekstra M, Biggar KK. Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference. Anal Biochem 2021; 633:114429. [PMID: 34678252 DOI: 10.1016/j.ab.2021.114429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 01/25/2023]
Abstract
A major regulatory influence over gene expression is the dynamic post translational methylation of histone proteins, with major implications from both lysine methylation and demethylation. The KDM5/JARID1 sub-family of Fe(II)/2-oxoglutarate dependent lysine-specific demethylases is, in part, responsible for the removal of tri/dimethyl modifications from lysine 4 of histone H3 (i.e., H3K4me3/2), a mark associated with active gene expression. Although the relevance of KDM5 activity to disease progression has been primarily established through its ability to regulate gene expression via histone methylation, there is evidence that these enzymes may also target non-histone proteins. To aid in the identification of new non-histone substrates, we examined KDM5A in vitro activity towards a library of 180 permutated peptide substrates derived from the H3K4me3 sequence. From this data, a recognition motif was identified and used to predict candidate KDM5A substrates from the methyllysine proteome. High-ranking candidate substrates were then validated for in vitro KDM5A activity using representative trimethylated peptides. Our approach correctly identified activity towards 90% of high-ranked substrates. Here, we have demonstrated the usefulness of our method in identifying candidate substrates that is applicable to any Fe(II)- and 2-oxoglutarate dependent demethylase.
Collapse
Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
| |
Collapse
|
23
|
Tariq A, Rehman HM, Mateen RM, Ali M, Mutahir Z, Afzal MS, Sajjad M, Gul R, Saleem M. A computer aided drug discovery based discovery of lead-like compounds against KDM5A for cancers using pharmacophore modeling and high-throughput virtual screening. Proteins 2021; 90:645-657. [PMID: 34642975 DOI: 10.1002/prot.26262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/17/2021] [Accepted: 10/03/2021] [Indexed: 12/11/2022]
Abstract
KDM5A over-expression mediates cancer cell proliferation and promotes resistance toward chemotherapy through epigenetic modifications. As its complete mechanism of action is still unknown, there is no KDM5A specific drug available at clinical level. In the current study, lead compounds for KDM5A were determined through pharmacophore modeling and high-throughput virtual screening from Asinex libraries containing 0.5 million compounds. These virtual hits were further evaluated and filtered for ADMET properties. Finally, 726 compounds were used for docking analysis against KDM5A. On the basis of docking score, 10 top-ranked compounds were selected and further evaluated for non-central nervous system (CNS) and CNS drug-like properties. Among these compounds, N-{[(7-Methyl-4-oxo-1,2,3,4-tetrahydrocyclopenta [c] chromen-9-yl) oxy]acetyl}-l-phenylalanine (G-score: -11.363 kcal/mol) was estimated to exhibit non-CNS properties while 2-(3,4-Dimethoxy-phenyl)-7-methoxy-chromen-4-one (G-score: -7.977 kcal/mol) was evaluated as CNS compound. Docked complexes of both compounds were finally selected for molecular dynamic simulation to examine the stability. This study concluded that both these compounds can serve as lead compounds in the quest of finding therapeutic agents against KDM5A associated cancers.
Collapse
Affiliation(s)
- Asma Tariq
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Rana Muhammad Mateen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Moazzam Ali
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Zeeshan Mutahir
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore, Punjab, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| |
Collapse
|
24
|
Zhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, McGeary MK, Song E, Blenman KRM, Micevic G, Jessel S, Zhang Y, Yin M, Booth CJ, Jilaveanu LB, Damsky W, Sznol M, Kluger HM, Iwasaki A, Bosenberg MW, Yan Q. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature 2021; 598:682-687. [PMID: 34671158 PMCID: PMC8555464 DOI: 10.1038/s41586-021-03994-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 09/03/2021] [Indexed: 01/22/2023]
Abstract
Tumours use various strategies to evade immune surveillance1,2. Immunotherapies targeting tumour immune evasion such as immune checkpoint blockade have shown considerable efficacy on multiple cancers3,4 but are ineffective for most patients due to primary or acquired resistance5-7. Recent studies showed that some epigenetic regulators suppress anti-tumour immunity2,8-12, suggesting that epigenetic therapies could boost anti-tumour immune responses and overcome resistance to current immunotherapies. Here we show that, in mouse melanoma models, depletion of KDM5B-an H3K4 demethylase that is critical for melanoma maintenance and drug resistance13-15-induces robust adaptive immune responses and enhances responses to immune checkpoint blockade. Mechanistically, KDM5B recruits the H3K9 methyltransferase SETDB1 to repress endogenous retroelements such as MMVL30 in a demethylase-independent manner. Derepression of these retroelements activates cytosolic RNA-sensing and DNA-sensing pathways and the subsequent type-I interferon response, leading to tumour rejection and induction of immune memory. Our results demonstrate that KDM5B suppresses anti-tumour immunity by epigenetic silencing of retroelements. We therefore reveal roles of KDM5B in heterochromatin regulation and immune evasion in melanoma, opening new paths for the development of KDM5B-targeting and SETDB1-targeting therapies to enhance tumour immunogenicity and overcome immunotherapy resistance.
Collapse
Affiliation(s)
- Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Wesley L. Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Current address: Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xiaoni Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Durga Thakral
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Jiesi Luo
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA,Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Lok Hei Chan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Meaghan K. McGeary
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kim RM Blenman
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA,Department of Medicine, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Goran Micevic
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Shlomit Jessel
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yangyi Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingzhu Yin
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Carmen J. Booth
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Lucia B. Jilaveanu
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Mario Sznol
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Harriet M. Kluger
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA,Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA,Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marcus W. Bosenberg
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Department of Dermatology, Yale School of Medicine, New Haven, CT, USA,Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA,Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA,Corresponding authors: ,
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA,Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA,Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA,Corresponding authors: ,
| |
Collapse
|
25
|
Liu XY, Guo CH, Xi ZY, Xu XQ, Zhao QY, Li LS, Wang Y. Histone methylation in pancreatic cancer and its clinical implications. World J Gastroenterol 2021; 27:6004-6024. [PMID: 34629816 PMCID: PMC8476335 DOI: 10.3748/wjg.v27.i36.6004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive human cancer. Appropriate methods for the diagnosis and treatment of PC have not been found at the genetic level, thus making epigenetics a promising research path in studies of PC. Histone methylation is one of the most complicated types of epigenetic modifications and has proved crucial in the development of PC. Histone methylation is a reversible process regulated by readers, writers, and erasers. Some writers and erasers can be recognized as potential biomarkers and candidate therapeutic targets in PC because of their unusual expression in PC cells compared with normal pancreatic cells. Based on the impact that writers have on the development of PC, some inhibitors of writers have been developed. However, few inhibitors of erasers have been developed and put to clinical use. Meanwhile, there is not enough research on the reader domains. Therefore, the study of erasers and readers is still a promising area. This review focuses on the regulatory mechanism of histone methylation, and the diagnosis and chemotherapy of PC based on it. The future of epigenetic modification in PC research is also discussed.
Collapse
Affiliation(s)
- Xing-Yu Liu
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Chuan-Hao Guo
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Zhi-Yuan Xi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Xin-Qi Xu
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Qing-Yang Zhao
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Li-Sha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Ying Wang
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| |
Collapse
|
26
|
Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, Ma DL, Chen J. The emerging role of KDM5A in human cancer. J Hematol Oncol 2021; 14:30. [PMID: 33596982 PMCID: PMC7888121 DOI: 10.1186/s13045-021-01041-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Histone methylation is a key posttranslational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Variations in the pattern of histone methylation influence both physiological and pathological events. Lysine-specific demethylase 5A (KDM5A, also known as JARID1A or RBP2) is a KDM5 Jumonji histone demethylase subfamily member that erases di- and tri-methyl groups from lysine 4 of histone H3. Emerging studies indicate that KDM5A is responsible for driving multiple human diseases, particularly cancers. In this review, we summarize the roles of KDM5A in human cancers, survey the field of KDM5A inhibitors including their anticancer activity and modes of action, and the current challenges and potential opportunities of this field.
Collapse
Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.,Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Yan-Jun Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, People's Republic of China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, People's Republic of China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China. .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China. .,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
| |
Collapse
|
27
|
Iida T, Itoh Y, Takahashi Y, Yamashita Y, Kurohara T, Miyake Y, Oba M, Suzuki T. Design, Synthesis, and Biological Evaluation of Lysine Demethylase 5 C Degraders. ChemMedChem 2021; 16:1609-1618. [PMID: 33470543 DOI: 10.1002/cmdc.202000933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/18/2022]
Abstract
Lysine demethylase 5 C (KDM5C) controls epigenetic gene expression and is attracting great interest in the field of chemical epigenetics. KDM5C has emerged as a therapeutic target for anti-prostate cancer agents, and recently we identified triazole 1 as an inhibitor of KDM5C. Compound 1 exhibited highly potent KDM5C-inhibitory activity in in vitro enzyme assays, but did not show strong anticancer effects. Therefore, a different approach is needed for the development of anticancer agents targeting KDM5C. Here, we attempted to identify KDM5C degraders by focusing on a protein-knockdown strategy. Compound 3 b, which was designed based on compound 1, degraded KDM5C and inhibited the growth of prostate cancer PC-3 cells more strongly than compound 1. These findings suggest that KDM5C degraders are more effective as anticancer agents than compounds that only inhibit the catalytic activity of KDM5C.
Collapse
Affiliation(s)
- Tetsuya Iida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yukari Takahashi
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yuka Miyake
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Makoto Oba
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| |
Collapse
|
28
|
Lee HR, Ann J, Kim YM, Lee J, Kim HJ. The KDM5 Inhibitor KDM5-C70 Induces Astrocyte Differentiation in Rat Neural Stem Cells. ACS Chem Neurosci 2021; 12:441-446. [PMID: 33482060 DOI: 10.1021/acschemneuro.0c00613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Members of the lysine-specific histone demethylase 5 (KDM5/JARID1) family are known to play important roles in stem cell fate determination. Here, using the KDM5 inhibitor C70 (KDM5-C70), we demonstrated that the histone demethylase activity of the KDM5 enzyme is essential for the repression of astrocytic differentiation of neural stem cells (NSCs). KDM5-C70 treatment activated the glial fibrillary acidic protein (Gfap) gene by increasing the trimethylation of histone H3 lysine 4 in the promoter regions and subsequently induced astrocytogenesis in NSCs. In addition, treatment of NSCs with KDM5-C70 activated Janus kinase-signal transducer and activator of transcription (JAK-STAT3) signaling and increased the mRNA expression of transforming growth factor-beta 1 (Tgf-β1). Our data provide evidence that KDM5 is a promising target for NSC fate modulation and suggest that epigenetic regulation is important for NSC fate determination.
Collapse
Affiliation(s)
- Ha-Rim Lee
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jihyae Ann
- College of Pharmacy, Seoul National University, Seoul151-742, Republic of Korea
| | - Young Min Kim
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jeewoo Lee
- College of Pharmacy, Seoul National University, Seoul151-742, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea
| |
Collapse
|
29
|
Zhou W, Chen W. Development of molecular intervention strategies for B-cell lymphoma. Expert Rev Hematol 2021; 14:241-252. [PMID: 33263441 DOI: 10.1080/17474086.2021.1856652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
INTRODUCTION There are many genetic mutations involved in B-cell lymphomagenesis. These mutations contribute to the prognosis of B-cell lymphomas and can be used for and targeted for intervention. AREAS COVERED This review provides an overview of targeted gene therapies for B-cell lymphoma that were newly approved or are under clinical development. These include, TP53 mutations and related pathways, such as BTK inhibitors, MDM2/4 inhibitors, and XPO1 inhibitors; new drugs targeting EZH2 mutations through competitive inhibition, such as tazemetostat and GSK126; BCL-2-targeted therapeutics, including venetoclax and ABT-263; BTK, IRAK 1/4, HCK, and myddosome complex that targets the MYD88 mutation and the related pathways. In addition, we have also discussed gene mutations that have been reported as potential therapeutic targets, such as TNFAIP3, CARD11. EXPERT OPINION The mechanisms underlying the role of several genetic mutations in lymphomagenesis have been reported, and several studies have designed and developed drugs targeting these mutations. Many of these drugs have been approved for clinical use, while several are still under clinical development. Recent studies have identified additional genetic mutations and gene targets for BCL-2 treatment; however, effective molecular interventions targeting these new targets are yet to be developed.
Collapse
Affiliation(s)
- Wenyujing Zhou
- Department of Hematology, The First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Weihong Chen
- Department of Hematology, The First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| |
Collapse
|
30
|
Abstract
2-Oxoglutarate-dependent dioxygenases (2OGDDs) are a superfamily of enzymes that play diverse roles in many biological processes, including regulation of hypoxia-inducible factor-mediated adaptation to hypoxia, extracellular matrix formation, epigenetic regulation of gene transcription and the reprogramming of cellular metabolism. 2OGDDs all require oxygen, reduced iron and 2-oxoglutarate (also known as α-ketoglutarate) to function, although their affinities for each of these co-substrates, and hence their sensitivity to depletion of specific co-substrates, varies widely. Numerous 2OGDDs are recurrently dysregulated in cancer. Moreover, cancer-specific metabolic changes, such as those that occur subsequent to mutations in the genes encoding succinate dehydrogenase, fumarate hydratase or isocitrate dehydrogenase, can dysregulate specific 2OGDDs. This latter observation suggests that the role of 2OGDDs in cancer extends beyond cancers that harbour mutations in the genes encoding members of the 2OGDD superfamily. Herein, we review the regulation of 2OGDDs in normal cells and how that regulation is corrupted in cancer.
Collapse
Affiliation(s)
- Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA.
| |
Collapse
|
31
|
Kirtana R, Manna S, Patra SK. Molecular mechanisms of KDM5A in cellular functions: Facets during development and disease. Exp Cell Res 2020; 396:112314. [PMID: 33010254 DOI: 10.1016/j.yexcr.2020.112314] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 12/12/2022]
Abstract
Gene expression is influenced at many layers by a fine-tuned crosstalk between multiple extrinsic signalling pathways and intrinsic regulatory molecules that respond to environmental stimuli. Epigenetic modifiers like DNA methyltransferases, histone modifying enzymes and chromatin remodellers are reported to act as triggering factors in many scenarios by exhibiting their control over most of the cellular processes. These epigenetic players can either directly regulate gene expression or interact with some effector molecules that harmonize the expression of downstream genes. One such epigenetic regulator which exhibits multifaceted regulation over gene expression is KDM5A. It is classically a transcriptional repressor acting as H3K4me3 demethylase, but also is reported to act as an activator in many contexts either by loss of activity due to inhibition manifested by other interacting proteins or by downregulating the negative players of a given physiological process thereby escalating the framework. Through this review, we draw attention to the remarkable modes of functioning laid by KDM5A on transcriptional and translational processes, affecting gene expression during differentiation and development and finally summing up on role in disease causation (Fig. 1). We also shed light on different orthologs of KDM5A and their organism specific roles, along with comparison of the sequence similarity to extrapolate some unanswered questions about this protein.
Collapse
Affiliation(s)
- R Kirtana
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
| |
Collapse
|
32
|
Histone Demethylase KDM5B as a Therapeutic Target for Cancer Therapy. Cancers (Basel) 2020; 12:cancers12082121. [PMID: 32751840 PMCID: PMC7465382 DOI: 10.3390/cancers12082121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
Lysine-specific demethylase 5B (KDM5B/PLU1/JARID1B) is found to be overexpressed in numerous malignancies, including breast, lung, skin, liver, and prostate cancer. Identification of molecules targeting the KDM5B enzyme could be a potential lead in cancer research. Although many KDM5B inhibitors with promising outcomes have been developed so far, its further application in clinical practice is limited due to toxicity and lack of target specificity. Here, we summarize the significance of targeting KDM5B in anticancer therapy and report the molecular docking studies of some known anti-viral agents, decitabine, entecavir, abacavir, penciclovir, and 3-deazaneplanocin A in the catalytic domain JmjC of KDM5B. These studies show the repurposing potential of identified anti-viral agents in cancer therapy.
Collapse
|
33
|
Arifuzzaman S, Khatun MR, Khatun R. Emerging of lysine demethylases (KDMs): From pathophysiological insights to novel therapeutic opportunities. Biomed Pharmacother 2020; 129:110392. [PMID: 32574968 DOI: 10.1016/j.biopha.2020.110392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, there have been remarkable scientific advancements in the understanding of lysine demethylases (KDMs) because of their demethylation of diverse substrates, including nucleic acids and proteins. Novel structural architectures, physiological roles in the gene expression regulation, and ability to modify protein functions made KDMs the topic of interest in biomedical research. These structural diversities allow them to exert their function either alone or in complex with numerous other bio-macromolecules. Impressive number of studies have demonstrated that KDMs are localized dynamically across the cellular and tissue microenvironment. Their dysregulation is often associated with human diseases, such as cancer, immune disorders, neurological disorders, and developmental abnormalities. Advancements in the knowledge of the underlying biochemistry and disease associations have led to the development of a series of modulators and technical compounds. Given the distinct biophysical and biochemical properties of KDMs, in this review we have focused on advances related to the structure, function, disease association, and therapeutic targeting of KDMs highlighting improvements in both the specificity and efficacy of KDM modulation.
Collapse
Affiliation(s)
- Sarder Arifuzzaman
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh; Everest Pharmaceuticals Ltd., Dhaka-1208, Bangladesh.
| | - Mst Reshma Khatun
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Rabeya Khatun
- Department of Pediatrics, TMSS Medical College and Rafatullah Community Hospital, Gokul, Bogura, 5800, Bangladesh
| |
Collapse
|
34
|
Matthews KA, Senagbe KM, Nötzel C, Gonzales CA, Tong X, Rijo-Ferreira F, Bhanu NV, Miguel-Blanco C, Lafuente-Monasterio MJ, Garcia BA, Kafsack BFC, Martinez ED. Disruption of the Plasmodium falciparum Life Cycle through Transcriptional Reprogramming by Inhibitors of Jumonji Demethylases. ACS Infect Dis 2020; 6:1058-1075. [PMID: 32272012 PMCID: PMC7748244 DOI: 10.1021/acsinfecdis.9b00455] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Little
is known about the role of the three Jumonji C (JmjC) enzymes
in Plasmodium falciparum (Pf). Here,
we show that JIB-04 and other established inhibitors of mammalian
JmjC histone demethylases kill asexual blood stage parasites and are
even more potent at blocking gametocyte development and gamete formation.
In late stage parasites, JIB-04 increased levels of trimethylated
lysine residues on histones, suggesting the inhibition of P. falciparum Jumonji demethylase activity. These epigenetic
defects coincide with deregulation of invasion, cell motor, and sexual
development gene programs, including gene targets coregulated by the
PfAP2-I transcription factor and chromatin-binding factor, PfBDP1.
Mechanistically, we demonstrate that PfJmj3 converts 2-oxoglutarate
to succinate in an iron-dependent manner consistent with mammalian
Jumonji enzymes, and this catalytic activity is inhibited by JIB-04
and other Jumonji inhibitors. Our pharmacological studies of Jumonji
activity in the malaria parasite provide evidence that inhibition
of these enzymatic activities is detrimental to the parasite.
Collapse
Affiliation(s)
- Krista A. Matthews
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Kossi M. Senagbe
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Christopher Nötzel
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
- Biochemistry, Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Christopher A. Gonzales
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Xinran Tong
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Natarajan V. Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, Pennsylvania 19104, United States
| | - Celia Miguel-Blanco
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, P.T.M. Severo Ochoa, Tres Cantos, Madrid 28760, Spain
| | | | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, Pennsylvania 19104, United States
| | - Björn F. C. Kafsack
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
- Biochemistry, Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Elisabeth D. Martinez
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| |
Collapse
|
35
|
Yoo J, Jeon YH, Cho HY, Lee SW, Kim GW, Lee DH, Kwon SH. Advances in Histone Demethylase KDM3A as a Cancer Therapeutic Target. Cancers (Basel) 2020; 12:cancers12051098. [PMID: 32354028 PMCID: PMC7280979 DOI: 10.3390/cancers12051098] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Lysine-specific histone demethylase 3 (KDM3) subfamily proteins are H3K9me2/me1 histone demethylases that promote gene expression. The KDM3 subfamily primarily consists of four proteins (KDM3A−D). All four proteins contain the catalytic Jumonji C domain (JmjC) at their C-termini, but whether KDM3C has demethylase activity is under debate. In addition, KDM3 proteins contain a zinc-finger domain for DNA binding and an LXXLL motif for interacting with nuclear receptors. Of the KDM3 proteins, KDM3A is especially deregulated or overexpressed in multiple cancers, making it a potential cancer therapeutic target. However, no KDM3A-selective inhibitors have been identified to date because of the lack of structural information. Uncovering the distinct physiological and pathological functions of KDM3A and their structure will give insight into the development of novel selective inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM3A in cancer. We also discuss existing KDM3A-related inhibitors and review their potential as therapeutic agents for overcoming cancer.
Collapse
Affiliation(s)
- Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Ha Young Cho
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-32-749-4513
| |
Collapse
|
36
|
Miyake Y, Itoh Y, Suzuma Y, Kodama H, Kurohara T, Yamashita Y, Narozny R, Hanatani Y, Uchida S, Suzuki T. Metalloprotein-Catalyzed Click Reaction for In Situ Generation of a Potent Inhibitor. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuka Miyake
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yoshinori Suzuma
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Hidehiko Kodama
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Remy Narozny
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yutaro Hanatani
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Shusaku Uchida
- Graduate School of Medicine, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
37
|
Petronikolou N, Longbotham JE, Fujimori DG. Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A. Biochemistry 2020; 59:647-651. [PMID: 31985200 DOI: 10.1021/acs.biochem.9b01036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human lysine demethylase KDM5A is a chromatin-modifying enzyme associated with transcriptional regulation, because of its ability to catalyze removal of methyl groups from methylated lysine 4 of histone H3 (H3K4me3). Amplification of KDM5A is observed in many cancers, including breast cancer, prostate cancer, hepatocellular carcinoma, lung cancer, and gastric cancer. In this study, we employed alanine scanning mutagenesis to investigate substrate recognition of KDM5A and identify the H3 tail residues necessary for KDM5A-catalyzed demethylation. Our data show that the H3Q5 residue is critical for substrate recognition by KDM5A. Our data also reveal that the protein-protein interactions between KDM5A and the histone H3 tail extend beyond the amino acids proximal to the substrate mark. Specifically, demethylation activity assays show that deletion or mutation of residues at positions 14-18 on the H3 tail results in an 8-fold increase in the KMapp, compared to wild-type 18mer peptide, suggesting that this distal epitope is important in histone engagement. Finally, we demonstrate that post-translational modifications on this distal epitope can modulate KDM5A-dependent demethylation. Our findings provide insights into H3K4-specific recognition by KDM5A, as well as how chromatin context can regulate KDM5A activity and H3K4 methylation status.
Collapse
Affiliation(s)
- Nektaria Petronikolou
- Department of Cellular and Molecular Pharmacology , University of California , 600 16th Street, Genentech Hall , San Francisco , California 94158 , United States
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology , University of California , 600 16th Street, Genentech Hall , San Francisco , California 94158 , United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology , University of California , 600 16th Street, Genentech Hall , San Francisco , California 94158 , United States.,Department of Pharmaceutical Chemistry , University of California , 600 16th Street, Genentech Hall , San Francisco , California 94158 , United States
| |
Collapse
|
38
|
Clarke TL, Tang R, Chakraborty D, Van Rechem C, Ji F, Mishra S, Ma A, Kaniskan HÜ, Jin J, Lawrence MS, Sadreyev RI, Whetstine JR. Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification. Cancer Discov 2019; 10:306-325. [PMID: 31776131 DOI: 10.1158/2159-8290.cd-19-0463] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022]
Abstract
Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplification are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMT) and demethylases (KDM) in regulating transient site-specific DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplification of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specific KMTs and KDMs are able to promote or block extrachromosomal EGFR amplification, which identifies potential therapeutic strategies for controlling EGFR copy-number heterogeneity in cancer, and, in turn, drug response. SIGNIFICANCE: This study identifies a network of epigenetic factors and cellular signals that directly control EGFR DNA amplification. We demonstrate that chemical inhibitors targeting enzymes controlling this amplification can be used to rheostat EGFR copy number, which uncovers therapeutic opportunities for controlling EGFR DNA amplification heterogeneity and the associated drug response.This article is highlighted in the In This Issue feature, p. 161.
Collapse
Affiliation(s)
- Thomas L Clarke
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.,School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Capucine Van Rechem
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sweta Mishra
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Anqi Ma
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, Charlestown, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
| |
Collapse
|
39
|
Zoeller EL, Pedro B, Konen J, Dwivedi B, Rupji M, Sundararaman N, Wang L, Horton JR, Zhong C, Barwick BG, Cheng X, Martinez ED, Torres MP, Kowalski J, Marcus AI, Vertino PM. Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes. J Cell Sci 2019; 132:jcs231514. [PMID: 31515279 PMCID: PMC6803364 DOI: 10.1242/jcs.231514] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
Collective invasion, the coordinated movement of cohesive packs of cells, has become recognized as a major mode of metastasis for solid tumors. These packs are phenotypically heterogeneous and include specialized cells that lead the invasive pack and others that follow behind. To better understand how these unique cell types cooperate to facilitate collective invasion, we analyzed transcriptomic sequence variation between leader and follower populations isolated from the H1299 non-small cell lung cancer cell line using an image-guided selection technique. We now identify 14 expressed mutations that are selectively enriched in leader or follower cells, suggesting a novel link between genomic and phenotypic heterogeneity within a collectively invading tumor cell population. Functional characterization of two phenotype-specific candidate mutations showed that ARP3 enhances collective invasion by promoting the leader cell phenotype and that wild-type KDM5B suppresses chain-like cooperative behavior. These results demonstrate an important role for distinct genetic variants in establishing leader and follower phenotypes and highlight the necessity of maintaining a capacity for phenotypic plasticity during collective cancer invasion.
Collapse
Affiliation(s)
- Elizabeth L Zoeller
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Brian Pedro
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Jessica Konen
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Bhakti Dwivedi
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Manali Rupji
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Niveda Sundararaman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chaojie Zhong
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Benjamin G Barwick
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeanne Kowalski
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Adam I Marcus
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Paula M Vertino
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
40
|
Khodaverdian V, Tapadar S, MacDonald IA, Xu Y, Ho PY, Bridges A, Rajpurohit P, Sanghani BA, Fan Y, Thangaraju M, Hathaway NA, Oyelere AK. Deferiprone: Pan-selective Histone Lysine Demethylase Inhibition Activity and Structure Activity Relationship Study. Sci Rep 2019; 9:4802. [PMID: 30886160 PMCID: PMC6423038 DOI: 10.1038/s41598-019-39214-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
Deferiprone (DFP) is a hydroxypyridinone-derived iron chelator currently in clinical use for iron chelation therapy. DFP has also been known to elicit antiproliferative activities, yet the mechanism of this effect has remained elusive. We herein report that DFP chelates the Fe2+ ion at the active sites of selected iron-dependent histone lysine demethylases (KDMs), resulting in pan inhibition of a subfamily of KDMs. Specifically, DFP inhibits the demethylase activities of six KDMs - 2A, 2B, 5C, 6A, 7A and 7B - with low micromolar IC50s while considerably less active or inactive against eleven KDMs - 1A, 3A, 3B, 4A-E, 5A, 5B and 6B. The KDM that is most sensitive to DFP, KDM6A, has an IC50 that is between 7- and 70-fold lower than the iron binding equivalence concentrations at which DFP inhibits ribonucleotide reductase (RNR) activities and/or reduces the labile intracellular zinc ion pool. In breast cancer cell lines, DFP potently inhibits the demethylation of H3K4me3 and H3K27me3, two chromatin posttranslational marks that are subject to removal by several KDM subfamilies which are inhibited by DFP in cell-free assay. These data strongly suggest that DFP derives its anti-proliferative activity largely from the inhibition of a sub-set of KDMs. The docked poses adopted by DFP at the KDM active sites enabled identification of new DFP-based KDM inhibitors which are more cytotoxic to cancer cell lines. We also found that a cohort of these agents inhibited HP1-mediated gene silencing and one lead compound potently inhibited breast tumor growth in murine xenograft models. Overall, this study identified a new chemical scaffold capable of inhibiting KDM enzymes, globally changing histone modification profiles, and with specific anti-tumor activities.
Collapse
Affiliation(s)
- Verjine Khodaverdian
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Subhasish Tapadar
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Ian A MacDonald
- The University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA
| | - Yuan Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Po-Yi Ho
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Allison Bridges
- Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Pragya Rajpurohit
- Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Bhakti A Sanghani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Yuhong Fan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | | | - Nathaniel A Hathaway
- The University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA.
| | - Adegboyega K Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
| |
Collapse
|
41
|
Research update and opportunity of non-hormonal male contraception: Histone demethylase KDM5B-based targeting. Pharmacol Res 2019; 141:1-20. [DOI: 10.1016/j.phrs.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/29/2018] [Accepted: 12/09/2018] [Indexed: 12/28/2022]
|
42
|
Liu X, Zhang SM, McGeary MK, Krykbaeva I, Lai L, Jansen DJ, Kales SC, Simeonov A, Hall MD, Kelly DP, Bosenberg MW, Yan Q. KDM5B Promotes Drug Resistance by Regulating Melanoma-Propagating Cell Subpopulations. Mol Cancer Ther 2019; 18:706-717. [PMID: 30523048 PMCID: PMC6397704 DOI: 10.1158/1535-7163.mct-18-0395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/09/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022]
Abstract
Tumor heterogeneity is a major challenge for cancer treatment, especially due to the presence of various subpopulations with stem cell or progenitor cell properties. In mouse melanomas, both CD34+p75- (CD34+) and CD34-p75- (CD34-) tumor subpopulations were characterized as melanoma-propagating cells (MPC) that exhibit some of those key features. However, these two subpopulations differ from each other in tumorigenic potential, ability to recapitulate heterogeneity, and chemoresistance. In this study, we demonstrate that CD34+ and CD34- subpopulations carrying the BRAFV600E mutation confer differential sensitivity to targeted BRAF inhibition. Through elevated KDM5B expression, melanoma cells shift toward a more drug-tolerant, CD34- state upon exposure to BRAF inhibitor or combined BRAF inhibitor and MEK inhibitor treatment. KDM5B loss or inhibition shifts melanoma cells to the more BRAF inhibitor-sensitive CD34+ state. These results support that KDM5B is a critical epigenetic regulator that governs the transition of key MPC subpopulations with distinct drug sensitivity. This study also emphasizes the importance of continuing to advance our understanding of intratumor heterogeneity and ultimately develop novel therapeutics by altering the heterogeneous characteristics of melanoma.
Collapse
Affiliation(s)
- Xiaoni Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Meaghan K McGeary
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Irina Krykbaeva
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Ling Lai
- Penn Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Daniel P Kelly
- Penn Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marcus W Bosenberg
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
| |
Collapse
|
43
|
Li ZR, Wang S, Yang L, Yuan XH, Suo FZ, Yu B, Liu HM. Experience-based discovery (EBD) of aryl hydrazines as new scaffolds for the development of LSD1/KDM1A inhibitors. Eur J Med Chem 2019; 166:432-444. [DOI: 10.1016/j.ejmech.2019.01.075] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/01/2019] [Accepted: 01/29/2019] [Indexed: 01/22/2023]
|
44
|
Mokou M, Klein J, Makridakis M, Bitsika V, Bascands JL, Saulnier-Blache JS, Mullen W, Sacherer M, Zoidakis J, Pieske B, Mischak H, Roubelakis MG, Schanstra JP, Vlahou A. Proteomics based identification of KDM5 histone demethylases associated with cardiovascular disease. EBioMedicine 2019; 41:91-104. [PMID: 30826357 PMCID: PMC6443027 DOI: 10.1016/j.ebiom.2019.02.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022] Open
Abstract
Background The increased prevalence of cardiovascular disease (CVD) indicates a demand for novel therapeutic approaches. Proteome analysis of vascular tissues from animal models and humans with CVD could lead to the identification of novel druggable targets. Methods LC-MS/MS analysis of thoracic aortas from three mouse models of non-diabetic and diabetic (streptozotocin (STZ)-induced) atherosclerosis followed by bioinformatics/pathway analysis was performed. Selected findings were confirmed by proteomics analysis of human vessels from patients with CVD as well as in vitro studies (migration, proliferation, angiogenesis assays) using endothelial (HUVEC) cells. Findings Comparative tissue proteomics of low density lipoprotein receptor deficient (Ldlr−/−) and diabetic Ldlr−/− (Ldlr−/−STZ) with wild type (WT) animals led to the identification of 284 differentially expressed proteins in both models. Among them, 177 proteins were also differentially expressed in diabetic apolipoprotein E deficient (ApoE−/−STZ) mice, suggesting expression changes associated with atherosclerosis independent of the model used. These proteins recapitulated the hallmarks of atherosclerosis. Comparison of these findings with differentially expressed proteins in human vessels with CVD enabled shortlisting of six commonly dysregulated proteins. Among them, lysine-specific demethylase 5D (KDM5D) exhibited pronounced overexpression accompanied by a reduction in the protein levels of its substrate, the trimethylated lysine 4 of histone H3 (H3K4me3), in patients with CVD. Functional interference studies applying a KDM5 inhibitor on HUVEC reduced cell proliferation, migration and tube-forming ability in vitro. Interpretation This high-throughput proteomics strategy identified KDM5 histone demethylases being potentially involved in CVD, possibly by affecting H3K4 methylation. Fund [SysVasc, HEALTH-2013 603288], [ERA-CVD PROACT: ANR-17-ECVD-0006, 01KL1805], [FRM, DEQ20170336759].
Collapse
Affiliation(s)
- Marika Mokou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Laboratory of Biology, University of Athens, School of Medicine, Athens, Greece
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier Toulouse, Toulouse, France
| | - Manousos Makridakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Bitsika
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jean-Loup Bascands
- INSERM, U1188, Sainte Clotilde, La Réunion, France; Université de La Réunion, Sainte Clotilde, La Réunion, France
| | - Jean Sebastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier Toulouse, Toulouse, France
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Michael Sacherer
- Department of Cardiology, Medical University of Graz, Graz, Austria
| | - Jerome Zoidakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Burkert Pieske
- Department of Internal Medicine and Cardiology, Charité University Medicine, Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site, Berlin, Germany; Department of Internal Medicine and Cardiology, German Heart Center, Berlin, Germany; Berlin Institute of Health (BIH), Germany
| | - Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom; Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Maria G Roubelakis
- Laboratory of Biology, University of Athens, School of Medicine, Athens, Greece
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier Toulouse, Toulouse, France.
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| |
Collapse
|
45
|
Structure-Based Discovery of a Selective KDM5A Inhibitor that Exhibits Anti-Cancer Activity via Inducing Cell Cycle Arrest and Senescence in Breast Cancer Cell Lines. Cancers (Basel) 2019; 11:cancers11010092. [PMID: 30650517 PMCID: PMC6360022 DOI: 10.3390/cancers11010092] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the one of the most frequent causes of female cancer mortality. KDM5A, a histone demethylase, can increase the proliferation, metastasis, and drug resistance of cancers, including breast cancer, and is thus an important therapeutic target. In the present work, we performed hierarchical virtual screening towards the KDM5A catalytic pocket from a chemical library containing 90,000 compounds. Using multiple biochemical methods, the cyclopenta[c]chromen derivative 1 was identified as the top candidate for KDM5A demethylase inhibitory activity. Compared with the well-known KDM5 inhibitor CPI-455 (18), 1 exhibited higher potency against KDM5A and much higher selectivity for KDM5A over both KDM4A and other KDM5 family members (KDM5B and KDM5C). Additionally, compound 1 repressed the proliferation of various KDM5A-overexpressing breast cancer cell lines. Mechanistically, 1 promoted accumulation of p16 and p27 by blocking KDM5A-mediated H3K4me3 demethylation, leading to cell cycle arrest and senescence. To date, compound 1 is the first cyclopenta[c]chromen-based KDM5A inhibitor reported, and may serve as a novel motif for developing more selective and efficacious pharmacological molecules targeting KDM5A. In addition, our research provides a possible anti-cancer mechanism of KDM5A inhibitors and highlights the feasibility and significance of KDM5A as a therapeutic target for KDM5A-overexpressing breast cancer.
Collapse
|
46
|
Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun 2019; 10:94. [PMID: 30626866 PMCID: PMC6327041 DOI: 10.1038/s41467-018-07829-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation. The demethylase activity of KDM5A is allosterically enhanced by binding of histone H3 to its PHD1 reader domain, through an unknown mechanism. Here the authors show that the PHD1 domain drives ligand-induced allosteric stimulation by stabilizing the binding of substrate to the catalytic domain.
Collapse
Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Cynthia M Chio
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | | | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Karen Ruiz
- TETRAD Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA. .,Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA.
| |
Collapse
|
47
|
Collins BE, Greer CB, Coleman BC, Sweatt JD. Histone H3 lysine K4 methylation and its role in learning and memory. Epigenetics Chromatin 2019; 12:7. [PMID: 30616667 PMCID: PMC6322263 DOI: 10.1186/s13072-018-0251-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dysregulation of various components of the epigenetic machinery causes cognitive deficits at the behavioral level, suggesting that proper epigenetic control is necessary for the fundamental processes of learning and memory. Histone H3 lysine K4 (H3K4) methylation comprises one component of such epigenetic control, and global levels of this mark are increased in the hippocampus during memory formation. Modifiers of H3K4 methylation are needed for memory formation, shown through animal studies, and many of the same modifiers are mutated in human cognitive diseases. Indeed, all of the known H3K4 methyltransferases and four of the known six H3K4 demethylases have been associated with impaired cognition in a neurologic or psychiatric disorder. Cognitive impairment in such patients often manifests as intellectual disability, consistent with a role for H3K4 methylation in learning and memory. As a modification quintessentially, but not exclusively, associated with transcriptional activity, H3K4 methylation provides unique insights into the regulatory complexity of writing, reading, and erasing chromatin marks within an activated neuron. The following review will discuss H3K4 methylation and connect it to transcriptional events required for learning and memory within the developed nervous system. This will include an initial discussion of the most recent advances in the developing methodology to analyze H3K4 methylation, namely mass spectrometry and deep sequencing, as well as how these methods can be applied to more deeply understand the biology of this mark in the brain. We will then introduce the core enzymatic machinery mediating addition and removal of H3K4 methylation marks and the resulting epigenetic signatures of these marks throughout the neuronal genome. We next foray into the brain, discussing changes in H3K4 methylation marks within the hippocampus during memory formation and retrieval, as well as the behavioral correlates of H3K4 methyltransferase deficiency in this region. Finally, we discuss the human cognitive diseases connected to each H3K4 methylation modulator and summarize advances in developing drugs to target them.
Collapse
Affiliation(s)
- Bridget E Collins
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Benjamin C Coleman
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
| |
Collapse
|
48
|
Horton JR, Woodcock CB, Chen Q, Liu X, Zhang X, Shanks J, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Cyr M, Pohida K, Hu X, Shah P, Xu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Cheng X. Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J Med Chem 2018; 61:10588-10601. [PMID: 30392349 PMCID: PMC6467790 DOI: 10.1021/acs.jmedchem.8b01219] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.
Collapse
Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Clayton B. Woodcock
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Qin Chen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew Cyr
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Departments of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| |
Collapse
|
49
|
Plch J, Hrabeta J, Eckschlager T. KDM5 demethylases and their role in cancer cell chemoresistance. Int J Cancer 2018; 144:221-231. [PMID: 30246379 DOI: 10.1002/ijc.31881] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/28/2022]
Abstract
Histone methylation is important in the regulation of genes expression, and thus its dysregulation has been observed in various cancers. KDM5 enzymes are capable of removing tri- and di- methyl marks from lysine 4 on histone H3 (H3K4) which makes them potential players in the downregulation of tumor suppressors, but could also suggest that their activity repress oncogenes. Depending on the methylation site, their effect on transcription can be either activating or repressing. There is emerging evidence for deregulation of KDM5A/B/C/D and important phenotypic consequences in various types of cancer. It has been suggested that the KDM5 family of demethylases plays a role in the appearance of drug tolerance. Drug resistance remains a challenge to successful cancer treatment. This review summarizes recent advances in understanding the functions of KDM5 histone demethylases in cancer chemoresistance and potential therapeutic targeting of these enzymes, which seems to prevent the emergence of a drug-resistant population.
Collapse
Affiliation(s)
- Johana Plch
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Jan Hrabeta
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Tomas Eckschlager
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| |
Collapse
|
50
|
Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol 2018; 57:79-85. [PMID: 30448242 DOI: 10.1016/j.semcancer.2018.11.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling stem cell function and tumorigenesis. The histone lysine demethylase, KDM5B, which catalyzes the demethylation of histone 3 lysine 4 (H3K4), is important for embryonic stem (ES) cell differentiation, and is a critical regulator of the H3K4-methylome during early mouse embryonic pre-implantation stage development. KDM5B is also overexpressed, amplified, or mutated in many cancer types. In cancer cells, KDM5B regulates expression of oncogenes and tumor suppressors by modulating H3K4 methylation levels. In this review, we examine how KDM5B regulates gene expression and cellular fates of stem cells and cancer cells by temporally and spatially controlling H3K4 methylation levels.
Collapse
Affiliation(s)
- Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
| |
Collapse
|