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Nomura T, Yoneda A, Kato Y. BAHD acyltransferase induced by histone deacetylase inhibitor catalyzes 3-O-hydroxycinnamoylquinic acid formation in bamboo cells. Plant J 2022; 112:1266-1280. [PMID: 36305861 DOI: 10.1111/tpj.16013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Suspension-cultured cells of a bamboo species (Bambusa multiplex; Bm) produce 3-O-feruloylquinic acid (3-FQA) and 3-O-p-coumaroylquinic acid (3-pCQA) by treatment with the histone deacetylase inhibitor suberoyl bis-hydroxamic acid (SBHA). Acyltransferases catalyzing the formation of 5-O-hydroxycinnamoylquinic acid esters by transesterification from hydroxycinnamoyl-CoAs to the C-5 hydroxy group of quinic acid (hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase, HQT) have been identified in the biosynthesis of chlorogenic acids and monolignols; however, an HQT that catalyzes the acylation of the C-3 hydroxy group of quinic acid has not been identified previously. In the present study, we purified a native HQT from SBHA-treated Bm cells. The purified enzyme preferentially accepted feruloyl-/p-coumaroyl-CoAs as acyl-donors and quinic acid as the acyl-acceptor, and the enzyme specifically formed 3-FQA and 3-pCQA but not 5-O-hydroxycinnamoylquinic acid esters or esters with shikimic acid. A cDNA (BmHQT1) encoding this HQT was isolated. Although BmHQT1 is a phylogenetically unique member of the BAHD acyltransferase superfamily that does not cluster with other HQTs, functional characterization of the recombinant enzyme verified that BmHQT1 catalyzes the regiospecific formation of 3-O-hydroxycinnamoylquinic acid esters. Transcript levels of BmHQT1 markedly increased in Bm cells cultured in the presence of SBHA. Moreover, elevated acetylation levels of histone H3 were observed in the coding region of BmHQT1 in the presence of SBHA, indicating that the induced accumulation of 3-FQA/3-pCQA by SBHA is caused by transcriptional activation of BmHQT1 by the action of SBHA as a histone deacetylase inhibitor. The results demonstrate the utility of HDAC inhibitors for discovery of cryptic secondary metabolites and unknown biosynthetic enzymes.
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Affiliation(s)
- Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Akari Yoneda
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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2
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Serrano R, González-Menéndez V, Martínez G, Toro C, Martín J, Genilloud O, Tormo JR. Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach. Molecules 2021; 26:molecules26144262. [PMID: 34299537 PMCID: PMC8305139 DOI: 10.3390/molecules26144262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.
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3
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Dang X, Zhou D, Meng L, Bi L. Blastic plasmacytoid dendritic cell neoplasm with genetic mutations in multiple epigenetic modifiers: a case report. J Int Med Res 2021; 49:300060520982667. [PMID: 33530792 PMCID: PMC7871073 DOI: 10.1177/0300060520982667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare, aggressive hematodermic malignancy derived from plasmacytoid dendritic cell precursors. Despite advances in our understanding of tumor cell surface markers, the pathogenesis of BPDCN remains largely unknown. No standard or optimal treatments are available for BPDCN, and the prognosis is usually poor. We report herein a case of BPDCN that harbored multiple genetic mutations in epigenetic modifiers such as TET2 and ZRSR2. Genetic studies in patients with BPDCN may provide insights into the underlying pathogenesis, prediction of clinical prognosis, and development of better targeted therapeutics for this rare clinical entity.
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Affiliation(s)
- Xinmei Dang
- Department of Hematology and Oncology, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Di Zhou
- Department of Hematology and Oncology, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Lingjun Meng
- Department of Hematology and Oncology, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Lintao Bi
- Department of Hematology and Oncology, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
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4
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Ameen F, Almansob A, Al Tami M, Al-Enazi N, Al-Sabri A, Orfali R. Epigenetic Modifiers Affect the Bioactive Compounds Secreted by an Endophyte of the Tropical Plant Piper longum. Molecules 2020; 26:E29. [PMID: 33374682 DOI: 10.3390/molecules26010029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Seven endophytic fungi were isolated from the tropical medicinal plant Piper longum L. After preliminary screening, Phomopsis heveicola was selected for the epigenetic activation treatments. The antibacterial, antifungal, and antioxidant potentials of crude extracts obtained from the treatments (with and without epigenetic modifiers) were analyzed in vitro. The extracts inhibited growth of the human pathogens Pseudomonas aeruginosa, Shigella sonnei, Streptococcus pyogenes, and Salmonella typhi, as well as the phytopathogens Puccinia recondita, Rhizoctonia solani, Phytophthora infestans, and Botrytis cinerea. Furthermore, DPPH-scavenging activity was higher in valproic acid treated extracts. Volatile chemicals with known biological activities (measured with GC-MS/MS), were released in the valproic acid treatment. The antimicrobial potentials of the extracts were confirmed using MRM/MS analysis. The experiments revealed a new promising endophytic fungus, P. heveicola, to be utilized in biological plant protection and in biomedical applications.
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Wada M, Kukita A, Sone K, Hamamoto R, Kaneko S, Komatsu M, Takahashi Y, Inoue F, Kojima M, Honjoh H, Taguchi A, Kashiyama T, Miyamoto Y, Tanikawa M, Tsuruga T, Mori-Uchino M, Wada-Hiraike O, Osuga Y, Fujii T. Epigenetic Modifier SETD8 as a Therapeutic Target for High-Grade Serous Ovarian Cancer. Biomolecules 2020; 10:E1686. [PMID: 33339442 DOI: 10.3390/biom10121686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
The histone methyltransferase SETD8, which methylates the lysine 20 of histone H4 (H4K20), is reportedly involved in human carcinogenesis along with nonhistone proteins such as p53. However, its expression profiles and functions in the context of high-grade serous ovarian carcinoma (HGSOC) are still unknown. The purpose of this study was to investigate the role of SETD8 in HGSOC. We performed quantitative real-time PCR and immunohistochemistry to detect the expression of SETD8 in HGSOC samples and normal ovarian specimens. Then, we assessed the effect of the inhibition of SETD8 expression using small interfering RNA (siRNA) and a selective inhibitor (UNC0379) on cell proliferation and apoptosis in HGSOC cells. The expression of SETD8 was significantly upregulated in clinical ovarian cancer specimens compared to that in the corresponding normal ovary. In addition, suppression of SETD8 expression in HGSOC cells with either siRNA or UNC0379 resulted in reduced levels of H4K20 monomethylation, inhibition of cell proliferation, and induction of apoptosis. Furthermore, UNC0379 showed a long-term antitumor effect against HGSOC cells, as demonstrated by colony-formation assays. SETD8 thus constitutes a promising therapeutic target for HGSOC, warranting further functional studies.
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6
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Lin H, Ma N, Zhao L, Yang G, Cao B. KDM5c Promotes Colon Cancer Cell Proliferation Through the FBXW7-c-Jun Regulatory Axis. Front Oncol 2020; 10:535449. [PMID: 33042830 PMCID: PMC7526003 DOI: 10.3389/fonc.2020.535449] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 08/18/2020] [Indexed: 01/16/2023] Open
Abstract
KDM5c is a histone demethylase that specifically demethylates trimethylated and dimethylated H3 Lys-4 to play a central role in transcriptional repression. C-Jun is a proto-oncogene and promotes cell proliferation when ectopically accumulated, but can be ubiquitinated by SCF (FBXW7), leading to its degradation. FBXW7 is an E3 ubiquitin ligase of c-Jun, and exhibits carcinostasis in colon cancer. Here, we report that overexpression of KDM5c in human colon cancer cells results in attenuated FBXW7 transcription and accumulated c-Jun protein, leading to increased proliferation of colon cancer cells. We show that overexpression of KDM5c can result in increased c-Jun protein levels and decreased ubiquitin levels, with no significant change in mRNA levels of c-Jun. KDM5c overexpression blocks the ubiquitin-proteasome proteolytic pathway of c-Jun by down-regulating the expression of FBXW7. KDM5c down-regulation of FBXW7 occurs by demethylation of H3K4me3 at TSS and downstream of the FBXW7 gene. And interaction of KDM5c with H3K4me3 downstream of FBXW7 gene may be followed by recruitment of DNMT3b to methylate the spatially close CpG island located near the FBXW7 TSS. This methylation represses FBXW7 gene expression, which can reduce c-Jun degradation via the ubiquitin-proteasome pathway. TCGA database analysis revealed high expression of KDM5c in colon cancer tissues. KDM5c expression in colon cancer was correlated with poor overall survival of patients in the first 7 years. Data from TCGA showed that high expression of KDM5c was correlated with high DNA methylation of the FBXW7 gene, but was not positively correlated with methylation of the Jun gene. These results suggest that KDM5c regulation of colon cell proliferation is mainly mediated by the KDM5c-FBXW7-c-Jun axis.
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Affiliation(s)
- Haishan Lin
- Cancer Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Nina Ma
- Cancer Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lei Zhao
- Cancer Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Guowei Yang
- Department of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Bangwei Cao
- Cancer Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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7
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Alam H, Tang M, Maitituoheti M, Dhar SS, Kumar M, Han CY, Ambati CR, Amin SB, Gu B, Chen TY, Lin YH, Chen J, Muller FL, Putluri N, Flores ER, DeMayo FJ, Baseler L, Rai K, Lee MG. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. Cancer Cell 2020; 37:599-617.e7. [PMID: 32243837 PMCID: PMC7178078 DOI: 10.1016/j.ccell.2020.03.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 11/08/2019] [Accepted: 03/04/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic modifiers frequently harbor loss-of-function mutations in lung cancer, but their tumor-suppressive roles are poorly characterized. Histone methyltransferase KMT2D (a COMPASS-like enzyme, also called MLL4) is among the most highly inactivated epigenetic modifiers in lung cancer. Here, we show that lung-specific loss of Kmt2d promotes lung tumorigenesis in mice and upregulates pro-tumorigenic programs, including glycolysis. Pharmacological inhibition of glycolysis preferentially impedes tumorigenicity of human lung cancer cells bearing KMT2D-inactivating mutations. Mechanistically, Kmt2d loss widely impairs epigenomic signals for super-enhancers/enhancers, including the super-enhancer for the circadian rhythm repressor Per2. Loss of Kmt2d decreases expression of PER2, which regulates multiple glycolytic genes. These findings indicate that KMT2D is a lung tumor suppressor and that KMT2D deficiency confers a therapeutic vulnerability to glycolytic inhibitors.
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Affiliation(s)
- Hunain Alam
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1901 East Road, Houston, TX 77054, USA
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1901 East Road, Houston, TX 77054, USA
| | - Shilpa S Dhar
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Manish Kumar
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chae Young Han
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chandrashekar R Ambati
- Advanced Technology Core and Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samir B Amin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1901 East Road, Houston, TX 77054, USA
| | - Bingnan Gu
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Tsai-Yu Chen
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Yu-Hsi Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX 77054, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Florian L Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX 77054, USA
| | - Nagireddy Putluri
- Advanced Technology Core and Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elsa R Flores
- Department of Molecular Oncology and Cancer Biology and Evolution Program, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, The National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Laura Baseler
- Department of Veterinary Medicine & Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1901 East Road, Houston, TX 77054, USA.
| | - Min Gyu Lee
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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8
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Bhargava A, Pathak N, Seshadri S, Bunkar N, Mishra DK, Lohiya NK, Mishra PK. Pre-clinical Validation of Mito-targeted Nano-engineered Flavonoids Isolated From Selaginella bryopteris (Sanjeevani) As A Novel Cancer Prevention Strategy. Anticancer Agents Med Chem 2019; 18:1860-1874. [PMID: 29298656 DOI: 10.2174/1871520618666171229223919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 02/13/2017] [Accepted: 11/24/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Novel bioactive plant secondary metabolites, including flavonoids, offer a spectrum of chemo-protective responses against a range of human tumor models. However, the clinical translation of these promising anti-cancer agents has been hindered largely by their poor solubility, rapid metabolism, or a combination of both, ultimately resulting in poor bioavailability upon oral administration. OBJECTIVE To circumvent the challenges associated with herbal drug development and for effective integration into clinical setting, nano-engineering is one of the emerging pragmatic strategies which has promise to deliver therapeutic concentrations of bio-actives upon oral administration. METHOD We assessed the nano-encapsulated flavonoid-rich fraction isolated from a traditional Indian herb Selaginella bryopteris (Sanjeevani) (NP.SB). Both in vitro and in vivo studies were performed to evidence the epigenetic protection mechanisms of NP.SB through a mitochondrial-targeted pre-clinical validation strategy. RESULTS The mito-protective activity of NP.SB revealed a dose-dependent effect when tested in GC-1 spg (mouse spermatogonial epithelial) and B/CMBA.Ov (mouse ovarian epithelial) following exposure to Nsuccinimidyl N-methylcarbamate, a potential human carcinogen. Smaller size, rapid internalization, faster mobility and site specific delivery conferred significant cancer protection in cultured cells. Notably, this encapsulated flavonoid supplementation; prevented emergence of neoplastic daughter clones from senescent mother phenotypes in pro-oxidant treated GC-1 spg and B/CMBA.Ov cells by selective abrogation of mitochondrial oxidative stress-induced aberrant epigenetic modifications. In vivo studies using a diethylnitrosamine and 2- acetylaminofluorene mouse model demonstrated that NP.SB has a significant inhibitory effect on tumor growth which clearly substantiated our in vitro findings. CONCLUSION Anti-carcinogenic property in conjunction with low toxicity of NP.SB, underscores the translational significance of dietary flavonoids as cancer-protective agents for preferential application in clinical settings.
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Affiliation(s)
- Arpit Bhargava
- Translational Research Laboratory, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, India.,Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neelam Pathak
- Centre for Advanced Studies in Zoology, University of Rajasthan, Jaipur, India
| | - Sriram Seshadri
- Department of Biochemistry, Nirma Univesity, Ahmedabad, India
| | - Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, India.,Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Dinesh K Mishra
- School of Pharmacy and Technology Management, Narsee Monjee Institute of Management Studies, Shirpur, India
| | - Nirmal K Lohiya
- Centre for Advanced Studies in Zoology, University of Rajasthan, Jaipur, India
| | - Pradyumna K Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, India.,Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
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9
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Bellini A, Bessoltane-Bentahar N, Bhalshankar J, Clement N, Raynal V, Baulande S, Bernard V, Danzon A, Chicard M, Colmet-Daage L, Pierron G, Le Roux L, Planchon JM, Combaret V, Lapouble E, Corradini N, Thebaud E, Gambart M, Valteau-Couanet D, Michon J, Louis-Brennetot C, Janoueix-Lerosey I, Defachelles AS, Bourdeaut F, Delattre O, Schleiermacher G. Study of chromatin remodeling genes implicates SMARCA4 as a putative player in oncogenesis in neuroblastoma. Int J Cancer 2019; 145:2781-2791. [PMID: 31018240 PMCID: PMC6771805 DOI: 10.1002/ijc.32361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/21/2019] [Accepted: 03/14/2019] [Indexed: 12/21/2022]
Abstract
In neuroblastoma (NB), genetic alterations in chromatin remodeling (CRGs) and epigenetic modifier genes (EMGs) have been described. We sought to determine their frequency and clinical impact. Whole exome (WES)/whole genome sequencing (WGS) data and targeted sequencing (TSCA®) of exonic regions of 33 CRGs/EMGs were analyzed in tumor samples from 283 NB patients, with constitutional material available for 55 patients. The frequency of CRG/EMG variations in NB cases was then compared to the Genome Aggregation Database (gnomAD). The sequencing revealed SNVs/small InDels or focal CNAs of CRGs/EMGs in 20% (56/283) of all cases, occurring at a somatic level in 4 (7.2%), at a germline level in 12 (22%) cases, whereas for the remaining cases, only tumor material could be analyzed. The most frequently altered genes were ATRX (5%), SMARCA4 (2.5%), MLL3 (2.5%) and ARID1B (2.5%). Double events (SNVs/small InDels/CNAs associated with LOH) were observed in SMARCA4 (n = 3), ATRX (n = 1) and PBRM1 (n = 1). Among the 60 variations, 24 (8.4%) targeted domains of functional importance for chromatin remodeling or highly conserved domains but of unknown function. Variations in SMARCA4 and ATRX occurred more frequently in the NB as compared to the gnomAD control cohort (OR = 4.49, 95%CI: 1.63-9.97, p = 0.038; OR 3.44, 95%CI: 1.46-6.91, p = 0.043, respectively). Cases with CRG/EMG variations showed a poorer overall survival compared to cases without variations. Genetic variations of CRGs/EMGs with likely functional impact were observed in 8.4% (24/283) of NB. Our case-control approach suggests a role of SMARCA4 as a player of NB oncogenesis.
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Affiliation(s)
- Angela Bellini
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadia Bessoltane-Bentahar
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Jaydutt Bhalshankar
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nathalie Clement
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Virginie Raynal
- Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Plateforme de Séquençage ICGex, Institut Curie, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, NGS Platform, Paris, France
| | - Virginie Bernard
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Adrien Danzon
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Mathieu Chicard
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Léo Colmet-Daage
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Laura Le Roux
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Julien M Planchon
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Valérie Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, Lyon, France
| | - Eve Lapouble
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Unité de Génétique Somatique, Institut Curie, Paris, France
| | | | - Estelle Thebaud
- Service d'Oncologie Pédiatrique, Hôpital de la Mère et l'enfant, Nantes, France
| | - Marion Gambart
- Unite d'Hemato-Oncologie, Hôpital des Enfants, Toulouse, France
| | | | - Jean Michon
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Caroline Louis-Brennetot
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Isabelle Janoueix-Lerosey
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | | | - Franck Bourdeaut
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
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10
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Fang Y, Zhang D, Hu T, Zhao H, Zhao X, Lou Z, He Y, Qin W, Xia J, Zhang X, Ye LC. KMT2A histone methyltransferase contributes to colorectal cancer development by promoting cathepsin Z transcriptional activation. Cancer Med 2019; 8:3544-3552. [PMID: 31090199 PMCID: PMC6601586 DOI: 10.1002/cam4.2226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence supports the notion that epigenetic modifiers are abnormal in carcinogenesis and have a fundamental role in cancer progression. Among these aberrant epigenetic modifiers, the function of histone methyltransferase KMT2A in somatic tumors is not well known. By analyzing KMT2A expression in patient tissues, we demonstrated that KMT2A was overexpressed in colorectal cancer tissues in comparison with adjacent normal tissues and its expression was positively correlated with cancer stages. In KMT2A-knockdown HCT116 and DLD1 cells, cell invasion and migration were consequently suppressed. In addition, KMT2A depletion effectively suppressed cancer metastasis in vivo. Mechanistically, cathepsin Z (CTSZ) was demonstrated to be an important downstream gene of KMT2A. Further studies showed that p65 could recruit KMT2A on the promoter region of the downstream gene CTSZ and knockdown of p65 could reduce the KMT2A on the promoter of CTSZ. Finally, our present study revealed that KMT2A epigenetically promotes cancer progression by targeting CTSZ, which has specific functions in cancer invasion and metastasis.
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Affiliation(s)
- Yang Fang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tingting Hu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongyan Zhao
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xuan Zhao
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhefeng Lou
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongshan He
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenzheng Qin
- Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianfu Xia
- Department of General Surgery, Wenzhou Central Hospital, Wenzhou, China
| | - Xiaohua Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Le-Chi Ye
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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11
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Triastuti A, Vansteelandt M, Barakat F, Trinel M, Jargeat P, Fabre N, Amasifuen Guerra CA, Mejia K, Valentin A, Haddad M. How Histone Deacetylase Inhibitors Alter the Secondary Metabolites of Botryosphaeria mamane, an Endophytic Fungus Isolated from Bixa orellana. Chem Biodivers 2019; 16:e1800485. [PMID: 30636097 DOI: 10.1002/cbdv.201800485] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022]
Abstract
Fungi are talented organisms able to produce several natural products with a wide range of structural and pharmacological activities. The conventional fungal cultivation used in laboratories is too poor to mimic the natural habitats of fungi, and this can partially explain why most of the genes responsible for the production of metabolites are transcriptionally silenced. The use of Histone Deacetylase inhibitors (HDACis) to perturb fungal secondary biosynthetic machinery has proven to be an effective approach for discovering new fungal natural products. The present study relates the effects of suberoylanilide hydroxamic acid (SAHA) and sodium valproate (VS) on the metabolome of Botryosphaeria mamane, an endophytic fungus isolated from Bixa orellana L. UHPLC/HR-MS analysis, integrated with four metabolomics tools: MS-DIAL, MS-FINDER, MetaboAnalyst and GNPS molecular networking, was established. This study highlighted that SAHA and VS changed metabolites in B. mamane, causing upregulation and downregulation of metabolites production. In addition, twelve compounds were detected in the extracts as metabolites structurally correlated to SAHA, indicating its important reactivity in the medium or its metabolism by the fungus. An addition of SAHA induced the production of eight metabolites while VS induced only two metabolites undetected in the control strain. This result illustrates the importance of adding HDACis to a fungal culture in order to induce metabolite production.
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Affiliation(s)
- Asih Triastuti
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France.,Laboratory Pharmaceutical Biology, Department of Pharmacy, UII, Yogyakarta, 55584, Indonesia
| | | | - Fatima Barakat
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Manon Trinel
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, UPS, 31062, Toulouse, France
| | - Nicolas Fabre
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Carlos A Amasifuen Guerra
- Escuela de Ingeniería Ambiental, Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Chachapoyas, Peru
| | - Kember Mejia
- Instituto de Investigaciones de la Amazonía Peruana, Avenida Abelardo Quiñonez Km. 4.5, Iquitos, Peru
| | - Alexis Valentin
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
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12
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Lemmers RJLF, van den Boogaard ML, van der Vliet PJ, Donlin-Smith CM, Nations SP, Ruivenkamp CAL, Heard P, Bakker B, Tapscott S, Cody JD, Tawil R, van der Maarel SM. Hemizygosity for SMCHD1 in Facioscapulohumeral Muscular Dystrophy Type 2: Consequences for 18p Deletion Syndrome. Hum Mutat 2015; 36:679-83. [PMID: 25820463 DOI: 10.1002/humu.22792] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is most often associated with variegated expression in somatic cells of the normally repressed DUX4 gene within the D4Z4-repeat array. The most common form, FSHD1, is caused by a D4Z4-repeat array contraction to a size of 1-10 units (normal range 10-100 units). The less common form, FSHD2, is characterized by D4Z4 CpG hypomethylation and is most often caused by loss-of-function mutations in the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene on chromosome 18p. The chromatin modifier SMCHD1 is necessary to maintain a repressed D4Z4 chromatin state. Here, we describe two FSHD2 families with a 1.2-Mb deletion encompassing the SMCHD1 gene. Numerical aberrations of chromosome 18 are relatively common and the majority of 18p deletion syndrome (18p-) cases have, such as these FSHD2 families, only one copy of SMCHD1. Our finding therefore raises the possibility that 18p- cases are at risk of developing FSHD. To address this possibility, we combined genome-wide array analysis data with D4Z4 CpG methylation and repeat array sizes in individuals with 18p- and conclude that approximately 1:8 18p- cases might be at risk of developing FSHD.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Colleen M Donlin-Smith
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York
| | - Sharon P Nations
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Patricia Heard
- University of Texas Health Science Center at San Antonio, Chromosome 18 Research Center, San Antonio, Texas
| | - Bert Bakker
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephen Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jannine D Cody
- University of Texas Health Science Center at San Antonio, Chromosome 18 Research Center, San Antonio, Texas
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York
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13
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Chen HJ, Awakawa T, Sun JY, Wakimoto T, Abe I. Epigenetic modifier-induced biosynthesis of novel fusaric acid derivatives in endophytic fungi from Datura stramonium L. Nat Prod Bioprospect 2013; 3:20-23. [PMCID: PMC4131616 DOI: 10.1007/s13659-013-0010-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 02/16/2013] [Indexed: 05/22/2023]
Abstract
Abstract The treatment of fungi with DNA methyltransferase (DNMT) and/or histone deacetylase (HDAC) inhibitors is a promising way to activate secondary metabolite biosynthetic pathways that are dormant under normal conditions. In this study, we included an HDAC inhibitor, suberoylanilide hydroxamic acid (SBHA), in the culture medium of endophytic fungi isolated from the medicinal plant Datura stramonium L. The production of two compounds was induced in the culture supplemented with SBHA, and their structures were determined to be the fusaric acid derivatives 5-butyl-6-oxo-1,6-dihydropyridine-2-carboxylic acid and 5-(but-9-enyl)-6-oxo-1,6-dihydropyridine-2-carboxylic acid. The result confirmed that the use of chemical epigenetic modifiers is an effective technique for promoting the expression of silent biosynthetic pathways to produce unique secondary metabolites. Graphical abstract ![]()
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Affiliation(s)
- Han-Jing Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Jie-Yin Sun
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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