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Ma X, Jiang N, Fu J, Li Y, Zhou L, Yuan L, Wang Y, Li Y. A cytosine analogue 5-azacitidine improves the accumulation of licochalcone A in licorice Glycyrrhiza inflata. J Plant Physiol 2024; 292:154145. [PMID: 38091890 DOI: 10.1016/j.jplph.2023.154145] [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: 11/18/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 02/10/2024]
Abstract
Licochalcone A (LCA) is a characteristic compound of Glycyrrhiza inflata with anti-inflammatory, antioxidant and antitumor activities. However, G. inflata produces LCA in low quantities that does not meet the market demand. In this study, we found that DNA methylation inhibitor 5-azacitidine (5-azaC) successfully improved the LCA contents in G. inflata seedlings. Transcriptome analysis revealed a series of differentially expressed genes (DEGs), including transcription factors such as MYB, ERF, WRKY, and some structural genes related to flavonoid biosynthesis. However, whole genome bisulfite sequencing (BS-seq) results showed little effect of the 5-azaC treatment on the alteration of DNA methylation on these genes, indicating the possibility that 5-azaC acts as a stimulus, but not an epigenetic modulation factor to improve the LCA content in G. inflata. Additionally, we applied the 5-azaC treatment to field plants and hairy roots and successfully increased the LCA contents in both cases. This research demonstrates the feasibility of 5-azaC treatments in future applications to improve plant production of LCA.
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Affiliation(s)
- Xiaoling Ma
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningxin Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingxian Fu
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuping Li
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijun Zhou
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Ying Wang
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongqing Li
- Guangdong Provincial Key Laboratory of Applied Botany & Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Rajesh V, Divya PK. Embryonic exposure to decitabine induces multiple neural tube defects in developing zebrafish. Fish Physiol Biochem 2023; 49:1357-1379. [PMID: 37982970 DOI: 10.1007/s10695-023-01261-x] [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: 05/20/2023] [Accepted: 11/01/2023] [Indexed: 11/21/2023]
Abstract
Neural tube defects are severe congenital disorders of the central nervous system that originate during embryonic development when the neural tube fails to close completely. It affects one to two infants per 1000 births. The aetiology is multifactorial with contributions from both genetic and environmental factors. Dysregulated epigenetic mechanisms, in particular the abnormal genome-wide methylation during embryogenesis, have been linked to developmental abnormalities including neural tube defects. The current study investigated the influence of decitabine (DCT), a DNA methylation inhibitor, on embryonic development in zebrafish, with a focus on neural tube formation. The developing zebrafish embryos were exposed to graded concentrations of decitabine (from 13.69 μM to 1 mM) before the onset of neurulation. The developmental process was monitored at regular time intervals post fertilization. At 120 h post fertilization, the developing embryos were inspected individually to determine the incidence and severity of neural tube defects. Using alizarin red staining, the cranial and caudal neural tube morphology was examined in formaldehyde fixed larvae. Anomalies in neural tube and somite development, as well as a delay in hatching, were discovered at an early stage of development. As development continued, neural tube defects became increasingly evident, and there was a concentration-dependent rise in the prevalence and severity of various neural tube defects. 90% of growing embryos in the group exposed to decitabine 1 mM had multiple neural tube malformations, and 10% had isolated neural tube defects. With several abnormalities, the caudal region of the neural tube was seriously compromised. The histopathological studies supported the malformations in neural tube. Our study revealed the harmful impact of decitabine on the development of the neural tube in growing zebrafish. Moreover, these findings support the hypothesis that the hypomethylation during embryonic development causes neural tube defects.
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Affiliation(s)
- Venugopalan Rajesh
- Department of Pharmacology, The Erode College of Pharmacy and Research Institute affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Veppampalayam, Vallipurathampalayam (Po), Erode, Chennai, Tamil Nadu, 638112, India.
| | - Pachangattupalayam Karuppusamy Divya
- Department of Pharmacology, The Erode College of Pharmacy and Research Institute affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Veppampalayam, Vallipurathampalayam (Po), Erode, Chennai, Tamil Nadu, 638112, India
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3
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Saha A, Chauhan MS, Manik RS, Palta P, Singla SK. Comparison the effects of 5-Aza-2'-deoxycytidine and zebularine on the in vitro development, blastocyst quality, methylation pattern and conception rate on handmade cloned buffalo embryos. Reprod Domest Anim 2023; 58:158-167. [PMID: 36214130 DOI: 10.1111/rda.14275] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/09/2022] [Indexed: 01/07/2023]
Abstract
In this study we treated the handmade cloned (HMC) buffalo embryos with the DNA methylation inhibitors; 5-aza-2'-deoxycytidine (AzadC) or Zebularine individually after post-fusion and during in vitro culture till eighth day. The blastocysts production rate significantly improved (p < .01) after treating embryos independently with 5 nM AzadC and 5 nM zebularine compared with 2 and 10 nM AzadC or zebularine groups, respectively. The highest cleavage rates were obtained for 5 nM treatment of AzadC and zebularine compared with other treatments and untreated control group. Quality of blastocysts were evaluated using total cell number (TCN) and the ratio of number of inner cell mass (ICM) cells/total cell number (ICM/TCN). Zebularine treatments (2/5/10 nM) significantly improved both TCN and ICM/TCN ratio compared with AzadC treatments (2/5/10 nM); however, control group TCN and ICM/TCN ratio was found lower. The methylation percentage of pDS4.1 and B. bubalis satellite DNA were comparatively more attenuated with 5 nM zebularine than 5 nM AzadC treatment. The increased in vitro development rates of the treated embryos were correlated with the decreased level of DNA methylation and the improved blastocyst quality. Following transfer of 5 nM zebularine treated embryos to 6 recipients, 4 were found to be pregnant, though the pregnancies were not carried to full term.
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Affiliation(s)
- Ambikaprasanna Saha
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India.,Dum Dum Motijheel College, Kolkata, India
| | - Manmohan S Chauhan
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Radhey S Manik
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Prabhat Palta
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Suresh K Singla
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
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Abstract
With the aging of the population, the incidence of colorectal cancer in China is increasing. One of the epigenetic alterations: CpG island methylator phenotype (CIMP) plays an important role in the incidence of colorectal cancer. Recent studies have shown that CIMP is closely related to some specific clinicopathological phenotypes and multiple molecular phenotypes in colorectal cancer. In this paper, the newest progress of CIMP colorectal cancer in chemotherapeutic drugs, targeted agents and small molecular methylation inhibitors are going to be introduced. We hope to provide potential clinical treatment strategies for personalized and precise treatment of colorectal cancer patients.
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Affiliation(s)
- Xiaofei Zhang
- Department of Medical Oncology, Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Wenjun Zhang
- Department of Colorectal Surgery, Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Pingan Cao
- Department of Medical Oncology, Dalian University Affiliated Xinhua Hospital, Dalian, China
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Zou Y, Hu X, Schewitz-Bowers LP, Stimpson M, Miao L, Ge X, Yang L, Li Y, Bible PW, Wen X, Li JJ, Liu Y, Lee RWJ, Wei L. The DNA Methylation Inhibitor Zebularine Controls CD4 + T Cell Mediated Intraocular Inflammation. Front Immunol 2019; 10:1950. [PMID: 31475011 PMCID: PMC6706956 DOI: 10.3389/fimmu.2019.01950] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023] Open
Abstract
CD4+ T cell mediated uveitis is conventionally treated with systemic immunosuppressive agents, including corticosteroids and biologics targeting key inflammatory cytokines. However, their long-term utility is limited due to various side effects. Here, we investigated whether DNA methylation inhibitor zebularine can target CD4+ T cells and control intraocular inflammation. Our results showed that zebularine restrained the expression of inflammatory cytokines IFN-γ and IL-17 in both human and murine CD4+ T cells in vitro. Importantly, it also significantly alleviated intraocular inflammation and retinal tissue damage in the murine experimental autoimmune uveitis (EAU) model in vivo, suggesting that the DNA methylation inhibitor zebularine is a candidate new therapeutic agent for uveitis.
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Affiliation(s)
- Yanli Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiao Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lauren P Schewitz-Bowers
- Translational Health Sciences, University of Bristol, Bristol, United Kingdom.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Madeleine Stimpson
- Translational Health Sciences, University of Bristol, Bristol, United Kingdom.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Li Miao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaofei Ge
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Liu Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Paul W Bible
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Wen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Richard W J Lee
- Translational Health Sciences, University of Bristol, Bristol, United Kingdom.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Chung W, Kelly AD, Kropf P, Fung H, Jelinek J, Su XY, Roboz GJ, Kantarjian HM, Azab M, Issa JPJ. Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia. Clin Epigenetics 2019; 11:106. [PMID: 31331399 PMCID: PMC6647096 DOI: 10.1186/s13148-019-0704-3] [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: 03/27/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background Guadecitabine is a novel DNA methyltransferase (DNMT) inhibitor with improved pharmacokinetics and clinical activity in a subset of patients with relapsed/refractory acute myeloid leukemia (r/r AML), but identification of this subset remains difficult. Methods To search for biomarkers of response, we measured genome-wide DNA methylation, mutations of 54 genes, and expression of a panel of 7 genes in pre-treatment samples from 128 patients treated at therapeutic doses in a phase I/II study. Results Response rate to guadecitabine was 17% (2 complete remission (CR), 3 CR with incomplete blood count recovery (CRi), or CR with incomplete platelets recovery (CRp)) in the phase I component and 23% (14 CR, 9 CRi/CRp) in phase II. There were no strong mutation or methylation predictors of response. Gene expression clustering defined a subset of patients (~ 20%) that had (i) high DNMT3B and low CDKN2B, CTCF, and CDA expression; (ii) enrichment for KRAS/NRAS mutations; (iii) frequent CpG island hypermethylation; (iv) low long interspersed nuclear element 1 (LINE-1) hypomethylation after treatment; and (v) resistance to guadecitabine in both phase I (response rate 0% vs. 33%, p = 0.07) and phase II components of the study (response rate 5% vs. 30%, p = 0.02). Multivariate analysis identified peripheral blood (PB) blasts and hemoglobin as predictors of response and cytogenetics, gene expression, RAS mutations, and hemoglobin as predictors of survival. Conclusions A subset of patients (~ 20%) with r/r AML is unlikely to benefit from guadecitabine as a single agent. In the remaining 80%, guadecitabine is a viable option with a median survival of 8 months and a 2-year survival rate of 21%. Trial registration NCT01261312. Electronic supplementary material The online version of this article (10.1186/s13148-019-0704-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA. .,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA.
| | - Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Henry Fung
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
| | | | - Gail J Roboz
- Weill Cornell Medicine, Division of Hematology and Oncology, The New York Presbyterian Hospital, New York, NY, USA
| | | | | | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
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7
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Kwon HM, Kang EJ, Kang K, Kim SD, Yang K, Yi JM. Combinatorial effects of an epigenetic inhibitor and ionizing radiation contribute to targeted elimination of pancreatic cancer stem cell. Oncotarget 2017; 8:89005-89020. [PMID: 29179494 PMCID: PMC5687664 DOI: 10.18632/oncotarget.21642] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/03/2023] Open
Abstract
Pancreatic cancer is associated with a high mortality rate, owing to de novo and acquired drug resistance, thereby leading to highly invasive and metastatic pancreatic cancer cells. Therefore, targeting pancreatic cancer stem cells (CSCs) may be a novel therapeutic strategy for the treatment of pancreatic cancer. Here, we combined a DNA methylation inhibitor (5-aza-2'-deoxycytidine; 5-aza-dC) and ionizing radiation (IR) to improve anti-cancer effects by inhibiting growth and proliferation and promoting apoptosis of pancreatic cancer cells in vitro and in vivo. Importantly, the combinatorial effect of 5-aza-dC with IR on sphere-forming pancreatic cancer cells was preferentially targeted toward CSCs through the downregulation of regulatory factors of self-renewal and CSC surface markers. We next performed the RNA sequencing to understand the underlying cellular mechanisms of the combined treatment with IR and 5-aza-dC in pancreatic cancer cells. Global transcriptome profiling indicated that the expression of the Oct4-centered transcriptional network of genes was significantly downregulated in cells with combination treatment. Our data suggested that combination treatment with DNA methylation inhibitor and IR may be a novel therapeutic strategy for pancreatic cancer. Overall, these findings support the use of epigenetic therapy in combination with radiotherapy to improve therapeutic efficacy by targeting and eradicating pancreatic CSCs.
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Affiliation(s)
- Hyun-Mi Kwon
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, South Korea
| | - Eun-Jin Kang
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, South Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook Universty, Cheonan 31116, South Korea
| | - Sung-Dae Kim
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, South Korea
| | - Kwangmo Yang
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, South Korea
| | - Joo Mi Yi
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, South Korea
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Seo JS, Choi YH, Moon JW, Kim HS, Park SH. Hinokitiol induces DNA demethylation via DNMT1 and UHRF1 inhibition in colon cancer cells. BMC Cell Biol 2017; 18:14. [PMID: 28241740 PMCID: PMC5327573 DOI: 10.1186/s12860-017-0130-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Received: 08/18/2016] [Accepted: 02/22/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND DNA hypermethylation is a key epigenetic mechanism for the silencing of many genes in cancer. Hinokitiol, a tropolone-related natural compound, is known to induce apoptosis and cell cycle arrest and has anti-inflammatory and anti-tumor activities. However, the relationship between hinokitiol and DNA methylation is not clear. The aim of our study was to explore whether hinokitiol has an inhibitory ability on the DNA methylation in colon cancer cells. RESULTS MTT data showed that hinokitiol had higher sensitivity in colon cancer cells, HCT-116 and SW480, than in normal colon cells, CCD18Co. Hinokitiol reduced DNA methyltransferase 1 (DNMT1) and ubiquitin-like plant homeodomain and RING finger domain 1 (UHRF1) expression in HCT-116 cells. In addition, the expression of ten-eleven translocation protein 1 (TET1), a known DNA demethylation initiator, was increased by hinokitiol treatment. ELISA and FACS data showed that hinokitiol increased the 5-hydroxymethylcytosine (5hmC) level in the both colon cancer cells, but 5-methylcytosine (5mC) level was not changed. Furthermore, hinokitiol significantly restored mRNA expression of O6-methylguanine DNA methyltransferase (MGMT), carbohydrate sulfotransferase 10 (CHST10), and B-cell translocation gene 4 (BTG4) concomitant with reduction of methylation status in HCT-116 cells. CONCLUSIONS These results indicate that hinokitiol may exert DNA demethylation by inhibiting the expression of DNMT1 and UHRF1 in colon cancer cells.
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Affiliation(s)
- Jung Seon Seo
- Department of Anatomy, Institute of Human Genetics, Korea University College of Medicine, 73, Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Young Ha Choi
- Department of Anatomy, Institute of Human Genetics, Korea University College of Medicine, 73, Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ji Wook Moon
- Department of Pathology, Korea University College of Medicine, 73, Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyeon Soo Kim
- Department of Anatomy, Institute of Human Genetics, Korea University College of Medicine, 73, Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sun-Hwa Park
- Department of Anatomy, Institute of Human Genetics, Korea University College of Medicine, 73, Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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Militello KT, Simon RD, Mandarano AH, DiNatale A, Hennick SM, Lazatin JC, Cantatore S. 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms. BMC Microbiol 2016; 16:130. [PMID: 27349222 PMCID: PMC4924334 DOI: 10.1186/s12866-016-0741-4] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 06/14/2016] [Indexed: 02/08/2023] Open
Abstract
Background Escherichia coli K-12 strains contain DNA cytosine methyltransferase (Dcm), which generates 5-methylcytosine at 5′CCWGG3′ sites. Although the role of 5-methylcytosine in eukaryotic gene expression is relatively well described, the role of 5-methylcytosine in bacterial gene expression is largely unknown. Results To identify genes that are controlled by 5-methylcytosine in E. coli, we compared the transcriptomes of cells grown in the absence and presence of the DNA methylation inhibitor 5-azacytidine. We observed expression changes for 63 genes. The majority of the gene expression changes occurred at early stationary phase and were up-regulations. To identify gene expression changes due to a loss of DNA methylation, we compared the expression of selected genes in a wild-type and dcm knockout strain via reverse transcription quantitative PCR. Conclusions Our data indicate that 5-azacytidine can influence gene expression by at least two distinct mechanisms: DNA methylation loss and a mechanism that is independent of DNA methylation loss. In addition, we have identified new targets of 5-methylcytosine-mediated regulation of gene expression. In summary, our data indicate that 5-azacytidine impacts the composition of the bacterial transcriptome, and the primary effect is increased gene expression at early stationary phase. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0741-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin T Militello
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
| | - Robert D Simon
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA
| | - Alexandra H Mandarano
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.,Cornell University, Ithaca, NY, 14853, USA
| | - Anthony DiNatale
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA
| | - Stacy M Hennick
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA
| | - Justine C Lazatin
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA
| | - Sarah Cantatore
- State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA
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Holleran JL, Beumer JH, McCormick DL, Johnson WD, Newman EM, Doroshow JH, Kummar S, Covey JM, Davis M, Eiseman JL. Oral and intravenous pharmacokinetics of 5-fluoro-2'-deoxycytidine and THU in cynomolgus monkeys and humans. Cancer Chemother Pharmacol 2015; 76:803-11. [PMID: 26321472 DOI: 10.1007/s00280-015-2857-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 05/06/2015] [Accepted: 08/25/2015] [Indexed: 11/24/2022]
Abstract
INTRODUCTION 5-Fluoro-2'-deoxycytidine (FdCyd; NSC48006), a fluoropyrimidine nucleoside inhibitor of DNA methylation, is degraded by cytidine deaminase (CD). Pharmacokinetic evaluation was carried out in cynomolgus monkeys in support of an ongoing phase I study of the PO combination of FdCyd and the CD inhibitor tetrahydrouridine (THU; NSC112907). METHODS Animals were dosed intravenously (IV) or per os (PO). Plasma samples were analyzed by LC-MS/MS for FdCyd, metabolites, and THU. Clinical chemistry and hematology were performed at various times after dosing. A pilot pharmacokinetic study was performed in humans to assess FdCyd bioavailability. RESULTS After IV FdCyd and THU administration, FdCyd C(max) and AUC increased with dose. FdCyd half-life ranged between 22 and 56 min, and clearance was approximately 15 mL/min/kg. FdCyd PO bioavailability after THU ranged between 9 and 25 % and increased with increasing THU dose. PO bioavailability of THU was less than 5 %, but did result in plasma concentrations associated with inhibition of its target CD. Human pilot studies showed comparable bioavailability for FdCyd (10 %) and THU (4.1 %). CONCLUSION Administration of THU with FdCyd increased the exposure to FdCyd and improved PO FdCyd bioavailability from <1 to 24 %. Concentrations of THU and FdCyd achieved after PO administration are associated with CD inhibition and hypomethylation, respectively. The schedule currently studied in phase I studies of PO FdCyd and THU is daily times three at the beginning of the first and second weeks of a 28-day cycle.
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Affiliation(s)
- Julianne L Holleran
- Cancer Therapeutics Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jan H Beumer
- Cancer Therapeutics Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,University of Pittsburgh Cancer Institute, Hillman Research Pavilion, Room G27E, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA.
| | - David L McCormick
- IIT Research Institute, 10 West 35th Street, Chicago, IL, 60616, USA
| | - William D Johnson
- IIT Research Institute, 10 West 35th Street, Chicago, IL, 60616, USA
| | - Edward M Newman
- Department of Cancer Biology, City of Hope Beckman Research Institute, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD, 20892, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD, 20892, USA
| | - Joseph M Covey
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD, 20892, USA
| | - Myrtle Davis
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD, 20892, USA
| | - Julie L Eiseman
- Cancer Therapeutics Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,University of Pittsburgh Cancer Institute, Hillman Research Pavilion, Room G27B, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA.
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