1
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Sharma S, Rani H, Mahesh Y, Jolly MK, Dixit J, Mahadevan V. Loss of p53 epigenetically modulates epithelial to mesenchymal transition in colorectal cancer. Transl Oncol 2024; 43:101848. [PMID: 38412660 PMCID: PMC10907866 DOI: 10.1016/j.tranon.2023.101848] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/21/2023] [Indexed: 02/29/2024] Open
Abstract
Epithelial to Mesenchymal transition (EMT) drives cancer metastasis and is governed by genetic and epigenetic alterations at multiple levels of regulation. It is well established that loss/mutation of p53 confers oncogenic function to cancer cells and promotes metastasis. Though transcription factors like ZEB1, SLUG, SNAIL and TWIST have been implied in EMT signalling, p53 mediated alterations in the epigenetic machinery accompanying EMT are not clearly understood. This work attempts to explore epigenetic signalling during EMT in colorectal cancer (CRC) cells with varying status of p53. Towards this, we have induced EMT using TGFβ on CRC cell lines with wild type, null and mutant p53 and have assayed epigenetic alterations after EMT induction. Transcriptomic profiling of the four CRC cell lines revealed that the loss of p53 confers more mesenchymal phenotype with EMT induction than its mutant counterparts. This was also accompanied by upregulation of epigenetic writer and eraser machinery suggesting an epigenetic signalling cascade triggered by TGFβ signalling in CRC. Significant agonist and antagonistic relationships observed between EMT factor SNAI1 and SNAI2 with epigenetic enzymes KDM6A/6B and the chromatin organiser SATB1 in p53 null CRC cells suggest a crosstalk between epigenetic and EMT factors. The observed epigenetic regulation of EMT factor SNAI1 correlates with poor clinical outcomes in 270 colorectal cancer patients taken from TCGA-COAD. This unique p53 dependent interplay between epigenetic enzymes and EMT factors in CRC cells may be exploited for development of synergistic therapies for CRC patients presenting to the clinic with loss of p53.
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Affiliation(s)
- Shreya Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, India
| | - Harsha Rani
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, India
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2
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Abu-Zaid A, Fang J, Jin H, Singh S, Pichavaram P, Wu Q, Tillman H, Janke L, Rosikiewicz W, Xu B, Van De Velde LA, Guo Y, Li Y, Shendy NAM, Delahunty IM, Rankovic Z, Chen T, Chen X, Freeman KW, Hatley ME, Durbin AD, Murray PJ, Murphy AJ, Thomas PG, Davidoff AM, Yang J. Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma. Cell Rep Med 2024; 5:101468. [PMID: 38508144 PMCID: PMC10983111 DOI: 10.1016/j.xcrm.2024.101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/21/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Neuroblastoma with MYCN amplification (MNA) is a high-risk disease that has a poor survival rate. Neuroblastoma displays cellular heterogeneity, including more differentiated (adrenergic) and more primitive (mesenchymal) cellular states. Here, we demonstrate that MYCN oncoprotein promotes a cellular state switch in mesenchymal cells to an adrenergic state, accompanied by induction of histone lysine demethylase 4 family members (KDM4A-C) that act in concert to control the expression of MYCN and adrenergic core regulatory circulatory (CRC) transcription factors. Pharmacologic inhibition of KDM4 blocks expression of MYCN and the adrenergic CRC transcriptome with genome-wide induction of transcriptionally repressive H3K9me3, resulting in potent anticancer activity against neuroblastomas with MNA by inducing neuroblastic differentiation and apoptosis. Furthermore, a short-term KDM4 inhibition in combination with conventional, cytotoxic chemotherapy results in complete tumor responses of xenografts with MNA. Thus, KDM4 blockade may serve as a transformative strategy to target the adrenergic CRC dependencies in MNA neuroblastomas.
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Affiliation(s)
- Ahmed Abu-Zaid
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jie Fang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Qiong Wu
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Tillman
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Janke
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lee-Ann Van De Velde
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yian Guo
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yimei Li
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Noha A M Shendy
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ian M Delahunty
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kevin W Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Mark E Hatley
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Adam D Durbin
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andrew J Murphy
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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3
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Jablonowski CM, Quarni W, Singh S, Tan H, Bostanthirige DH, Jin H, Fang J, Chang TC, Finkelstein D, Cho JH, Hu D, Pagala V, Sakurada SM, Pruett-Miller SM, Wang R, Murphy A, Freeman K, Peng J, Davidoff AM, Wu G, Yang J. Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing associated with therapeutic response to splicing inhibitor. eLife 2024; 12:RP90993. [PMID: 38488852 PMCID: PMC10942784 DOI: 10.7554/elife.90993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that jumonji domain containing 6, arginine demethylase, and lysine hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven human neuroblastoma. JMJD6 cooperates with MYC in cellular transformation of murine neural crest cells by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a 'molecular glue' that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
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Affiliation(s)
| | - Waise Quarni
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | | | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jie Fang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - David Finkelstein
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Dongli Hu
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Sadie Miki Sakurada
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s HospitalColumbusUnited States
| | - Andrew Murphy
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Kevin Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center (UTHSC)MemphisUnited States
| | - Junmin Peng
- Department of Structural Biology, St Jude Children’s Research HospitalMemphisUnited States
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
- College of Graduate Health Sciences, University of Tennessee Health Science CenterMemphisUnited States
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4
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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.
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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.
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5
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Kataria A, Tyagi S. Domain architecture and protein-protein interactions regulate KDM5A recruitment to the chromatin. Epigenetics 2023; 18:2268813. [PMID: 37838974 PMCID: PMC10578193 DOI: 10.1080/15592294.2023.2268813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023] Open
Abstract
Tri-methylation of Histone 3 lysine 4 (H3K4) is an important epigenetic modification whose deposition and removal can affect the chromatin at structural and functional levels. KDM5A is one of the four known H3K4-specific demethylases. It is a part of the KDM5 family, which is characterized by a catalytic Jumonji domain capable of removing H3K4 di- and tri-methylation marks. KDM5A has been found to be involved in multiple cellular processes such as differentiation, metabolism, cell cycle, and transcription. Its link to various diseases, including cancer, makes KDM5A an important target for drug development. However, despite several studies outlining its significance in various pathways, our lack of understanding of its recruitment and function at the target sites on the chromatin presents a challenge in creating effective and targeted treatments. Therefore, it is essential to understand the recruitment mechanism of KDM5A to chromatin, and its activity therein, to comprehend how various roles of KDM5A are regulated. In this review, we discuss how KDM5A functions in a context-dependent manner on the chromatin, either directly through its structural domain, or through various interacting partners, to bring about a diverse range of functions.
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Affiliation(s)
- Avishek Kataria
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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6
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Gaeta R, Righi A, Gambarotti M, Aretini P, Lessi F, Mazzanti CM, Mancini I, Pinzani P, Belgio B, Sbaraglia M, Dei Tos AP, Franchi A. Chondroblastoma‐like osteosarcoma: a clinicopathologic and molecular study of a rare osteosarcoma variant. Histopathology 2022; 81:389-401. [DOI: 10.1111/his.14721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Raffaele Gaeta
- Department of Translational Research University of Pisa Pisa Italy
| | | | - Marco Gambarotti
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli Bologna Italy
| | | | | | | | - Irene Mancini
- Molecular and Clinical Biochemistry Unit Careggi University Hospital Florence Italy
| | - Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio" University of Florence Florence Italy
| | - Beatrice Belgio
- Department of Translational Research University of Pisa Pisa Italy
| | - Marta Sbaraglia
- Department of Pathology, Azienda Ospedale‐Università Padova Padua Italy
| | - Angelo Paolo Dei Tos
- Department of Pathology, Azienda Ospedale‐Università Padova Padua Italy
- Department of Medicine (DIMED) University of Padua School of Medicine
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7
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Hou R, Yu Y, Sluter MN, Li L, Hao J, Fang J, Yang J, Jiang J. Targeting EP2 receptor with multifaceted mechanisms for high-risk neuroblastoma. Cell Rep 2022; 39:111000. [PMID: 35732130 PMCID: PMC9282716 DOI: 10.1016/j.celrep.2022.111000] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/02/2022] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Prostaglandin E2 (PGE2) promotes tumor cell proliferation, migration, and invasion, fostering an inflammation-enriched microenvironment that facilitates angiogenesis and immune evasion. However, the PGE2 receptor subtype (EP1–EP4) involved in neuroblastoma (NB) growth remains elusive. Herein, we show that the EP2 receptor highly correlates with NB aggressiveness and acts as a predominant Gαs-coupled receptor mediating PGE2-initiated cyclic AMP (cAMP) signaling in NB cells with high-risk factors, including 11q deletion and MYCN amplification. Knockout of EP2 in NB cells blocks the development of xenografts, and its conditional knockdown prevents established tumors from progressing. Pharmacological inhibition of EP2 by our recently developed antagonist TG6-129 suppresses the growth of NB xenografts in nude mice and syngeneic allografts in immunocompetent hosts, accompanied by anti-inflammatory, antiangiogenic, and apoptotic effects. This proof-of-concept study suggests that the PGE2/EP2 signaling pathway contributes to NB malignancy and that EP2 inhibition by our drug-like compounds provides a promising strategy to treat this deadly pediatric cancer. Hou et al. discover that prostaglandin receptor EP2 highly correlates with the aggressiveness of neuroblastoma, where it acts as the primary PGE2 receptor mediating cAMP signaling. EP2 deficiency or inhibition suppresses neuroblastoma with high-risk factors including 11q deletion and MYCN amplification, demonstrating EP2 as a promising therapeutic target for neuroblastoma.
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Affiliation(s)
- Ruida Hou
- Department of Pharmaceutical Sciences, Drug Discovery Center, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ying Yu
- Department of Pharmaceutical Sciences, Drug Discovery Center, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Madison N Sluter
- Department of Pharmaceutical Sciences, Drug Discovery Center, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lexiao Li
- Department of Pharmaceutical Sciences, Drug Discovery Center, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jiukuan Hao
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Jie Fang
- Department of Surgery, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianxiong Jiang
- Department of Pharmaceutical Sciences, Drug Discovery Center, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Anatomy and Neurobiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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8
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Sanchez A, Buck-Koehntop BA, Miller KM. Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?). Bioessays 2022; 44:e2200015. [PMID: 35532219 DOI: 10.1002/bies.202200015] [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: 01/19/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/05/2022]
Abstract
The lysine demethylase KDM5A collaborates with PARP1 and the histone variant macroH2A1.2 to modulate chromatin to promote DNA repair. Indeed, KDM5A engages poly(ADP-ribose) (PAR) chains at damage sites through a previously uncharacterized coiled-coil domain, a novel binding mode for PAR interactions. While KDM5A is a well-known transcriptional regulator, its function in DNA repair is only now emerging. Here we review the molecular mechanisms that regulate this PARP1-macroH2A1.2-KDM5A axis in DNA damage and consider the potential involvement of this pathway in transcription regulation and cancer. Using KDM5A as an example, we discuss how multifunctional chromatin proteins transition between several DNA-based processes, which must be coordinated to protect the integrity of the genome and epigenome. The dysregulation of chromatin and loss of genome integrity that is prevalent in human diseases including cancer may be related and could provide opportunities to target multitasking proteins with these pathways as therapeutic strategies.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, The University of Texas at Austin, Austin, Texas, USA
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, The University of Texas at Austin, Austin, Texas, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
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9
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The Emerging Significance of Histone Lysine Demethylases as Prognostic Markers and Therapeutic Targets in Head and Neck Cancers. Cells 2022; 11:cells11061023. [PMID: 35326475 PMCID: PMC8946939 DOI: 10.3390/cells11061023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic aberrations, associated with altered DNA methylation profiles and global changes in the level of histone modifications, are commonly detected in head and neck squamous cell carcinomas (HNSCC). Recently, histone lysine demethylases have been implicated in the pathogenesis of HNSCC and emerged as potential molecular targets. Histone lysine demethylases (KDMs) catalyze the removal of methyl groups from lysine residues in histones. By affecting the methylation of H3K4, H3K9, H3K27, or H3K36, these enzymes take part in transcriptional regulation, which may result in changes in the level of expression of tumor suppressor genes and protooncogenes. KDMs are involved in many biological processes, including cell cycle control, senescence, DNA damage response, and heterochromatin formation. They are also important regulators of pluripotency. The overexpression of most KDMs has been observed in HNSCC, and their inhibition affects cell proliferation, apoptosis, cell motility, invasiveness, and stemness. Of all KDMs, KDM1, KDM4, KDM5, and KDM6 proteins are currently regarded as the most promising prognostic and therapeutic targets in head and neck cancers. The aim of this review is to present up-to-date knowledge on the significance of histone lysine demethylases in head and neck carcinogenesis and to discuss the possibility of using them as prognostic markers and pharmacological targets in patients’ treatment.
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10
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Wang C, Jia Q, Guo X, Li K, Chen W, Shen Q, Xu C, Fu Y. microRNA-34 Family: From Mechanism to Potential Applications. Int J Biochem Cell Biol 2022; 144:106168. [DOI: 10.1016/j.biocel.2022.106168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/04/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023]
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11
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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.
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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.
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12
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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.
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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.
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13
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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.
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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
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14
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Transcriptional Reprogramming in Rumen Epithelium during the Developmental Transition of Pre-Ruminant to the Ruminant in Cattle. Animals (Basel) 2021; 11:ani11102870. [PMID: 34679891 PMCID: PMC8532853 DOI: 10.3390/ani11102870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary The rumen is the critical organ mediating nutrient uptake and use in cattle. Health development is essential to ensure animal feed efficiency. In this report, we present an analysis of gene expression dynamic in rumen epithelium during the transition from pre-ruminant to ruminant in cattle fed with hay or concentrated diets at weaning. The global shifts in gene expression and correlated transcription factors activities indicate transcriptional reprogramming during weaning. Transcriptional reprogramming in rumen epithelial tissue reflects critical nutrient-gene interactions occurring during the developmental progression. The results unveiled that nutrient-gene interactions compel transcriptional reprogramming. Our findings also suggest that this transcriptional reprogramming is the molecular basis of the transitional development of pre-ruminant to the ruminant in cattle. Abstract We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways. The dietary shift from liquid to solid feeds prompted the shifting of gene activity. The number of differentially expressed genes increased significantly after weaning. Bioinformatic analysis revealed gene activity shifts underline the functional transitions in the ruminal epithelium and signify the transcriptomic reprogramming. Gene ontogeny (GO) term enrichment shows extensively activated biological functions of differentially expressed genes in the ruminal epithelium after weaning were predominant metabolic functions. The transcriptomic reprogramming signifies a correlation between gene activity and changes in metabolism and energy production in the rumen epithelium, which occur at weaning when transitioning from glucose use to VFA use by epithelium during the weaning.
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15
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Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop BA, Miller KM. Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. J Cell Biol 2021; 220:212163. [PMID: 34003252 PMCID: PMC8135068 DOI: 10.1083/jcb.202006149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.
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Affiliation(s)
- Ramhari Kumbhar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Jullian Perren
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Fade Gong
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX
| | - David Corujo
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain
| | - Frank Medina
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Sravan K Devanathan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Marcus Buschbeck
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Spain
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
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16
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Abstract
The p53 protein is a transcription factor that prevents tumors from developing. In spontaneous and inherited cancers there are many different missense mutations in the DNA binding domain of the TP53 gene that contributes to tumor formation. These mutations produce a wide distribution in the transcriptional capabilities of the mutant p53 proteins with over four logs differences in the efficiencies of forming cancers in many diverse tissue types. These inherited and spontaneous TP53 mutations produce proteins that interact with both genetic and epigenetic cellular modifiers of p53 function and their inherited polymorphisms to produce a large number of diverse phenotypes in individual patients. This manuscript reviews these variables and discusses how the combinations of TP53 genetic alterations interact with genetic polymorphisms, epigenetic alterations, and environmental factors to begin predicting and modifying patient outcomes and provide a better understanding for new therapeutic opportunities.
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Affiliation(s)
- Arnold J. Levine
- grid.78989.370000 0001 2160 7918Institute for Advanced Study, Princeton, NJ USA
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17
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Moore TM, Zhou Z, Strumwasser AR, Cohn W, Lin AJ, Cory K, Whitney K, Ho T, Ho T, Lee JL, Rucker DH, Hoang AN, Widjaja K, Abrishami AD, Charugundla S, Stiles L, Whitelegge JP, Turcotte LP, Wanagat J, Hevener AL. Age-induced mitochondrial DNA point mutations are inadequate to alter metabolic homeostasis in response to nutrient challenge. Aging Cell 2020; 19:e13166. [PMID: 33049094 PMCID: PMC7681042 DOI: 10.1111/acel.13166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/10/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction is frequently associated with impairment in metabolic homeostasis and insulin action, and is thought to underlie cellular aging. However, it is unclear whether mitochondrial dysfunction is a cause or consequence of insulin resistance in humans. To determine the impact of intrinsic mitochondrial dysfunction on metabolism and insulin action, we performed comprehensive metabolic phenotyping of the polymerase gamma (PolG) D257A “mutator” mouse, a model known to accumulate supraphysiological mitochondrial DNA (mtDNA) point mutations. We utilized the heterozygous PolG mutator mouse (PolG+/mut) because it accumulates mtDNA point mutations ~ 500‐fold > wild‐type mice (WT), but fails to develop an overt progeria phenotype, unlike PolGmut/mut animals. To determine whether mtDNA point mutations induce metabolic dysfunction, we examined male PolG+/mut mice at 6 and 12 months of age during normal chow feeding, after 24‐hr starvation, and following high‐fat diet (HFD) feeding. No marked differences were observed in glucose homeostasis, adiposity, protein/gene markers of metabolism, or oxygen consumption in muscle between WT and PolG+/mut mice during any of the conditions or ages studied. However, proteomic analyses performed on isolated mitochondria from 12‐month‐old PolG+/mut mouse muscle revealed alterations in the expression of mitochondrial ribosomal proteins, electron transport chain components, and oxidative stress‐related factors compared with WT. These findings suggest that mtDNA point mutations at levels observed in mammalian aging are insufficient to disrupt metabolic homeostasis and insulin action in male mice.
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Affiliation(s)
- Timothy M. Moore
- Department of Biological Sciences Dana & David Dornsife College of Letters, Arts, and Sciences University of Southern California Los Angeles CA USA
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Zhenqi Zhou
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Alexander R. Strumwasser
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Whitaker Cohn
- Department of Psychiatry and Biobehavioral Sciences & The Semel Institute for Neuroscience and Human Behavior University of California Los Angeles CA USA
| | - Amanda J. Lin
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Kevin Cory
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Kate Whitney
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Theodore Ho
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Timothy Ho
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Joseph L. Lee
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Daniel H. Rucker
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Austin N. Hoang
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Kevin Widjaja
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Aaron D. Abrishami
- Division of Cardiology Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Sarada Charugundla
- Division of Cardiology Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Linsey Stiles
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Julian P. Whitelegge
- Department of Psychiatry and Biobehavioral Sciences & The Semel Institute for Neuroscience and Human Behavior University of California Los Angeles CA USA
| | - Lorraine P. Turcotte
- Department of Biological Sciences Dana & David Dornsife College of Letters, Arts, and Sciences University of Southern California Los Angeles CA USA
| | - Jonathan Wanagat
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
| | - Andrea L. Hevener
- Division of Endocrinology, Diabetes, and Hypertension Department of Medicine David Geffen School of Medicine University of California Los Angeles CA USA
- Iris Cantor‐UCLA Women's Health Center University of California Los Angeles CA USA
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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.
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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.
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19
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Ren F, Shrestha C, Shi H, Sun F, Zhang M, Cao Y, Li G. Targeting of KDM5A by miR-421 in Human Ovarian Cancer Suppresses the Progression of Ovarian Cancer Cells. Onco Targets Ther 2020; 13:9419-9428. [PMID: 33061428 PMCID: PMC7520141 DOI: 10.2147/ott.s266211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The retinoblastoma binding protein RBP2 (KDM5A) is a histone demethylase that promotes cell growth in many human cancers. A series of functional experiments were conducted to explore the role of miR-421/KDM5A in ovarian cancer cells and their underlying molecular mechanisms. MATERIALS AND METHODS Public microarray databases were analyzed to assess KDM5A and miR-421 expression in ovarian cancer. KDM5A was predicted to be a target of miR-421 using software analysis. The expression of the miR-421/KDM5A regulatory axis in ovarian cancer and the mechanisms of its effects on proliferation, migration, and invasion of ovarian cancer cell lines were investigated. RESULTS Compared with normal ovarian tissues, the expression of KDM5A mRNA and protein was elevated (P<0.05), and miR-421 expression was reduced in ovarian cancer tissue (P<0.05). miR-421 was found to bind specifically to the KDM5A gene. Silencing KDM5A or overexpressing miR-421 significantly inhibited proliferation, migration, and invasion of OVCAR-8 and SKOV-3 cells. Similarly, compared with nude mice injected with cells transfected with empty capsids, the in vivo proliferation rate of OVCAR-8 cells after miR-421 overexpression was reduced significantly. CONCLUSION The miR-421/KDM5A regulatory axis plays an important role in the development and progression of ovarian cancer cells.
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Affiliation(s)
- Fang Ren
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Christina Shrestha
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Huirong Shi
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Fangfang Sun
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Minghui Zhang
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Yuan Cao
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Gailing Li
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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20
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Li M, Deng Y, Zhuo M, Zhou H, Kong X, Xia X, Su Z, Chen Q, Guo P, Mo P, Yu C, Li W. Demethylase-independent function of JMJD2D as a novel antagonist of p53 to promote Liver Cancer initiation and progression. Am J Cancer Res 2020; 10:8863-8879. [PMID: 32754284 PMCID: PMC7392006 DOI: 10.7150/thno.45581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/28/2020] [Indexed: 12/13/2022] Open
Abstract
Background: As a histone demethylase, JMJD2D can enhance gene expression by specifically demethylating H3K9me2/3 and plays an important role in promoting colorectal cancer progression. However, its role in liver cancer remains unclear. Methods: The expression of JMJD2D was examined in human liver cancer specimens and non-tumorous liver tissues by immunohistochemical or immunoblot analysis. JMJD2D expression was knocked down in liver cancer cells using small hairpin RNAs, and cells were analyzed with Western blot, real-time PCR, cell viability, colony formation, and flow cytometry assays. Cells were also grown as tumor xenografts in nude mice, and the tumor cell proliferation and apoptosis were measured by immunohistochemical analysis. The relationship between JMJD2D and p53 was studied by co-immunoprecipitation, chromatin immunoprecipitation, and electric mobility shift assay. Wild-type and JMJD2D-knockout mice were intraperitoneally injected with diethylnitrosamine (DEN) to induce liver tumors and the liver cancer initiation and progression were investigated. Results: JMJD2D was frequently upregulated in human liver cancer specimens compared with non-tumorous liver tissues. The overall survival of liver cancer patients with high JMJD2D expression was significantly decreased compared to that with low JMJD2D expression. JMJD2D knockdown reduced liver cancer cell proliferation and xenograft tumor growth, sensitized cells to chemotherapeutic drug-induced apoptosis, and increased the expression of cell cycle inhibitor p21 and pro-apoptosis gene PUMA. Genetically, JMJD2D deficiency protected mice against DEN-induced liver cancer initiation and progression. Knockout of tumor suppressor p53 significantly reduced the effects of JMJD2D knockdown on cell proliferation, apoptosis, and the expression of p21 and PUMA, suggesting that JMJD2D regulates liver cancer cell functions in part through inhibiting p53 signaling pathway. Mechanistically, JMJD2D directly interacted with p53 and inhibited p53 recruitment to the p21 and PUMA promoters in a demethylation activity-independent manner, implicating a demethylase-independent function of JMJD2D as a novel p53 antagonist. In addition, JMJD2D could activate Wnt/β-catenin signaling to promote liver cancer cell proliferation. Conclusion: Our study demonstrates that JMJD2D can antagonize the tumor suppressor p53 and activate an oncogenic signaling pathway (such as Wnt/β-catenin signaling pathway) simultaneously to promote liver cancer initiation and progression, suggesting that JMJD2D may serve as a novel target for liver cancer treatment.
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Jaikhan P, Buranrat B, Itoh Y, Chotitumnavee J, Kurohara T, Suzuki T. Identification of ortho-hydroxy anilide as a novel scaffold for lysine demethylase 5 inhibitors. Bioorg Med Chem Lett 2019; 29:1173-1176. [DOI: 10.1016/j.bmcl.2019.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 01/06/2023]
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22
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Raman P, Zimmerman S, Rathi KS, de Torrenté L, Sarmady M, Wu C, Leipzig J, Taylor DM, Tozeren A, Mar JC. A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data. Cancer Genet 2019; 235-236:1-12. [PMID: 31296308 DOI: 10.1016/j.cancergen.2019.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 01/29/2023]
Abstract
Identifying genetic biomarkers of patient survival remains a major goal of large-scale cancer profiling studies. Using gene expression data to predict the outcome of a patient's tumor makes biomarker discovery a compelling tool for improving patient care. As genomic technologies expand, multiple data types may serve as informative biomarkers, and bioinformatic strategies have evolved around these different applications. For categorical variables such as a gene's mutation status, biomarker identification to predict survival time is straightforward. However, for continuous variables like gene expression, the available methods generate highly-variable results, and studies on best practices are lacking. We investigated the performance of eight methods that deal specifically with continuous data. K-means, Cox regression, concordance index, D-index, 25th-75th percentile split, median-split, distribution-based splitting, and KaplanScan were applied to four RNA-sequencing (RNA-seq) datasets from the Cancer Genome Atlas. The reliability of the eight methods was assessed by splitting each dataset into two groups and comparing the overlap of the results. Gene sets that had been identified from the literature for a specific tumor type served as positive controls to assess the accuracy of each biomarker using receiver operating characteristic (ROC) curves. Artificial RNA-Seq data were generated to test the robustness of these methods under fixed levels of gene expression noise. Our results show that methods based on dichotomizing tend to have consistently poor performance while C-index, D-index, and k-means perform well in most settings. Overall, the Cox regression method had the strongest performance based on tests of accuracy, reliability, and robustness.
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Affiliation(s)
- Pichai Raman
- School of Biomedical Engineering, Sciences and Health Systems, Drexel University, Philadelphia, PA, United States; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
| | - Samuel Zimmerman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Komal S Rathi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
| | - Laurence de Torrenté
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Chao Wu
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.
| | - Jeremy Leipzig
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; College of Computing and Informatics, Drexel University, Philadelphia, PA, United States.
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; The Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Aydin Tozeren
- School of Biomedical Engineering, Sciences and Health Systems, Drexel University, Philadelphia, PA, United States.
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.
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McCann TS, Sobral LM, Self C, Hsieh J, Sechler M, Jedlicka P. Biology and targeting of the Jumonji-domain histone demethylase family in childhood neoplasia: a preclinical overview. Expert Opin Ther Targets 2019; 23:267-280. [PMID: 30759030 DOI: 10.1080/14728222.2019.1580692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Epigenetic mechanisms of gene regulatory control play fundamental roles in developmental morphogenesis, and, as more recently appreciated, are heavily implicated in the onset and progression of neoplastic disease, including cancer. Many epigenetic mechanisms are therapeutically targetable, providing additional incentive for understanding of their contribution to cancer and other types of neoplasia. Areas covered: The Jumonji-domain histone demethylase (JHDM) family exemplifies many of the above traits. This review summarizes the current state of knowledge of the functions and pharmacologic targeting of JHDMs in cancer and other neoplastic processes, with an emphasis on diseases affecting the pediatric population. Expert opinion: To date, the JHDM family has largely been studied in the context of normal development and adult cancers. In contrast, comparatively few studies have addressed JHDM biology in cancer and other neoplastic diseases of childhood, especially solid (non-hematopoietic) neoplasms. Encouragingly, the few available examples support important roles for JHDMs in pediatric neoplasia, as well as potential roles for JHDM pharmacologic inhibition in disease management. Further investigations of JHDMs in cancer and other types of neoplasia of childhood can be expected to both enlighten disease biology and inform new approaches to improve disease outcomes.
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Affiliation(s)
- Tyler S McCann
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Lays M Sobral
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Chelsea Self
- b Department of Pediatrics , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Joseph Hsieh
- c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Marybeth Sechler
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Paul Jedlicka
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
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