51
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Halib N, Pavan N, Trombetta C, Dapas B, Farra R, Scaggiante B, Grassi M, Grassi G. An Overview of siRNA Delivery Strategies for Urological Cancers. Pharmaceutics 2022; 14:pharmaceutics14040718. [PMID: 35456552 PMCID: PMC9030829 DOI: 10.3390/pharmaceutics14040718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
The treatment of urological cancers has been significantly improved in recent years. However, for the advanced stages of these cancers and/or for those developing resistance, novel therapeutic options need to be developed. Among the innovative strategies, the use of small interfering RNA (siRNA) seems to be of great therapeutic interest. siRNAs are double-stranded RNA molecules which can specifically target virtually any mRNA of pathological genes. For this reason, siRNAs have a great therapeutic potential for human diseases including urological cancers. However, the fragile nature of siRNAs in the biological environment imposes the development of appropriate delivery systems to protect them. Thus, ensuring siRNA reaches its deep tissue target while maintaining structural and functional integrity represents one of the major challenges. To reach this goal, siRNA-based therapies require the development of fine, tailor-made delivery systems. Polymeric nanoparticles, lipid nanoparticles, nanobubbles and magnetic nanoparticles are among nano-delivery systems studied recently to meet this demand. In this review, after an introduction about the main features of urological tumors, we describe siRNA characteristics together with representative delivery systems developed for urology applications; the examples reported are subdivided on the basis of the different delivery materials and on the different urological cancers.
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Affiliation(s)
- Nadia Halib
- Department of Basic Sciences & Oral Biology, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur 55100, Malaysia;
| | - Nicola Pavan
- Urology Clinic, Department of Medical, Surgical and Health Science, University of Trieste, I-34149 Trieste, Italy; (N.P.); (C.T.)
| | - Carlo Trombetta
- Urology Clinic, Department of Medical, Surgical and Health Science, University of Trieste, I-34149 Trieste, Italy; (N.P.); (C.T.)
| | - Barbara Dapas
- Department of Life Sciences, Cattinara University Hospital, Trieste University, Strada di Fiume 447, I-34149 Trieste, Italy; (B.D.); (R.F.); (B.S.)
| | - Rossella Farra
- Department of Life Sciences, Cattinara University Hospital, Trieste University, Strada di Fiume 447, I-34149 Trieste, Italy; (B.D.); (R.F.); (B.S.)
| | - Bruna Scaggiante
- Department of Life Sciences, Cattinara University Hospital, Trieste University, Strada di Fiume 447, I-34149 Trieste, Italy; (B.D.); (R.F.); (B.S.)
| | - Mario Grassi
- Department of Engineering and Architecture, Trieste University, Via Valerio 6, I-34127 Trieste, Italy;
| | - Gabriele Grassi
- Department of Life Sciences, Cattinara University Hospital, Trieste University, Strada di Fiume 447, I-34149 Trieste, Italy; (B.D.); (R.F.); (B.S.)
- Correspondence: ; Tel.: +39-040-399-3227
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52
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Hara N, Sawada Y. Epigenetics of Cutaneous T-Cell Lymphomas. Int J Mol Sci 2022; 23:ijms23073538. [PMID: 35408897 PMCID: PMC8998216 DOI: 10.3390/ijms23073538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Epigenetic modifications rarely occur in isolation (as single “epigenetic modifications”). They usually appear together and form a network to control the epigenetic system. Cutaneous malignancies are usually affected by epigenetic changes. However, there is limited knowledge regarding the epigenetic changes associated with cutaneous lymphomas. In this review, we focused on cutaneous T-cell lymphomas such as mycosis fungoides, Sézary syndrome, and anaplastic large cell lymphoma. With regard to epigenetic changes, we summarize the detailed chemical modifications categorized into DNA methylation and histone acetylation and methylation. We also summarize the epigenetic modifications and characteristics of the drug for cutaneous T-cell lymphoma (CTCL). Furthermore, we discuss current research on epigenetic-targeted therapy against cutaneous T-cell lymphomas. Although the current method of treatment with histone deacetylase inhibitors does not exhibit sufficient therapeutic benefits in all cases of CTCL, epigenetic-targeted combination therapy might overcome this limitation for patients with CTCL.
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Son J, Huang S, Zeng Q, Bricker TL, Case JB, Zhou J, Zang R, Liu Z, Chang X, Darling TL, Xu J, Harastani HH, Chen L, Gomez Castro MF, Zhao Y, Kohio HP, Hou G, Fan B, Niu B, Guo R, Rothlauf PW, Bailey AL, Wang X, Shi PY, Martinez ED, Brody SL, Whelan SPJ, Diamond MS, Boon ACM, Li B, Ding S. JIB-04 Has Broad-Spectrum Antiviral Activity and Inhibits SARS-CoV-2 Replication and Coronavirus Pathogenesis. mBio 2022; 13:e0337721. [PMID: 35038906 PMCID: PMC8764536 DOI: 10.1128/mbio.03377-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/09/2021] [Indexed: 01/18/2023] Open
Abstract
Pathogenic coronaviruses are a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified small-molecule inhibitors that potently block the replication of severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with a 50% effective concentration of 695 nM, with a specificity index of greater than 1,000. JIB-04 showed in vitro antiviral activity in multiple cell types, including primary human bronchial epithelial cells, against several DNA and RNA viruses, including porcine coronavirus transmissible gastroenteritis virus. In an in vivo porcine model of coronavirus infection, administration of JIB-04 reduced virus infection and associated tissue pathology, which resulted in improved weight gain and survival. These results highlight the potential utility of JIB-04 as an antiviral agent against SARS-CoV-2 and other viral pathogens. IMPORTANCE The coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2 infection, is an ongoing public health disaster worldwide. Although several vaccines are available as a preventive measure and the FDA approval of an orally bioavailable drug is on the horizon, there remains a need for developing antivirals against SARS-CoV-2 that could work on the early course of infection. By using infectious reporter viruses, we screened small-molecule inhibitors for antiviral activity against SARS-CoV-2. Among the top hits was JIB-04, a compound previously studied for its anticancer activity. Here, we showed that JIB-04 inhibits the replication of SARS-CoV-2 as well as different DNA and RNA viruses. Furthermore, JIB-04 conferred protection in a porcine model of coronavirus infection, although to a lesser extent when given as therapeutic rather than prophylactic doses. Our findings indicate a limited but still promising utility of JIB-04 as an antiviral agent in the combat against COVID-19 and potentially other viral diseases.
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Affiliation(s)
- Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Program in Molecular Cell Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shimeng Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Traci L. Bricker
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - James Brett Case
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xinjian Chang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Tamarand L. Darling
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jian Xu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Houda H. Harastani
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Yongxiang Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Hinissan P. Kohio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Beibei Niu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam L. Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xin Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Steven L. Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S. Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adrianus C. M. Boon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Therapeutical interference with the epigenetic landscape of germ cell tumors: a comparative drug study and new mechanistical insights. Clin Epigenetics 2022; 14:5. [PMID: 34996497 PMCID: PMC8742467 DOI: 10.1186/s13148-021-01223-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/18/2021] [Indexed: 12/18/2022] Open
Abstract
Background Type II germ cell tumors (GCT) are the most common solid cancers in males of age 15 to 35 years. Treatment of these tumors includes cisplatin-based therapy achieving high cure rates, but also leading to late toxicities. As mainly young men are suffering from GCTs, late toxicities play a major role regarding life expectancy, and the development of therapy resistance emphasizes the need for alternative therapeutic options. GCTs are highly susceptible to interference with the epigenetic landscape; therefore, this study focuses on screening of drugs against epigenetic factors as a treatment option for GCTs.
Results We present seven different epigenetic inhibitors efficiently decreasing cell viability in GCT cell lines including cisplatin-resistant subclones at low concentrations by targeting epigenetic modifiers and interactors, like histone deacetylases (Quisinostat), histone demethylases (JIB-04), histone methyltransferases (Chaetocin), epigenetic readers (MZ-1, LP99) and polycomb-repressive complexes (PRT4165, GSK343). Mass spectrometry-based analyses of the histone modification landscape revealed effects beyond the expected mode-of-action of each drug, suggesting a wider spectrum of activity than initially assumed. Moreover, we characterized the effects of each drug on the transcriptome of GCT cells by RNA sequencing and found common deregulations in gene expression of ion transporters and DNA-binding factors. A kinase array revealed deregulations of signaling pathways, like cAMP, JAK-STAT and WNT. Conclusion Our study identified seven drugs against epigenetic modifiers to treat cisplatin-resistant GCTs. Further, we extensively analyzed off-target effects and modes-of-action, which are important for risk assessment of the individual drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01223-1.
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55
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Lapidot M, Saladi SV, Salgia R, Sattler M. Novel Therapeutic Targets and Immune Dysfunction in Malignant Pleural Mesothelioma. Front Pharmacol 2022; 12:806570. [PMID: 35069219 PMCID: PMC8776703 DOI: 10.3389/fphar.2021.806570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Advances in the treatment of malignant pleural mesothelioma (MPM) have been disappointing, despite the apparent need for new therapeutic options for this rare and devastating cancer. Drug resistance is common and surgical intervention has brought benefits only to a subset of patients. MPM is a heterogenous disease with a surprisingly low mutation rate and recent sequencing efforts have confirmed alterations in a limited number of tumor suppressors that do not provide apparent insights into the molecular mechanisms that drive this malignancy. There is increasing evidence that epigenetic regulation leads to immune evasion and transformation in MPM. Further, the low efficacy of immune checkpoint inhibitors is consistent with a suppression of genes involved in the anti-tumor immune response. We review three promising emerging therapeutic targets (STAT3, KDM4A, heparanase) and highlight their potential effects on the immune response.
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Affiliation(s)
- Moshe Lapidot
- Department of Thoracic Surgery, Galilee Medical Center, Nahariya, Israel
| | - Srinivas Vinod Saladi
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, United States
| | - Martin Sattler
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
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56
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Tran TA, Zhang QJ, Wang L, Gonzales C, Girard L, May H, Gillette T, Liu ZP, Martinez ED. Inhibition of Jumonji demethylases reprograms severe dilated cardiomyopathy and prolongs survival. J Biol Chem 2021; 298:101515. [PMID: 34933013 PMCID: PMC8803621 DOI: 10.1016/j.jbc.2021.101515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022] Open
Abstract
Hypertrophic/dilated cardiomyopathy, often a prequel to heart failure, is accompanied by maladaptive transcriptional changes that contribute to arrythmias and contractile misfunction. Transgenic mice constitutively expressing high levels of calcineurin are known to develop extreme heart hypertrophy, which progresses to dilated cardiomyopathy, and to die several weeks after birth. Here, we characterized aberrant transcriptional and epigenetic pathways in this mouse model and established a pharmacological approach to treat established cardiomyopathy. We found that H3K4me3 (trimethyl histone 3 lysine 4) and H3K9me3 (trimethyl histone 3 lysine 9) Jumonji histone demethylases are markedly increased at the protein level and show enhanced enzymatic activity in diseased hearts. These epigenetic regulators continued to increase with time, further affecting cardiac gene expression. Our findings parallel the lower H3K4me3 and H3K9me3 levels seen in human patients. Inhibition of Jumonji demethylase activities in vivo results in lower histone demethylase enzymatic function in the heart and higher histone methylation levels and leads to partial reduction of heart size, reversal of maladaptive transcriptional programs, improved heart function, and prolonged survival. At the molecular level, target genes of transcription factor myocyte enhancer factor 2 are specifically regulated in response to pharmacological or genetic inhibition of Jumonji demethylases. Similar transcriptional reversal of disease-associated genes is seen in a second disease model based on cardiac mechanical overload. Our findings validate pharmacological inhibitors of Jumonji demethylases as potential therapeutics for the treatment of cardiomyopathies across disease models and provide evidence of the reversal of maladaptive transcriptional reprogramming leading to partial restoration of cardiac function. In addition, this study defines pathways of therapeutic resistance upregulated with disease progression.
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Affiliation(s)
- Tram Anh Tran
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX; Department of Pharmacology, UT Southwestern Medical Center, Dallas TX
| | - Qing-Jun Zhang
- Department of Cardiology, UT Southwestern Medical Center, Dallas TX
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX
| | - Christopher Gonzales
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX
| | - Herman May
- Department of Cardiology, UT Southwestern Medical Center, Dallas TX
| | - Thomas Gillette
- Department of Cardiology, UT Southwestern Medical Center, Dallas TX
| | - Zhi-Ping Liu
- Department of Cardiology, UT Southwestern Medical Center, Dallas TX.
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX; Department of Pharmacology, UT Southwestern Medical Center, Dallas TX.
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57
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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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PCBP1 regulates the transcription and alternative splicing of metastasis‑related genes and pathways in hepatocellular carcinoma. Sci Rep 2021; 11:23356. [PMID: 34857818 PMCID: PMC8640068 DOI: 10.1038/s41598-021-02642-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/03/2021] [Indexed: 02/08/2023] Open
Abstract
PCBP1 is a multifunctional RNA-binding protein (RBP) expressed in most human cells and is involved in posttranscriptional gene regulation. PCBP1 regulates the alternative splicing, translation and RNA stability of many cancer-related genes and has been identified as a potential tumour suppressor gene. PCBP1 inhibits the invasion of hepatocellular carcinoma (HCC) cells, but there are few studies on the specific regulatory target and mechanism of RBPs in HCC, and it is unclear whether PCBP1 plays a role in tumour metastasis as a splicing factor. We analysed the regulation of gene expression by PCBP1 at the transcriptional level. We obtained and analysed PCBP1-knockdown RNA-seq data and eCLIP-seq data of PCBP1 in HepG2 cells and found that PCBP1 widely regulates the alternative splicing and expression of genes enriched in cancer-related pathways, including extracellular matrix, cell adhesion, small molecule metabolic process and apoptosis. We validated five regulated alternative splicing events affected by PCBP1 using RT-qPCR and found that there was a significant difference in the expression of APOC1 and SPHK1 between tumour and normal tissues. In this study, we provided convincing evidence that human PCBP1 profoundly regulates the splicing of genes associated with tumour metastasis. These findings provide new insight into potential markers or therapeutic targets for HCC treatment.
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59
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Moorlag SJCFM, Matzaraki V, van Puffelen JH, van der Heijden C, Keating S, Groh L, Röring RJ, Bakker OB, Koeken VACM, de Bree LCJ, Smeekens SP, Oosting M, Gamboa RA, Riksen NP, Xavier RJ, Wijmenga C, Kumar V, van Crevel R, Novakovic B, Joosten LAB, Li Y, Netea MG. An integrative genomics approach identifies KDM4 as a modulator of trained immunity. Eur J Immunol 2021; 52:431-446. [PMID: 34821391 PMCID: PMC9299854 DOI: 10.1002/eji.202149577] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 09/29/2021] [Accepted: 11/19/2021] [Indexed: 01/21/2023]
Abstract
Innate immune cells are able to build memory characteristics via a process termed “trained immunity.” Host factors that influence the magnitude of the individual trained immunity response remain largely unknown. Using an integrative genomics approach, our study aimed to prioritize and understand the role of specific genes in trained immunity responses. In vitro‐induced trained immunity responses were assessed in two independent population‐based cohorts of healthy individuals, the 300 Bacillus Calmette‐Guérin (300BCG; n = 267) and 200 Functional Genomics (200FG; n = 110) cohorts from the Human Functional Genomics Project. Genetic loci that influence cytokine responses upon trained immunity were identified by conducting a meta‐analysis of QTLs identified in the 300BCG and 200FG cohorts. From the identified QTL loci, we functionally validated the role of PI3K‐Akt signaling pathway and two genes that belong to the family of Siglec receptors (Siglec‐5 and Siglec‐14). Furthermore, we identified the H3K9 histone demethylases of the KDM4 family as major regulators of trained immunity responses. These data pinpoint an important role of metabolic and epigenetic processes in the regulation of trained immunity responses, and these findings may open new avenues for vaccine design and therapeutic interventions.
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Affiliation(s)
- Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelmer H van Puffelen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sam Keating
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laszlo Groh
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rutger Jan Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark.,Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raúl Aguirre Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands.,K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Norway
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Boris Novakovic
- Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, and Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hannover, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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60
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Silva VR, Santos LDS, Dias RB, Quadros CA, Bezerra DP. Emerging agents that target signaling pathways to eradicate colorectal cancer stem cells. Cancer Commun (Lond) 2021; 41:1275-1313. [PMID: 34791817 PMCID: PMC8696218 DOI: 10.1002/cac2.12235] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/28/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) represents the third most commonly diagnosed cancer and the second leading cause of cancer death worldwide. The modern concept of cancer biology indicates that cancer is formed of a small population of cells called cancer stem cells (CSCs), which present both pluripotency and self-renewal properties. These cells are considered responsible for the progression of the disease, recurrence and tumor resistance. Interestingly, some cell signaling pathways participate in CRC survival, proliferation, and self-renewal properties, and most of them are dysregulated in CSCs, including the Wingless (Wnt)/β-catenin, Notch, Hedgehog, nuclear factor kappa B (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), peroxisome proliferator-activated receptor (PPAR), phosphatidyl-inositol-3-kinase/Akt/mechanistic target of rapamycin (PI3K/Akt/mTOR), and transforming growth factor-β (TGF-β)/Smad pathways. In this review, we summarize the strategies for eradicating CRC stem cells by modulating these dysregulated pathways, which will contribute to the study of potential therapeutic schemes, combining conventional drugs with CSC-targeting drugs, and allowing better cure rates in anti-CRC therapy.
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Affiliation(s)
- Valdenizia R Silva
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Luciano de S Santos
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Rosane B Dias
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Claudio A Quadros
- São Rafael Hospital, Rede D'Or/São Luiz, Salvador, Bahia, 41253-190, Brazil.,Bahia State University, Salvador, Bahia, 41150-000, Brazil
| | - Daniel P Bezerra
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
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61
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Fang W, Liao C, Shi R, Simon JM, Ptacek TS, Zurlo G, Ye Y, Han L, Fan C, Bao L, Ortiz CL, Lin HR, Manocha U, Luo W, Peng Y, Kim WY, Yang LW, Zhang Q. ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer. eLife 2021; 10:e70412. [PMID: 34779768 PMCID: PMC8673836 DOI: 10.7554/elife.70412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/14/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease, which warrants the critical need to identify new therapeutic targets. We show that Zinc Fingers and Homeoboxes 2 (ZHX2) is amplified or overexpressed in TNBC cell lines and patients. Functionally, depletion of ZHX2 inhibited TNBC cell growth and invasion in vitro, orthotopic tumor growth, and spontaneous lung metastasis in vivo. Mechanistically, ZHX2 bound with hypoxia-inducible factor (HIF) family members and positively regulated HIF1α activity in TNBC. Integrated ChIP-seq and gene expression profiling demonstrated that ZHX2 co-occupied with HIF1α on transcriptionally active promoters marked by H3K4me3 and H3K27ac, thereby promoting gene expression. Among the identified ZHX2 and HIF1α coregulated genes, overexpression of AP2B1, COX20, KDM3A, or PTGES3L could partially rescue TNBC cell growth defect by ZHX2 depletion, suggested that these downstream targets contribute to the oncogenic role of ZHX2 in an accumulative fashion. Furthermore, multiple residues (R491, R581, and R674) on ZHX2 are important in regulating its phenotype, which correspond with their roles on controlling ZHX2 transcriptional activity in TNBC cells. These studies establish that ZHX2 activates oncogenic HIF1α signaling, therefore serving as a potential therapeutic target for TNBC.
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Affiliation(s)
- Wentong Fang
- Department of Pharmacy, The First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Rachel Shi
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- Department of Genetics, Neuroscience Center; University of North Carolina School of MedicineChapel HillUnited States
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
| | - Giada Zurlo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Youqiong Ye
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical SchoolHoustonUnited States
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lei Bao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Christopher Llynard Ortiz
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Department of Chemistry, National Tsing-Hua UniversityHsinchuTaiwan
| | - Hong-Rui Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Weibo Luo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Physics Division, National Center for Theoretical SciencesHsinchuTaiwan
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
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62
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Carter DM, Specker E, Małecki PH, Przygodda J, Dudaniec K, Weiss MS, Heinemann U, Nazaré M, Gohlke U. Enhanced Properties of a Benzimidazole Benzylpyrazole Lysine Demethylase Inhibitor: Mechanism-of-Action, Binding Site Analysis, and Activity in Cellular Models of Prostate Cancer. J Med Chem 2021; 64:14266-14282. [PMID: 34555281 DOI: 10.1021/acs.jmedchem.1c00693] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Jumonji domain-containing lysine demethylase (KDM) enzymes are encoded by genes of the KDM superfamily. Activities of the KDM4 subfamily promote aggressive phenotypes associated with prostate cancer (PCa). Previously, we discovered a benzimidazole pyrazole molecule that inhibited KDM4 isoforms with properties tractable for development. Here, we demonstrate that a benzyl-substituted variant of this inhibitor exhibits improved potency in biochemical assays, is cell-permeable, and kills PCa cells at low micromolar concentrations. By X-ray crystallography and kinetics-based assays, we demonstrate that the mechanism of inhibition is complex, proceeding via competition with the enzyme for binding of active-site Fe2+ and by populating a distal site on the enzyme surface. Furthermore, we provide evidence that the inhibitor's cytostatic properties arise from direct intracellular inhibition of KDM4 enzymes. PCa cells treated with the inhibitor exhibit reduced expression of genes regulated by the androgen receptor, an outcome accompanied by epigenetic maintenance of a heterochromatic state.
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Affiliation(s)
- David M Carter
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Piotr H Małecki
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany.,Helmholtz-Zentrum Berlin (HZB) Macromolecular Crystallography, Berlin 14109, Germany
| | - Jessica Przygodda
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Krystyna Dudaniec
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin (HZB) Macromolecular Crystallography, Berlin 14109, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
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63
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Essential role of the histone lysine demethylase KDM4A in the biology of malignant pleural mesothelioma (MPM). Br J Cancer 2021; 125:582-592. [PMID: 34088988 PMCID: PMC8368004 DOI: 10.1038/s41416-021-01441-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with a dismal prognosis. There is increasing interest in targeting chromatin regulatory pathways in difficult-to-treat cancers. In preliminary studies, we found that KDM4A (lysine-specific histone demethylase 4) was overexpressed in MPM. METHODS KDM4A protein expression was determined by immunohistochemistry or immunoblotting. Functional inhibition of KDM4A by targeted knockdown and small molecule drugs was correlated to cell growth using cell lines and a xenograft mouse model. Gene expression profiling was performed to identify KDM4A-dependent signature pathways. RESULTS Levels of KDM4A were found to be significantly elevated in MPM patients compared to normal mesothelial tissue. Inhibiting the enzyme activity efficiently reduced cell growth in vitro and reduced tumour growth in vivo. KDM4A inhibitor-induced apoptosis was further enhanced by the BH3 mimetic navitoclax. KDM4A expression was associated with pathways involved in cell growth and DNA repair. Interestingly, inhibitors of the DNA damage and replication checkpoint regulators CHK1 (prexasertib) and WEE1 (adavosertib) within the DNA double-strand break repair pathway, cooperated in the inhibition of cell growth. CONCLUSIONS The results establish a novel and essential role for KDM4A in growth in preclinical models of MPM and identify potential therapeutic approaches to target KDM4A-dependent vulnerabilities.
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64
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Fang Z, Liu Y, Zhang R, Chen Q, Wang T, Yang W, Fan Y, Yu C, Xiang R, Yang S. Discovery of a potent and selective inhibitor of histone lysine demethylase KDM4D. Eur J Med Chem 2021; 223:113662. [PMID: 34237635 DOI: 10.1016/j.ejmech.2021.113662] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/03/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023]
Abstract
Histone lysine demethylase 4D (KDM4D) plays an important role in the regulation of tumorigenesis, progression and drug resistance and has been considered a potential target for cancer treatment. However, there is still a lack of potent and selective KDM4D inhibitors. In this investigation, we report a new class of KDM4D inhibitors containing the 2-(aryl(pyrrolidine-1-yl)methyl)phenol scaffold, identified through AlphaLisa-based screening, structural optimization, and structure-activity relationship analyses. Among these inhibitors, 24s was the most potent, with an IC50 value of 0.023 ± 0.004 μM. This compound exhibited more than 1500-fold selectivity towards KDM4D versus KDM4A as well as other JMJD subfamily members, indicating good selectivity for KDM4D. Kinetic analysis indicated that 24s did not occupy the 2-oxoglutarate binding pocket. In an in vitro assay, 24s significantly suppressed the proliferation and migration of colorectal cancer (CRC) cells. Overall, this study has identified a good tool compound to explore the biological function of KDM4D and a good lead compound for drug discovery targeting KDM4D.
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Affiliation(s)
- Zhen Fang
- Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China
| | - Yang Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China
| | - Rong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China
| | - Qiang Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Fujian, 361102, China
| | - Tianqi Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Wei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China
| | - Yan Fan
- Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Chundong Yu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Fujian, 361102, China.
| | - Rong Xiang
- Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China.
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65
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Punnia-Moorthy G, Hersey P, Emran AA, Tiffen J. Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers. Front Genet 2021; 12:680633. [PMID: 34220955 PMCID: PMC8242339 DOI: 10.3389/fgene.2021.680633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been implicated in a variety of pathological processes including carcinogenesis. A major group of enzymes that influence epigenetic modifications are lysine demethylases (KDMs) also known as "erasers" which remove methyl groups on lysine (K) amino acids of histones. Numerous studies have implicated aberrant lysine demethylase activity in a variety of cancers, including melanoma. This review will focus on the structure, classification and functions of KDMs in normal biology and the current knowledge of how KDMs are deregulated in cancer pathogenesis, emphasizing our interest in melanoma. We highlight the current knowledge gaps of KDMs in melanoma pathobiology and describe opportunities to increases our understanding of their importance in this disease. We summarize the progress of several pre-clinical compounds that inhibit KDMs and represent promising candidates for further investigation in oncology.
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Affiliation(s)
- Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Abdullah Al Emran
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Jessamy Tiffen
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
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66
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Son J, Huang S, Zeng Q, Bricker TL, Case JB, Zhou J, Zang R, Liu Z, Chang X, Harastani HH, Chen L, Castro MFG, Zhao Y, Kohio HP, Hou G, Fan B, Niu B, Guo R, Rothlauf PW, Bailey AL, Wang X, Shi PY, Martinez ED, Whelan SP, Diamond MS, Boon AC, Li B, Ding S. JIB-04 has broad-spectrum antiviral activity and inhibits SARS-CoV-2 replication and coronavirus pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.09.24.312165. [PMID: 32995798 PMCID: PMC7523209 DOI: 10.1101/2020.09.24.312165] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pathogenic coronaviruses represent a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified several small-molecule inhibitors that potently block the replication of the newly emerged severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with an EC50 of 695 nM, with a specificity index of greater than 1,000. JIB-04 showed in vitro antiviral activity in multiple cell types against several DNA and RNA viruses, including porcine coronavirus transmissible gastroenteritis virus. In an in vivo porcine model of coronavirus infection, administration of JIB-04 reduced virus infection and associated tissue pathology, which resulted in improved weight gain and survival. These results highlight the potential utility of JIB-04 as an antiviral agent against SARS-CoV-2 and other viral pathogens.
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Affiliation(s)
- Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Program in Molecular Cell Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Shimeng Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Traci L. Bricker
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xinjian Chang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Houda H. Harastani
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | - Yongxiang Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hinissan P. Kohio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Beibei Niu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Adam L. Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S. Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrianus C.M. Boon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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Baby S, Gurukkala Valapil D, Shankaraiah N. Unravelling KDM4 histone demethylase inhibitors for cancer therapy. Drug Discov Today 2021; 26:1841-1856. [PMID: 34051367 DOI: 10.1016/j.drudis.2021.05.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic enzyme-targeted therapy is a promising new development in the field of drug discovery. To date, histone deacetylases and DNA methyltransferases have been investigated as druggable epigenetic enzyme targets in cancer therapeutics. Histone methyltransferases and lysine demethylase inhibitors are the latest groups of epi-drugs being actively studied in clinical trials. KDM4s are JmjC domain-containing histone H3 lysine 9/36 demethylase enzymes, belonging to the 2-OG-dependent oxygenases, which are upregulated in multiple malignancies. In the recent years, these enzymes have captured much attention as a novel target in cancer therapy. Herein, we traverse the discovery path and current challenges in designing potent KDM4 inhibitors as potential anticancer agents. We discuss the considerable efforts and proposed future strategies to develop selective small molecule inhibitors of KDM4s, highlighting scaffold candidates and cyclic skeletons for which activity data, selectivity profiles and structure-activity relationships (SARs) have been studied.
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Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Durgesh Gurukkala Valapil
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India.
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68
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From Laboratory Studies to Clinical Trials: Temozolomide Use in IDH-Mutant Gliomas. Cells 2021; 10:cells10051225. [PMID: 34067729 PMCID: PMC8157002 DOI: 10.3390/cells10051225] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss the use of the alkylating agent temozolomide (TMZ) in the treatment of IDH-mutant gliomas. We describe the challenges associated with TMZ in clinical (drug resistance and tumor recurrence) and preclinical settings (variabilities associated with in vitro models) in treating IDH-mutant glioma. Lastly, we summarize the emerging therapeutic targets that can potentially be used in combination with TMZ.
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69
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Bhan A, Ansari KI, Chen MY, Jandial R. Inhibition of Jumonji Histone Demethylases Selectively Suppresses HER2 + Breast Leptomeningeal Carcinomatosis Growth via Inhibition of GMCSF Expression. Cancer Res 2021; 81:3200-3214. [PMID: 33941612 DOI: 10.1158/0008-5472.can-20-3317] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/17/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
HER2+ breast leptomeningeal carcinomatosis (HER2+ LC) occurs when tumor cells spread to cerebrospinal fluid-containing leptomeninges surrounding the brain and spinal cord, a complication with a dire prognosis. HER2+ LC remains incurable, with few treatment options. Currently, much effort is devoted toward development of therapies that target mutations. However, targeting epigenetic or transcriptional states of HER2+ LC tumors might efficiently target HER2+ LC growth via inhibition of oncogenic signaling; this approach remains promising but is less explored. To test this possibility, we established primary HER2+ LC (Lepto) cell lines from nodular HER2+ LC tissues. These lines are phenotypically CD326+CD49f-, confirming that they are derived from HER2+ LC tumors, and express surface CD44+CD24-, a cancer stem cell (CSC) phenotype. Like CSCs, Lepto lines showed greater drug resistance and more aggressive behavior compared with other HER2+ breast cancer lines in vitro and in vivo. Interestingly, the three Lepto lines overexpressed Jumonji domain-containing histone lysine demethylases KDM4A/4C. Treatment with JIB04, a selective inhibitor of Jumonji demethylases, or genetic loss of function of KDM4A/4C induced apoptosis and cell-cycle arrest and reduced Lepto cell viability, tumorsphere formation, regrowth, and invasion in vitro. JIB04 treatment of patient-derived xenograft mouse models in vivo reduced HER2+ LC tumor growth and prolonged animal survival. Mechanistically, KDM4A/4C inhibition downregulated GMCSF expression and prevented GMCSF-dependent Lepto cell proliferation. Collectively, these results establish KDM4A/4C as a viable therapeutic target in HER2+ LC and spotlight the benefits of targeting the tumorigenic transcriptional network. SIGNIFICANCE: HER2+ LC tumors overexpress KDM4A/4C and are sensitive to the Jumonji demethylase inhibitor JIB04, which reduces the viability of primary HER2+ LC cells and increases survival in mouse models.
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Affiliation(s)
- Arunoday Bhan
- Division of Neurosurgery, Beckman Research Institute, City of Hope, Duarte, California
| | - Khairul I Ansari
- Division of Neurosurgery, Beckman Research Institute, City of Hope, Duarte, California.,Celcuity, Minneapolis, Minnesota
| | - Mike Y Chen
- Division of Neurosurgery, Beckman Research Institute, City of Hope, Duarte, California
| | - Rahul Jandial
- Division of Neurosurgery, Beckman Research Institute, City of Hope, Duarte, California.
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70
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Krstic A, Konietzny A, Halasz M, Cain P, Oppermann U, Kolch W, Duffy DJ. A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma. Front Cell Dev Biol 2021; 9:612518. [PMID: 33968920 PMCID: PMC8097097 DOI: 10.3389/fcell.2021.612518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
Although a rare disease, neuroblastoma accounts for the highest proportion of childhood cancer deaths. There is a lack of recurrent somatic mutations in neuroblastoma embryonal tumours, suggesting a possible role for epigenetic alterations in driving this cancer. While an increasing number of reports suggest an association of MYCN with epigenetic machinery, the mechanisms of these interactions are poorly understood in the neuroblastoma setting. Utilising chemo-genomic approaches we revealed global MYCN-epigenetic interactions and identified numerous epigenetic proteins as MYCN targets. The epigenetic regulators HDAC2, CBX8 and CBP (CREBBP) were all MYCN target genes and also putative MYCN interactors. MYCN-related epigenetic genes included SMARCs, HDACs, SMYDs, BRDs and CREBBP. Expression levels of the majority of MYCN-related epigenetic genes showed predictive ability for neuroblastoma patient outcome. Furthermore, a compound library screen targeting epigenetic proteins revealed broad susceptibility of neuroblastoma cells to all classes of epigenetic regulators, belonging to families of bromodomains, HDACs, HATs, histone methyltransferases, DNA methyltransferases and lysin demethylases. Ninety-six percent of the compounds reduced MYCN-amplified neuroblastoma cell viability. We show that the C646 (CBP-bromodomain targeting compound) exhibits switch-like temporal and dose response behaviour and is effective at reducing neuroblastoma viability. Responsiveness correlates with MYCN expression, with MYCN-amplified cells being more susceptible to C646 treatment. Thus, exploiting the broad vulnerability of neuroblastoma cells to epigenetic targeting compounds represents an exciting strategy in neuroblastoma treatment, particularly for high-risk MYCN-amplified tumours.
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Affiliation(s)
- Aleksandar Krstic
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Anja Konietzny
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Molecular Neurobiology Hamburg (ZMNH), Emmy-Noether Group "Neuronal Protein Transport", University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Melinda Halasz
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Peter Cain
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Institute of Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Institute of Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Walter Kolch
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - David J Duffy
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, United States.,Department of Biology, University of Florida, Gainesville, FL, United States
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71
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Walters ZS, Aladowicz E, Villarejo-Balcells B, Nugent G, Selfe JL, Eve P, Blagg J, Rossanese O, Shipley J. Role for the Histone Demethylase KDM4B in Rhabdomyosarcoma via CDK6 and CCNA2: Compensation by KDM4A and Apoptotic Response of Targeting Both KDM4B and KDM4A. Cancers (Basel) 2021; 13:1734. [PMID: 33917420 PMCID: PMC8038694 DOI: 10.3390/cancers13071734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 01/10/2023] Open
Abstract
Histone demethylases are epigenetic modulators that play key roles in regulating gene expression related to many critical cellular functions and are emerging as promising therapeutic targets in a number of tumor types. We previously identified histone demethylase family members as overexpressed in the pediatric sarcoma, rhabdomyosarcoma. Here we show high sensitivity of rhabdomyosarcoma cells to a pan-histone demethylase inhibitor, JIB-04 and identify a key role for the histone demethylase KDM4B in rhabdomyosarcoma cell growth through an RNAi-screening approach. Decreasing KDM4B levels affected cell cycle progression and transcription of G1/S and G2/M checkpoint genes including CDK6 and CCNA2, which are bound by KDM4B in their promoter regions. However, after sustained knockdown of KDM4B, rhabdomyosarcoma cell growth recovered. We show that this can be attributed to acquired molecular compensation via recruitment of KDM4A to the promoter regions of CDK6 and CCNA2 that are otherwise bound by KDM4B. Furthermore, upfront silencing of both KDM4B and KDM4A led to RMS cell apoptosis, not seen by reducing either alone. To circumvent compensation and elicit stronger therapeutic responses, our study supports targeting histone demethylase sub-family proteins through selective poly-pharmacology as a therapeutic approach.
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Affiliation(s)
- Zoë S. Walters
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
- Cancer Sciences, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Ewa Aladowicz
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Barbara Villarejo-Balcells
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Gary Nugent
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Joanna L. Selfe
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Paul Eve
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Julian Blagg
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Olivia Rossanese
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
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72
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Connacher J, Josling GA, Orchard LM, Reader J, Llinás M, Birkholtz LM. H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum. Epigenetics Chromatin 2021; 14:19. [PMID: 33794978 PMCID: PMC8017609 DOI: 10.1186/s13072-021-00393-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program. However, the processes that drive the differentiation and development of the gametocyte post-commitment, remain largely unexplored. A previous study reported enrichment of H3K36 di- and tri-methylated (H3K36me2&3) histones in early-stage gametocytes. Using chromatin immunoprecipitation followed by high-throughput sequencing, we identify a stage-specific association between these repressive histone modifications and transcriptional reprogramming that define a stage II gametocyte transition point. Results Here, we show that H3K36me2 and H3K36me3 from stage II gametocytes are associated with repression of genes involved in asexual proliferation and sexual commitment, indicating that H3K36me2&3-mediated repression of such genes is essential to the transition from early gametocyte differentiation to intermediate development. Importantly, we show that the gene encoding the transcription factor AP2-G as commitment master regulator is enriched with H3K36me2&3 and actively repressed in stage II gametocytes, providing the first evidence of ap2-g gene repression in post-commitment gametocytes. Lastly, we associate the enhanced potency of the pan-selective Jumonji inhibitor JIB-04 in gametocytes with the inhibition of histone demethylation including H3K36me2&3 and a disruption of normal transcriptional programs. Conclusions Taken together, our results provide the first description of an association between global gene expression reprogramming and histone post-translational modifications during P. falciparum early sexual development. The stage II gametocyte-specific abundance of H3K36me2&3 manifests predominantly as an independent regulatory mechanism targeted towards genes that are repressed post-commitment. H3K36me2&3-associated repression of genes is therefore involved in key transcriptional shifts that accompany the transition from early gametocyte differentiation to intermediate development. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00393-9.
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Affiliation(s)
- Jessica Connacher
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Gabrielle A Josling
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lindsey M Orchard
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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73
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Khaliq M, Manikkam M, Martinez ED, Fallahi-Sichani M. Epigenetic modulation reveals differentiation state specificity of oncogene addiction. Nat Commun 2021; 12:1536. [PMID: 33750776 PMCID: PMC7943789 DOI: 10.1038/s41467-021-21784-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
Hyperactivation of the MAPK signaling pathway motivates the clinical use of MAPK inhibitors for BRAF-mutant melanomas. Heterogeneity in differentiation state due to epigenetic plasticity, however, results in cell-to-cell variability in the state of MAPK dependency, diminishing the efficacy of MAPK inhibitors. To identify key regulators of such variability, we screen 276 epigenetic-modifying compounds, individually or combined with MAPK inhibitors, across genetically diverse and isogenic populations of melanoma cells. Following single-cell analysis and multivariate modeling, we identify three classes of epigenetic inhibitors that target distinct epigenetic states associated with either one of the lysine-specific histone demethylases Kdm1a or Kdm4b, or BET bromodomain proteins. While melanocytes remain insensitive, the anti-tumor efficacy of each inhibitor is predicted based on melanoma cells' differentiation state and MAPK activity. Our systems pharmacology approach highlights a path toward identifying actionable epigenetic factors that extend the BRAF oncogene addiction paradigm on the basis of tumor cell differentiation state.
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Affiliation(s)
- Mehwish Khaliq
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Mohan Manikkam
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
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74
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Oner E, Kotmakci M, Baird AM, Gray SG, Debelec Butuner B, Bozkurt E, Kantarci AG, Finn SP. Development of EphA2 siRNA-loaded lipid nanoparticles and combination with a small-molecule histone demethylase inhibitor in prostate cancer cells and tumor spheroids. J Nanobiotechnology 2021; 19:71. [PMID: 33685469 PMCID: PMC7938557 DOI: 10.1186/s12951-021-00781-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND siRNAs hold a great potential for cancer therapy, however, poor stability in body fluids and low cellular uptake limit their use in the clinic. To enhance the bioavailability of siRNAs in tumors, novel, safe, and effective carriers are needed. RESULTS Here, we developed cationic solid lipid nanoparticles (cSLNs) to carry siRNAs targeting EphA2 receptor tyrosine kinase (siEphA2), which is overexpressed in many solid tumors including prostate cancer. Using DDAB cationic lipid instead of DOTMA reduced nanoparticle size and enhanced both cellular uptake and gene silencing in prostate cancer cells. DDAB-cSLN showed better cellular uptake efficiency with similar silencing compared to commercial transfection reagent (Dharmafect 2). After verifying the efficacy of siEphA2-loaded nanoparticles, we further evaluated a potential combination with a histone lysine demethylase inhibitor, JIB-04. Silencing EphA2 by siEphA2-loaded DDAB-cSLN did not affect the viability (2D or 3D culture), migration, nor clonogenicity of PC-3 cells alone. However, upon co-administration with JIB-04, there was a decrease in cellular responses. Furthermore, JIB-04 decreased EphA2 expression, and thus, silencing by siEphA2-loaded nanoparticles was further increased with co-treatment. CONCLUSIONS We have successfully developed a novel siRNA-loaded lipid nanoparticle for targeting EphA2. Moreover, preliminary results of the effects of JIB-04, alone and in combination with siEphA2, on prostate cancer cells and prostate cancer tumor spheroids were presented for the first time. Our delivery system provides high transfection efficiency and shows great promise for targeting other genes and cancer types in further in vitro and in vivo studies.
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Affiliation(s)
- Ezgi Oner
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Izmir Katip Celebi University, Balatcik, Izmir, Turkey
| | - Mustafa Kotmakci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Bilge Debelec Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Emir Bozkurt
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Ayse Gulten Kantarci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland. .,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland. .,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland. .,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland.
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75
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Wang Z, Wu R, Nie Q, Bouchonville KJ, Diasio RB, Offer SM. Chromatin assembly factor 1 suppresses epigenetic reprogramming toward adaptive drug resistance. JOURNAL OF THE NATIONAL CANCER CENTER 2021. [DOI: 10.1016/j.jncc.2020.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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76
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SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS. Blood 2021; 135:2271-2285. [PMID: 32202636 DOI: 10.1182/blood.2019001963] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/08/2020] [Indexed: 02/06/2023] Open
Abstract
SETD2, the histone H3 lysine 36 methyltransferase, previously identified by us, plays an important role in the pathogenesis of hematologic malignancies, but its role in myelodysplastic syndromes (MDSs) has been unclear. In this study, low expression of SETD2 correlated with shortened survival in patients with MDS, and the SETD2 levels in CD34+ bone marrow cells of those patients were increased by decitabine. We knocked out Setd2 in NUP98-HOXD13 (NHD13) transgenic mice, which phenocopies human MDS, and found that loss of Setd2 accelerated the transformation of MDS into acute myeloid leukemia (AML). Loss of Setd2 enhanced the ability of NHD13+ hematopoietic stem and progenitor cells (HSPCs) to self-renew, with increased symmetric self-renewal division and decreased differentiation and cell death. The growth of MDS-associated leukemia cells was inhibited though increasing the H3K36me3 level by using epigenetic modifying drugs. Furthermore, Setd2 deficiency upregulated hematopoietic stem cell signaling and downregulated myeloid differentiation pathways in the NHD13+ HSPCs. Our RNA-seq and chromatin immunoprecipitation-seq analysis indicated that S100a9, the S100 calcium-binding protein, is a target gene of Setd2 and that the addition of recombinant S100a9 weakens the effect of Setd2 deficiency in the NHD13+ HSPCs. In contrast, downregulation of S100a9 leads to decreases of its downstream targets, including Ikba and Jnk, which influence the self-renewal and differentiation of HSPCs. Therefore, our results demonstrated that SETD2 deficiency predicts poor prognosis in MDS and promotes the transformation of MDS into AML, which provides a potential therapeutic target for MDS-associated acute leukemia.
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77
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Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans 2021; 49:93-105. [PMID: 33492339 PMCID: PMC7925003 DOI: 10.1042/bst20191219] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
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78
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Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells. Sci Rep 2021; 11:884. [PMID: 33441614 PMCID: PMC7806742 DOI: 10.1038/s41598-020-79601-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Trophoblast stem cell (TSC) is crucial to the formation of placenta in mammals. Histone demethylase JMJD2 (also known as KDM4) family proteins have been previously shown to support self-renewal and differentiation of stem cells. However, their roles in the context of the trophoblast lineage remain unclear. Here, we find that knockdown of Jmjd2b resulted in differentiation of TSCs, suggesting an indispensable role of JMJD2B/KDM4B in maintaining the stemness. Through the integration of transcriptome and ChIP-seq profiling data, we show that JMJD2B is associated with a loss of H3K36me3 in a subset of embryonic lineage genes which are marked by H3K9me3 for stable repression. By characterizing the JMJD2B binding motifs and other transcription factor binding datasets, we discover that JMJD2B forms a protein complex with AP-2 family transcription factor TFAP2C and histone demethylase LSD1. The JMJD2B-TFAP2C-LSD1 complex predominantly occupies active gene promoters, whereas the TFAP2C-LSD1 complex is located at putative enhancers, suggesting that these proteins mediate enhancer-promoter interaction for gene regulation. We conclude that JMJD2B is vital to the TSC transcriptional program and safeguards the trophoblast cell fate via distinctive protein interactors and epigenetic targets.
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79
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Wang Y, Ma J, Martinez ED, Liang D, Xie H. A UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma: Development, validation and application to pharmacokinetics study. J Pharm Biomed Anal 2020; 191:113587. [PMID: 32892084 PMCID: PMC7581536 DOI: 10.1016/j.jpba.2020.113587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
Methylation of lysine by histone methyltransferases can be reversed by lysine demethylases (KDMs). Different KDMs have distinct oncogenic functions based on their cellular localization, stimulating cancer cell proliferation, reducing the expression of tumor suppressors, and/or promoting the development of drug resistance. JIB-04 is a small molecule that pan-selectively inhibits KDMs, showing maximal inhibitory activity against KDM5A, and as secondary targets, KDM4D/4B/4A/6B/4C. Recently, it was found that JIB-04 also potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines via the inhibition of a new target, serine hydroxymethyltransferase 2. Pharmacokinetic characterization and an analytical method for the quantification of JIB-04 are necessary for the further development of this small molecule. Herein, a sensitive, specific, fast and reliable UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma samples was developed and fully validated using a SCIEX 6500+ triple QUAD LC-MS system equipped with an ExionLC UHPLC unit. The chromatographic separation was achieved on a reverse phase ACE Excel 2 Super C18 column with a flow rate of 0.5 mL/min under gradient elution. The calibration curves were linear (r2 > 0.999) over concentrations from 0.5 to 1000 ng/mL. The accuracy (RE%) was between -7.4% and 3.7%, and the precision (CV%) was 10.2% or less. The stability data showed that no significant degradation occurred under the experimental conditions. This method was successfully applied to the pharmacokinetic study of JIB-04 in rat plasma after intravenous and oral administration and the oral bioavailability of JIB-04 was found to be 44.4%.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Jing Ma
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dong Liang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Huan Xie
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA.
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80
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Okabe K, Nawaz A, Nishida Y, Yaku K, Usui I, Tobe K, Nakagawa T. NAD+ Metabolism Regulates Preadipocyte Differentiation by Enhancing α-Ketoglutarate-Mediated Histone H3K9 Demethylation at the PPARγ Promoter. Front Cell Dev Biol 2020; 8:586179. [PMID: 33330464 PMCID: PMC7732485 DOI: 10.3389/fcell.2020.586179] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/03/2020] [Indexed: 01/07/2023] Open
Abstract
Obesity has become a serious problem in public health worldwide, causing numerous metabolic diseases. Once the differentiation to mature adipocytes is disrupted, adipocyte hypertrophy and ectopic lipid accumulation leads to the inflammation in adipose tissue and systemic metabolic disorders. Intracellular metabolic state is known to change during cell differentiation and it affects the cell fate or the differentiation through epigenetic mechanism. Although the mechanism of preadipocyte differentiation has been well established, it is unknown how metabolic state changes and how it affects the differentiation in predipocyte differentiation. Nicotinamide adenine dinucleotide (NAD+) plays crucial roles in energy metabolism as a coenzyme in multiple redox reactions in major catabolic pathways and as a substrate of sirtuins or poly(ADP-ribose)polymerases. NAD+ is mainly synthesized from salvage pathway mediated by two enzymes, Nampt and Nmnat. The manipulation to NAD+ metabolism causes metabolic change in each tissue and changes in systemic metabolism. However, the role of NAD+ and Nampt in adipocyte differentiation remains unknown. In this study, we employed liquid chromatography-mass spectrometry (LC-MS)- and gas chromatography-mass spectrometry (GC-MS)-based targeted metabolomics to elucidate the metabolic reprogramming events that occur during 3T3-L1 preadipocyte differentiation. We found that the tricarboxylic acid (TCA) cycle was enhanced, which correlated with upregulated NAD+ synthesis. Additionally, increased alpha-ketoglutarate (αKG) contributed to histone H3K9 demethylation in the promoter region of PPARγ, leading to its transcriptional activation. Thus, we concluded that NAD+-centered metabolic reprogramming is necessary for the differentiation of 3T3-L1 preadipocytes.
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Affiliation(s)
- Keisuke Okabe
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan.,First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Allah Nawaz
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan.,First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Yasuhiro Nishida
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Keisuke Yaku
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Isao Usui
- Department of Endocrinology and Metabolism, Dokkyo Medical University, Tochigi, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Toyama, Japan.,Research Center for Pre-Disease Science, University of Toyama, Toyama, Japan
| | - Takashi Nakagawa
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan.,Research Center for Pre-Disease Science, University of Toyama, Toyama, Japan
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81
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Alpha-ketoglutarate ameliorates age-related osteoporosis via regulating histone methylations. Nat Commun 2020; 11:5596. [PMID: 33154378 PMCID: PMC7645772 DOI: 10.1038/s41467-020-19360-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 10/05/2020] [Indexed: 02/05/2023] Open
Abstract
Age-related osteoporosis is characterized by the deterioration in bone volume and strength, partly due to the dysfunction of bone marrow mesenchymal stromal/stem cells (MSCs) during aging. Alpha-ketoglutarate (αKG) is an essential intermediate in the tricarboxylic acid (TCA) cycle. Studies have revealed that αKG extends the lifespan of worms and maintains the pluripotency of embryonic stem cells (ESCs). Here, we show that the administration of αKG increases the bone mass of aged mice, attenuates age-related bone loss, and accelerates bone regeneration of aged rodents. αKG ameliorates the senescence-associated (SA) phenotypes of bone marrow MSCs derived from aged mice, as well as promoting their proliferation, colony formation, migration, and osteogenic potential. Mechanistically, αKG decreases the accumulations of H3K9me3 and H3K27me3, and subsequently upregulates BMP signaling and Nanog expression. Collectively, our findings illuminate the role of αKG in rejuvenating MSCs and ameliorating age-related osteoporosis, with a promising therapeutic potential in age-related diseases. α-ketoglutarate is an intermediate of the Krebs Cycle that was recently reported to extend lifespan in C.Elegans. Here, the authors show that administration of α-ketoglutarate to mice reduces age-related bone loss, by ameliorating senescence of bone-marrow derived mesenchymal stem cells.
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82
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Pezone A, Taddei ML, Tramontano A, Dolcini J, Boffo FL, De Rosa M, Parri M, Stinziani S, Comito G, Porcellini A, Raugei G, Gackowski D, Zarakowska E, Olinski R, Gabrielli A, Chiarugi P, Avvedimento EV. Targeted DNA oxidation by LSD1-SMAD2/3 primes TGF-β1/ EMT genes for activation or repression. Nucleic Acids Res 2020; 48:8943-8958. [PMID: 32697292 PMCID: PMC7498341 DOI: 10.1093/nar/gkaa599] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is a complex transcriptional program induced by transforming growth factor β1 (TGF-β1). Histone lysine-specific demethylase 1 (LSD1) has been recognized as a key mediator of EMT in cancer cells, but the precise mechanism that underlies the activation and repression of EMT genes still remains elusive. Here, we characterized the early events induced by TGF-β1 during EMT initiation and establishment. TGF-β1 triggered, 30–90 min post-treatment, a nuclear oxidative wave throughout the genome, documented by confocal microscopy and mass spectrometry, mediated by LSD1. LSD1 was recruited with phosphorylated SMAD2/3 to the promoters of prototypic genes activated and repressed by TGF-β1. After 90 min, phospho-SMAD2/3 downregulation reduced the complex and LSD1 was then recruited with the newly synthesized SNAI1 and repressors, NCoR1 and HDAC3, to the promoters of TGF-β1-repressed genes such as the Wnt soluble inhibitor factor 1 gene (WIF1), a change that induced a late oxidative burst. However, TGF-β1 early (90 min) repression of transcription also required synchronous signaling by reactive oxygen species and the stress-activated kinase c-Jun N-terminal kinase. These data elucidate the early events elicited by TGF-β1 and the priming role of DNA oxidation that marks TGF-β1-induced and -repressed genes involved in the EMT.
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Affiliation(s)
- Antonio Pezone
- To whom correspondence should be addressed. Tel: +39 0817463614; ;
| | | | | | - Jacopo Dolcini
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, Università Federico II, 80131 Napoli, Italy
- Dipartimento di Scienze Cliniche e Molecolari, Clinica Medica, Università Politecnica delle Marche, 60100, Ancona, Italy
| | - Francesca Ludovica Boffo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, Università Federico II, 80131 Napoli, Italy
| | - Mariarosaria De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, Università Federico II, 80131 Napoli, Italy
| | - Matteo Parri
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, viale Morgagni 50, 50134 Firenze, Italy
| | - Stefano Stinziani
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, viale Morgagni 50, 50134 Firenze, Italy
| | - Giuseppina Comito
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, viale Morgagni 50, 50134 Firenze, Italy
| | | | - Giovanni Raugei
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, viale Morgagni 50, 50134 Firenze, Italy
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095 Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095 Bydgoszcz, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-095 Bydgoszcz, Poland
| | - Armando Gabrielli
- Dipartimento di Scienze Cliniche e Molecolari, Clinica Medica, Università Politecnica delle Marche, 60100, Ancona, Italy
| | - Paola Chiarugi
- Correspondence may also be addressed to Paola Chiarugi. Tel: +39 0552751247;
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83
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Ishak Gabra MB, Yang Y, Li H, Senapati P, Hanse EA, Lowman XH, Tran TQ, Zhang L, Doan LT, Xu X, Schones DE, Fruman DA, Kong M. Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth. Nat Commun 2020; 11:3326. [PMID: 32620791 PMCID: PMC7335172 DOI: 10.1038/s41467-020-17181-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. In melanoma, tumour cells often experience low glutamine levels, which promote cell dedifferentiation. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in a transgenic melanoma mouse model, and increases sensitivity to a BRAF inhibitor. Metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine in tumours and its downstream metabolite, αKG, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome in tumours. Our data further demonstrate that increase in intra-tumoural αKG concentration drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.
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Affiliation(s)
- Mari B Ishak Gabra
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Haiqing Li
- Center for Informatics, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Department of Computational & Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Parijat Senapati
- Department of Diabetes and Metabolic Disease, Beckman Research Institute of City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Eric A Hanse
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Xazmin H Lowman
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Thai Q Tran
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Lishi Zhang
- Institute for Clinical and Translational Science, University of California, Irvine, CA, 92687, USA
| | - Linda T Doan
- UCI Health Dermatology Center, Irvine, CA, 92697, USA
| | - Xiangdong Xu
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dustin E Schones
- Department of Diabetes and Metabolic Disease, Beckman Research Institute of City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - David A Fruman
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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84
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Lam HY, Arumugam S, Bae HG, Wang CC, Jung S, St John AL, Hong W, Han W, Tergaonkar V. ELKS1 controls mast cell degranulation by regulating the transcription of Stxbp2 and Syntaxin 4 via Kdm2b stabilization. SCIENCE ADVANCES 2020; 6:6/31/eabb2497. [PMID: 32937583 PMCID: PMC7531903 DOI: 10.1126/sciadv.abb2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/09/2020] [Indexed: 05/06/2023]
Abstract
ELKS1 is a protein with proposed roles in regulated exocytosis in neurons and nuclear factor κB (NF-κB) signaling in cancer cells. However, how these two potential roles come together under physiological settings remain unknown. Since both regulated exocytosis and NF-κB signaling are determinants of mast cell (MC) functions, we generated mice lacking ELKS1 in connective tissue MCs (Elks1f/f Mcpt5-Cre) and found that while ELKS1 is dispensable for NF-κB-mediated cytokine production, it is essential for MC degranulation both in vivo and in vitro. Impaired degranulation was caused by reduced transcription of Syntaxin 4 (STX4) and Syntaxin binding protein 2 (Stxpb2), resulting from a lack of ELKS1-mediated stabilization of lysine-specific demethylase 2B (Kdm2b), which is an essential regulator of STX4 and Stxbp2 transcription. These results suggest a transcriptional role for active-zone proteins like ELKS1 and suggest that they may regulate exocytosis through a novel mechanism involving transcription of key exocytosis proteins.
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Affiliation(s)
- Hiu Yan Lam
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117596, Singapore
| | - Surendar Arumugam
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Han Gyu Bae
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, #02-02 Helios, 11 Biopolis Way, Singapore 138667, Singapore
| | - Cheng Chun Wang
- Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Sangyong Jung
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, #02-02 Helios, 11 Biopolis Way, Singapore 138667, Singapore
| | - Ashley Lauren St John
- Program in Emerging Infectious Diseases, Duke-NUS, Singapore 169857, Singapore
- Department of Microbiology and Immunology, NUS, Singapore 119077, Singapore
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Wanjin Hong
- Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Weiping Han
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, #02-02 Helios, 11 Biopolis Way, Singapore 138667, Singapore
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 119074, Singapore
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85
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Activity of Epigenetic Inhibitors against Plasmodium falciparum Asexual and Sexual Blood Stages. Antimicrob Agents Chemother 2020; 64:AAC.02523-19. [PMID: 32366713 DOI: 10.1128/aac.02523-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Earlier genetic and inhibitor studies showed that epigenetic regulation of gene expression is critical for malaria parasite survival in multiple life stages and a promising target for new antimalarials. We therefore evaluated the activity of 350 diverse epigenetic inhibitors against multiple stages of Plasmodium falciparum We observed ≥90% inhibition at 10 μM for 28% of compounds against asexual blood stages and early gametocytes, of which a third retained ≥90% inhibition at 1 μM.
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86
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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.
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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
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87
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Abstract
Specific chemical modifications of biological molecules are an efficient way of regulating molecular function, and a plethora of downstream signalling pathways are influenced by the modification of DNA and proteins. Many of the enzymes responsible for regulating protein and DNA modifications are targets of current cancer therapies. RNA epitranscriptomics, the study of RNA modifications, is the new frontier of this arena. Despite being known since the 1970s, eukaryotic RNA modifications were mostly identified on transfer RNA and ribosomal RNA until the last decade, when they have been identified and characterized on mRNA and various non-coding RNAs. Increasing evidence suggests that RNA modification pathways are also misregulated in human cancers and may be ideal targets of cancer therapy. In this Review we highlight the RNA epitranscriptomic pathways implicated in cancer, describing their biological functions and their connections to the disease.
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Affiliation(s)
- Isaia Barbieri
- The Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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88
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Brewitz L, Tumber A, Pfeffer I, McDonough MA, Schofield CJ. Aspartate/asparagine-β-hydroxylase: a high-throughput mass spectrometric assay for discovery of small molecule inhibitors. Sci Rep 2020; 10:8650. [PMID: 32457455 PMCID: PMC7251097 DOI: 10.1038/s41598-020-65123-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
The human 2-oxoglutarate dependent oxygenase aspartate/asparagine-β-hydroxylase (AspH) catalyses the hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs). AspH is upregulated on the surface of malign cancer cells; increased AspH levels correlate with tumour invasiveness. Due to a lack of efficient assays to monitor the activity of isolated AspH, there are few reports of studies aimed at identifying small-molecule AspH inhibitors. Recently, it was reported that AspH substrates have a non-canonical EGFD disulfide pattern. Here we report that a stable synthetic thioether mimic of AspH substrates can be employed in solid phase extraction mass spectrometry based high-throughput AspH inhibition assays which are of excellent robustness, as indicated by high Z'-factors and good signal-to-noise/background ratios. The AspH inhibition assay was applied to screen approximately 1500 bioactive small-molecules, including natural products and active pharmaceutical ingredients of approved human therapeutics. Potent AspH inhibitors were identified from both compound classes. Our AspH inhibition assay should enable the development of potent and selective small-molecule AspH inhibitors and contribute towards the development of safer inhibitors for other 2OG oxygenases, e.g. screens of the hypoxia-inducible factor prolyl-hydroxylase inhibitors revealed that vadadustat inhibits AspH with moderate potency.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Inga Pfeffer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom.
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89
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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: 18] [Impact Index Per Article: 4.5] [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.
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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
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90
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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.
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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
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91
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Nava MM, Miroshnikova YA, Biggs LC, Whitefield DB, Metge F, Boucas J, Vihinen H, Jokitalo E, Li X, García Arcos JM, Hoffmann B, Merkel R, Niessen CM, Dahl KN, Wickström SA. Heterochromatin-Driven Nuclear Softening Protects the Genome against Mechanical Stress-Induced Damage. Cell 2020; 181:800-817.e22. [PMID: 32302590 PMCID: PMC7237863 DOI: 10.1016/j.cell.2020.03.052] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/02/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Tissue homeostasis requires maintenance of functional integrity under stress. A central source of stress is mechanical force that acts on cells, their nuclei, and chromatin, but how the genome is protected against mechanical stress is unclear. We show that mechanical stretch deforms the nucleus, which cells initially counteract via a calcium-dependent nuclear softening driven by loss of H3K9me3-marked heterochromatin. The resulting changes in chromatin rheology and architecture are required to insulate genetic material from mechanical force. Failure to mount this nuclear mechanoresponse results in DNA damage. Persistent, high-amplitude stretch induces supracellular alignment of tissue to redistribute mechanical energy before it reaches the nucleus. This tissue-scale mechanoadaptation functions through a separate pathway mediated by cell-cell contacts and allows cells/tissues to switch off nuclear mechanotransduction to restore initial chromatin state. Our work identifies an unconventional role of chromatin in altering its own mechanical state to maintain genome integrity in response to deformation. Stretch triggers amplitude-dependent supracellular and nuclear mechanoresponses H3K9me3 heterochromatin mediates nuclear stiffness and membrane tension Nuclear deformation-triggered Ca2+ alters chromatin rheology to prevent DNA damage Supracellular alignment redistributes stress to restore chromatin state
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Affiliation(s)
- Michele M Nava
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Yekaterina A Miroshnikova
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Leah C Biggs
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daniel B Whitefield
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Franziska Metge
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Jorge Boucas
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Xinping Li
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Juan Manuel García Arcos
- Institut Curie, PSL Research University, CNRS, UMR 144 and Institut Pierre-Gilles de Gennes, PSL Research University, 75005 Paris, France
| | - Bernd Hoffmann
- Forschungszentrum Jülich, Institute of Biological Information Processing-2: Mechanobiology, 52428 Jülich, Germany
| | - Rudolf Merkel
- Forschungszentrum Jülich, Institute of Biological Information Processing-2: Mechanobiology, 52428 Jülich, Germany
| | - Carien M Niessen
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Department of Dermatology, Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Kris Noel Dahl
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sara A Wickström
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.
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92
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Sun J, Chen J, Mohagheghian E, Wang N. Force-induced gene up-regulation does not follow the weak power law but depends on H3K9 demethylation. SCIENCE ADVANCES 2020; 6:eaay9095. [PMID: 32270037 PMCID: PMC7112933 DOI: 10.1126/sciadv.aay9095] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/08/2020] [Indexed: 05/25/2023]
Abstract
Mechanical forces play important roles in development, physiology, and diseases, but how force is transduced into gene transcription remains elusive. Here, we show that transcription of transgene DHFR or endogenous genes egr-1 and Cav1 is rapidly up-regulated in response to cyclic forces applied via integrins at low frequencies but not at 100 Hz. Gene up-regulation does not follow the weak power law with force frequency. Force-induced transcription up-regulation at the nuclear interior is associated with demethylation of histone H3 lysine-9 trimethylation (H3K9me3), whereas no transcription up-regulation near the nuclear periphery is associated with H3K9me3 that inhibits Pol II recruitment to the promoter site. H3K9me3 demethylation induces Pol II recruitment and increases force-induced transcription of egr-1 and Cav1 at the nuclear interior and activates mechano-nonresponsive gene FKBP5 near the nuclear periphery, whereas H3K9me3 hypermethylation has opposite effects. Our findings demonstrate that rapid up-regulation of endogenous mechanoresponsive genes depends on H3K9me3 demethylation.
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Affiliation(s)
- Jian Sun
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Junwei Chen
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Laboratory for Cellular Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Erfan Mohagheghian
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ning Wang
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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93
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Zhang S, Lu Y, Jiang C. Inhibition of histone demethylase JMJD1C attenuates cardiac hypertrophy and fibrosis induced by angiotensin II. J Recept Signal Transduct Res 2020; 40:339-347. [PMID: 32122211 DOI: 10.1080/10799893.2020.1734819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Pathological cardiac hypertrophy is a major risk factor for cardiovascular morbidity and mortality. Histone demethylases (KDMs) are emerging regulators of transcriptional reprograming in cancer, however, their potential role in abnormal heart growth and fibrosis remains largely unknown. The aim of this current study was to examine the role of JMJD1C, an H3K9me2 specific demethylase, in angiotensin II (Ang II) induced cardiac hypertrophy and fibrosis. In this study, we observed that Ang II could increase the expression of JMJD1C detected by Western blot and RT-qPCR in vitro and in vivo. Immunofluorescence staining showed that the treatment of Ang II could increase cardiomyocyte size. RT-qPCR results have shown that Ang II could increase the expression of cell hypertrophic and fibrotic markers in H9c2 cells. Whereas, inhibition of JMJD1C by shRNA and JIB-04, a small molecule histone demethylase inhibitor, significantly reduced Ang II-induced cell hypertrophy, and hypertrophic and fibrotic marker overexpression. Furthermore, cardiomyocyte JMJD1C knockdown decreased Tissue Inhibitor of Metalloproteinases 1 (TIMP1) transcription with pro-fibrotic activity. In conclusion, JMJD1C plays an important role in Ang II-induced cardiac hypertrophy and fibrosis by activating TIMP1 transcription, targeting of JMJD1C may be an effective strategy for the treatment of Ang II-associated cardiac diseases.
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Affiliation(s)
- Shenqian Zhang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Electrocardiogram Room of Department of Functional Examination, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Ying Lu
- Electrocardiogram Room of Department of Functional Examination, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chenyang Jiang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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94
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Saraç H, Morova T, Pires E, McCullagh J, Kaplan A, Cingöz A, Bagci-Onder T, Önder T, Kawamura A, Lack NA. Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer. Oncogene 2020; 39:2187-2201. [PMID: 31822799 PMCID: PMC7056651 DOI: 10.1038/s41388-019-1116-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/28/2022]
Abstract
Androgen deprivation therapy (ADT) is the standard care for prostate cancer (PCa) patients who fail surgery or radiotherapy. While initially effective, the cancer almost always recurs as a more aggressive castration resistant prostate cancer (CRPC). Previous studies have demonstrated that chromatin modifying enzymes can play a critical role in the conversion to CRPC. However, only a handful of these potential pharmacological targets have been tested. Therefore, in this study, we conducted a focused shRNA screen of chromatin modifying enzymes previously shown to be involved in cellular differentiation. We found that altering the balance between histone methylation and demethylation impacted growth and proliferation. Of all genes tested, KDM3B, a histone H3K9 demethylase, was found to have the most antiproliferative effect. These results were phenocopied with a KDM3B CRISPR/Cas9 knockout. When tested in several PCa cell lines, the decrease in proliferation was remarkably specific to androgen-independent cells. Genetic rescue experiments showed that only the enzymatically active KDM3B could recover the phenotype. Surprisingly, despite the decreased proliferation of androgen-independent cell no alterations in the cell cycle distribution were observed following KDM3B knockdown. Whole transcriptome analyses revealed changes in the gene expression profile following loss of KDM3B, including downregulation of metabolic enzymes such as ARG2 and RDH11. Metabolomic analysis of KDM3B knockout showed a decrease in several critical amino acids. Overall, our work reveals, for the first time, the specificity and the dependence of KDM3B in CRPC proliferation.
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Affiliation(s)
- Hilal Saraç
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Tunç Morova
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Anıl Kaplan
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Ahmet Cingöz
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | | | - Tamer Önder
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nathan A Lack
- School of Medicine, Koç University, Istanbul, 34450, Turkey.
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada.
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95
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Sobral LM, Sechler M, Parrish JK, McCann TS, Jones KL, Black JC, Jedlicka P. KDM3A/Ets1/MCAM axis promotes growth and metastatic properties in Rhabdomyosarcoma. Genes Cancer 2020; 11:53-65. [PMID: 32577157 PMCID: PMC7289905 DOI: 10.18632/genesandcancer.200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy of childhood. RMS exists as two major disease subtypes, with oncofusion-positive RMS (FP-RMS) typically carrying a worse prognosis than oncofusion-negative RMS (FN-RMS), in part due to higher propensity for metastasis. Epigenetic mechanisms have recently emerged as critical players in the pathogenesis of pediatric cancers, as well as potential new therapeutic vulnerabilities. Herein, we show that the epigenetic regulator KDM3A, a member of the Jumonji-domain histone demethylase (JHDM) family, is overexpressed, potently promotes colony formation and transendothelial invasion, and activates the expression of genes involved in cell growth, migration and metastasis, in both FN-RMS and FP-RMS. In mechanistic studies, we demonstrate that both RMS subtypes utilize a KDM3A/Ets1/MCAM disease-promoting axis recently discovered in Ewing Sarcoma, another aggressive pediatric cancer of distinct cellular and molecular origin. We further show that KDM3A depletion in FP-RMS cells inhibits both tumor growth and metastasis in vivo, and that RMS cells are highly sensitive to colony growth inhibition by the pan-JHDM inhibitor JIB-04. Together, our studies reveal an important role for the KDM3A/Ets1/MCAM axis in pediatric sarcomas of distinct cellular and molecular ontogeny, and identify new targetable vulnerabilities in RMS.
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Affiliation(s)
- Lays Martin Sobral
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Marybeth Sechler
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Cancer Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Janet K Parrish
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Tyler S McCann
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Black
- Department of Pharmacology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Paul Jedlicka
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Cancer Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
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96
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Lee DH, Kim GW, Jeon YH, Yoo J, Lee SW, Kwon SH. Advances in histone demethylase KDM4 as cancer therapeutic targets. FASEB J 2020; 34:3461-3484. [PMID: 31961018 DOI: 10.1096/fj.201902584r] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The KDM4 subfamily H3K9 histone demethylases are epigenetic regulators that control chromatin structure and gene expression by demethylating histone H3K9, H3K36, and H1.4K26. The KDM4 subfamily mainly consists of four proteins (KDM4A-D), all harboring the Jumonji C domain (JmjC) but with differential substrate specificities. KDM4A-C proteins also possess the double PHD and Tudor domains, whereas KDM4D lacks these domains. KDM4 proteins are overexpressed or deregulated in multiple cancers, cardiovascular diseases, and mental retardation and are thus potential therapeutic targets. Despite extensive efforts, however, there are very few KDM4-selective inhibitors. Defining the exact physiological and oncogenic functions of KDM4 demethylase will provide the foundation for the discovery of novel potent inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM4s and the interplay between KDM4-mediated epigenetic and metabolic pathways in cancer. We also review currently available KDM4 inhibitors and discuss their potential as therapeutic agents for cancer treatment.
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Affiliation(s)
- Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea
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97
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Celarain N, Tomas-Roig J. Aberrant DNA methylation profile exacerbates inflammation and neurodegeneration in multiple sclerosis patients. J Neuroinflammation 2020; 17:21. [PMID: 31937331 PMCID: PMC6961290 DOI: 10.1186/s12974-019-1667-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune and demyelinating disease of the central nervous system characterised by incoordination, sensory loss, weakness, changes in bladder capacity and bowel function, fatigue and cognitive impairment, creating a significant socioeconomic burden. The pathogenesis of MS involves both genetic susceptibility and exposure to distinct environmental risk factors. The gene x environment interaction is regulated by epigenetic mechanisms. Epigenetics refers to a complex system that modifies gene expression without altering the DNA sequence. The most studied epigenetic mechanism is DNA methylation. This epigenetic mark participates in distinct MS pathophysiological processes, including blood-brain barrier breakdown, inflammatory response, demyelination, remyelination failure and neurodegeneration. In this study, we also accurately summarised a list of environmental factors involved in the MS pathogenesis and its clinical course. A literature search was conducted using MEDLINE through PubMED and Scopus. In conclusion, an exhaustive study of DNA methylation might contribute towards new pharmacological interventions in MS by use of epigenetic drugs.
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Affiliation(s)
- Naiara Celarain
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital and Girona Biomedical Research Institute (IDIBGI), Girona, Spain.
| | - Jordi Tomas-Roig
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital and Girona Biomedical Research Institute (IDIBGI), Girona, Spain.
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98
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Kang S, Long K, Wang S, Sada A, Tumbar T. Histone H3 K4/9/27 Trimethylation Levels Affect Wound Healing and Stem Cell Dynamics in Adult Skin. Stem Cell Reports 2019; 14:34-48. [PMID: 31866458 PMCID: PMC6962642 DOI: 10.1016/j.stemcr.2019.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 01/03/2023] Open
Abstract
Epigenetic mechanisms controlling adult mammalian stem cell (SC) dynamics might be critical for tissue regeneration but are poorly understood. Mouse skin and hair follicle SCs (HFSCs) display reduced histone H3 K4me3, K9me3, and K27me3 methylation levels (hypomethylation) preceding hair growth. Chemical inhibition of relevant histone demethylases impairs subsequent differentiation and growth of HFs and delays wound healing. In wounding, this impairs epithelial cell differentiation and blood vessel recruitment, but not proliferation and fibroblast recruitment. With Aspm-CreER as a newfound inter-follicular epidermis lineage-labeling tool, and Lgr5-CreER for hair follicles, we demonstrate a reduced contribution of both lineages to wound healing after interfering with hypomethylation. Blocked hypomethylation increases BMP4 expression and selectively upregulates H3 K4me3 on the Bmp4 promoter, which may explain the effects on HFSC quiescence, hair cycle, and injury repair. Thus, transient hypomethylation of histone H3 K4/9/27me3 is essential for adult skin epithelial SC dynamics for proper tissue homeostasis and repair. H3 K4/9/27me3 hypomethylation is necessary for proper subsequent wound healing Hypomethylation affects dynamics of both hair follicle and inter-follicular lineages Hypomethylation affects hair follicle stem cell activation and differentiation Aspm-CreER, a genetic driver specific to inter-follicular epidermis in mouse skin
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Affiliation(s)
- Sangjo Kang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kylie Long
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sherry Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Aiko Sada
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; International Research Center for Medical Sciences, Kumamoto University, Kumamoto City 860-0811, Japan
| | - Tudorita Tumbar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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99
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Bayo J, Tran TA, Wang L, Peña-Llopis S, Das AK, Martinez ED. Jumonji Inhibitors Overcome Radioresistance in Cancer through Changes in H3K4 Methylation at Double-Strand Breaks. Cell Rep 2019; 25:1040-1050.e5. [PMID: 30355483 PMCID: PMC6245670 DOI: 10.1016/j.celrep.2018.09.081] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/17/2018] [Accepted: 09/25/2018] [Indexed: 01/10/2023] Open
Abstract
We have uncovered a role for Jumonji inhibitors in overcoming radioresistance through KDM5B inhibition. Pharmacological blockade of Jumonji demethy-lases with JIB-04 leads to specific accumulation of H3K4me3 at sites marked by γH2AX and impaired recruitment of DNA repair factors, preventing resolution of damage and resulting in robust sensitization to radiation therapy. In DNA-repair-proficient cancer cells, knockdown of the H3K4me3 demethylase KDM5B, but not other Jumonji enzymes, mimics pharmacological inhibition, and KDM5B overexpression rescues this phenotype and increases radioresistance. The H3K4me3 demethylase inhibitor PBIT also sensitizes cancer cells to radiation, while an H3K27me3 demethylase inhibitor does not. In vivo co-administration of radiation with JIB-04 significantly prolongs the survival of mice with tumors even long after cessation of treatment. In human patients, lung squamous cell carcinomas highly ex-pressing KDM5B respond poorly to radiation. Thus, we propose the use of Jumonji KDM inhibitors as potent radiosensitizers. Radioresistance is an obstacle to lung cancer cures. Bayo et al. reveal that JARID1B removes H3K4me3 marks at sites of DNA damage. Genetic or pharmacological inhibition of JARID1B robustly radiosensitizes cancers in vitro and in vivo through defects in DNA repair, providing a therapeutic option for radioresistant tumors.
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Affiliation(s)
- Juan Bayo
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Instituto de Investigaciones en Medicina Traslacional, CONICET, Universidad Austral, Argentina
| | - Tram Anh Tran
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel Peña-Llopis
- Division of Translational Oncology, Essen University Hospital, German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amit K Das
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.
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100
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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.
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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
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