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Deng L, Zhou J, Sun Y, Hu Y, Qiao J, Liu Z, Gu L, Lin D, Zhang L, Deng D. CDKN2A somatic copy number amplification in normal tissues surrounding gastric carcinoma reduces cancer metastasis risk in droplet digital PCR analysis. Gastric Cancer 2024; 27:986-997. [PMID: 38822931 DOI: 10.1007/s10120-024-01515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The CDKN2A gene is frequently affected by somatic copy number variations (SCNVs, including deletions and amplifications [SCNdel and SCNamp]) in the cancer genome. Using surgical gastric margin tissue samples (SMs) as the diploid reference in SCNV analysis via CDKN2A/P16-specific real-time PCR (P16-Light), we previously reported that the CDKN2A SCNdel was associated with a high risk of metastasis of gastric carcinoma (GC). However, the status of CDKN2A SCNVs in SMs and their clinical significance have not been reported. METHODS Peripheral white blood cell (WBC) and frozen GC and SM tissue samples were collected from patients (n = 80). Droplet digital PCR (ddPCR) was used to determine the copy number (CN) of the CDKN2A gene in tissue samples using paired WBCs as the diploid reference. RESULTS A novel P16-ddPCR system was initially established with a minimal proportion (or limit, 10%) of the detection of CDKN2A CN alterations. While CDKN2A SCNamp events were detected in both SMs and GCs, fewer CDKN2A SCNdel events were detected in SMs than in GCs (15.0% vs. 41.3%, P = 4.77E-04). Notably, significantly more SCNamp and fewer SCNdel of the CDKN2A gene were detected in SMs from GC patients without metastasis than in those from patients with lymph node metastasis by P16-ddPCR (P = 0.023). The status of CDKN2A SCNVs in SM samples was significantly associated with overall survival (P = 0.032). No cancer deaths were observed among the 11 patients with CDKN2A SCNamp. CONCLUSION CDKN2A SCNVs in SMs identified by P16-ddPCR are prevalent and significantly associated with GC metastasis and overall survival.
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Affiliation(s)
- Lewen Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yu Sun
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Ying Hu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dongmei Lin
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Debernardi S, Liszka L, Ntala C, Steiger K, Esposito I, Carlotti E, Baker A, McDonald S, Graham T, Dmitrovic B, Feakins RM, Crnogorac‐Jurcevic T. Molecular characteristics of early-onset pancreatic ductal adenocarcinoma. Mol Oncol 2024; 18:677-690. [PMID: 38145461 PMCID: PMC10920080 DOI: 10.1002/1878-0261.13576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023] Open
Abstract
The median age of patients with pancreatic ductal adenocarcinoma (PDAC) at diagnosis is 71 years; however, around 10% present with early-onset pancreatic cancer (EOPC), i.e., before age 50. The molecular mechanisms underlying such an early onset are unknown. We assessed the role of common PDAC drivers (KRAS, TP53, CDKN2A and SMAD4) and determined their mutational status and protein expression in 90 formalin-fixed, paraffin-embedded tissues, including multiple primary and matched metastases, from 37 EOPC patients. KRAS was mutated in 88% of patients; p53 was altered in 94%, and p16 and SMAD4 were lost in 86% and 71% of patients, respectively. Meta-synthesis showed a higher rate of p53 alterations in EOPC than in late-onset PDAC (94% vs. 69%, P = 0.0009) and significantly higher loss of SMAD4 (71% vs. 44%, P = 0.0025). The majority of EOPC patients accumulated aberrations in all four drivers; in addition, high tumour heterogeneity was observed across all tissues. The cumulative effect of an exceptionally high rate of alterations in all common PDAC driver genes combined with high tumour heterogeneity suggests an important mechanism underlying the early onset of PDAC.
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Affiliation(s)
- Silvana Debernardi
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Lukasz Liszka
- Department of Pathomorphology and Molecular DiagnosticsMedical University of SilesiaKatowicePoland
| | | | - Katja Steiger
- Institute of Pathology, School of Medicine and HealthTechnical University of MunichGermany
| | - Irene Esposito
- Institute of PathologyHeinrich‐Heine University and University Hospital of DusseldorfGermany
| | - Emanuela Carlotti
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Ann‐Marie Baker
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Stuart McDonald
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Trevor Graham
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Branko Dmitrovic
- Department of Pathology and Forensic MedicineClinical Hospital Center OsijekCroatia
| | - Roger M. Feakins
- Department of Cellular PathologyRoyal Free London NHS Foundation TrustUK
| | - Tatjana Crnogorac‐Jurcevic
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer InstituteQueen Mary University of LondonUK
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Zhang X, Li P, Gan Y, Xiang S, Gu L, Zhou J, Zhou X, Wu P, Zhang B, Deng D. Driving effect of P16 methylation on telomerase reverse transcriptase-mediated immortalization and transformation of normal human fibroblasts. Chin Med J (Engl) 2024:00029330-990000000-00975. [PMID: 38420748 DOI: 10.1097/cm9.0000000000003004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND P16 inactivation is frequently accompanied by telomerase reverse transcriptase (TERT) amplification in human cancer genomes. P16 inactivation by DNA methylation often occurs automatically during immortalization of normal cells by TERT. However, direct evidence remains to be obtained to support the causal effect of epigenetic changes, such as P16 methylation, on cancer development. This study aimed to provide experimental evidence that P16 methylation directly drives cancer development. METHODS A zinc finger protein-based P16-specific DNA methyltransferase (P16-Dnmt) vector containing a "Tet-On" switch was used to induce extensive methylation of P16 CpG islands in normal human fibroblast CCD-18Co cells. Battery assays were used to evaluate cell immortalization and transformation throughout their lifespan. Cell subcloning and DNA barcoding were used to track the diversity of cell evolution. RESULTS Leaking P16-Dnmt expression (without doxycycline-induction) could specifically inactivate P16 expression by DNA methylation. P16 methylation only promoted proliferation and prolonged lifespan but did not induce immortalization of CCD-18Co cells. Notably, cell immortalization, loss of contact inhibition, and anchorage-independent growth were always prevalent in P16-Dnmt&TERT cells, indicating cell transformation. In contrast, almost all TERT cells died in the replicative crisis. Only a few TERT cells recovered from the crisis, in which spontaneous P16 inactivation by DNA methylation occurred. Furthermore, the subclone formation capacity of P16-Dnmt&TERT cells was two-fold that of TERT cells. DNA barcoding analysis showed that the diversity of the P16-Dnmt&TERT cell population was much greater than that of the TERT cell population. CONCLUSION P16 methylation drives TERT-mediated immortalization and transformation of normal human cells that may contribute to cancer development.
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Affiliation(s)
- Xuehong Zhang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Paiyun Li
- Division of Etiology, Beijing Cancer Hospital, Beijing 100142, China
- Radiation Oncology Department, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ying Gan
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Shengyan Xiang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaorui Zhou
- Department of Biomedical Engineering, Peking University Cancer Hospital and Institute, Beijing 100871, China
| | - Peihuang Wu
- Department of Biomedical Engineering, Peking University Cancer Hospital and Institute, Beijing 100871, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
- Division of Etiology, Beijing Cancer Hospital, Beijing 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
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Peng H, Fu W, Chang C, Gao H, He Q, Liu Z, Cui M, Wang H, Yu Y, Wu Y, Zhang X, Jiang S, Xu C, Shen X, Zhang Z, Zhou Y, Li D, Wang Q. The transcription activity of OTX2 on p16 expression is significantly blocked by methylation of CpG shore in non-promoter of lung cancer cell lines. Transl Cancer Res 2023; 12:2582-2595. [PMID: 37969391 PMCID: PMC10643975 DOI: 10.21037/tcr-23-909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/13/2023] [Indexed: 11/17/2023]
Abstract
Background The aberrant expression of the classical tumor suppressor gene p16 is a frequent event in lung cancer mainly due to the hypermethylation of its 5'-cytosine-phosphate-guanine-3' island (Cgi). However, whether methylation happens in other regions and how p16 expression and function are affected are largely unknown. Methods Clustered Regularly Interspaced Short Palindromic Repeats/dCas9 (CRISPR/dCas9) technology was used for methylation editing at specific site of p16. The effects of methylation editing were detected by 3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethoxyphenyl)-2-(4-sulfopheny)-2H-tetrazolium, inner salt (MTS), transwell migration and wound healing tests. Chromatin immnoprecipitation-quantitative polymerase chain reaction (CHIP-qPCR) was performed to explore the impact of Cgi shore methylation on the binding abilities of transcription factors (TFs) including YY1, SP1, ZNF148 and OTX2 to p16 gene. A rescue experiment was performed to verify the regulatory effect of OTX2 on p16. The negative relationship between p16 expression and the methylation level of Cgi shore in non-promoter region was further verified with datasets from The Cancer Genome Atlas (TCGA) program and lung adenocarcinoma (LUAD) patients' samples. Results The suppressive effect of p16 Cgi shore methylation on its expression was demonstrated in both HEK293 and A549 cells using CRISPR/dCas9-mediated specific site methylation editing. Methylation of the Cgi shore in the p16 non-promoter region significantly decreased its expression and promoted cell growth and migration. The ability of OTX2 bound to p16 was significantly reduced by 19.35% after methylation modification. Over-expression of OTX2 in A549 cells partly reversed the inhibitory effect of methylation on p16 expression by 19.04%. The verification results with TCGA and LUAD patients' samples supported that the p16 Cgi shore is a key methylation regulatory region. Conclusions Our findings suggested that methylation of the Cgi shore in the p16 non-promoter region can hamper the transcriptional activity of OTX2, leading to a reduction in the expression of p16, which might contribute to the development of lung cancer.
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Affiliation(s)
- Honghao Peng
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wenfan Fu
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Chong Chang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Huan Gao
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qianmei He
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ziqi Liu
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Mengxing Cui
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Han Wang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongjiang Yu
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yonghui Wu
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Xue Zhang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shuyun Jiang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Chi Xu
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyu Shen
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhihan Zhang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yixiang Zhou
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, Li Y, Gao N, Jung SY, Creighton CJ, Li JJ, Cui Y, Arimura S, Lei Y, Li W, Shen L. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res 2023; 42:113. [PMID: 37143122 PMCID: PMC10157929 DOI: 10.1186/s13046-023-02689-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Methylation of the p16 promoter resulting in epigenetic gene silencing-known as p16 epimutation-is frequently found in human colorectal cancer and is also common in normal-appearing colonic mucosa of aging individuals. Thus, to improve clinical care of colorectal cancer (CRC) patients, we explored the role of age-related p16 epimutation in intestinal tumorigenesis. METHODS We established a mouse model that replicates two common genetic and epigenetic events observed in human CRCs: Apc mutation and p16 epimutation. We conducted long-term survival and histological analysis of tumor development and progression. Colonic epithelial cells and tumors were collected from mice and analyzed by RNA sequencing (RNA-seq), quantitative PCR, and flow cytometry. We performed single-cell RNA sequencing (scRNA-seq) to characterize tumor-infiltrating immune cells throughout tumor progression. We tested whether anti-PD-L1 immunotherapy affects overall survival of tumor-bearing mice and whether inhibition of both epigenetic regulation and immune checkpoint is more efficacious. RESULTS Mice carrying combined Apc mutation and p16 epimutation had significantly shortened survival and increased tumor growth compared to those with Apc mutation only. Intriguingly, colon tumors with p16 epimutation exhibited an activated interferon pathway, increased expression of programmed death-ligand 1 (Pdl1), and enhanced infiltration of immune cells. scRNA-seq further revealed the presence of Foxp3+ Tregs and γδT17 cells, which contribute to an immunosuppressive tumor microenvironment (TME). Furthermore, we showed that a combined therapy using an inhibitor of DNA methylation and a PD-L1 immune checkpoint inhibitor is more effective for improving survival in tumor-bearing mice than blockade of either pathway alone. CONCLUSIONS Our study demonstrated that age-dependent p16 epimutation creates a permissive microenvironment for malignant transformation of polyps to colon cancer. Our findings provide a mechanistic rationale for future targeted therapy in patients with p16 epimutation.
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Affiliation(s)
- Li Yang
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Xiaomin Chen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Christy Lee
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jiejun Shi
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
- Present address: Department of General Surgery, Shanghai Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Emily B Lawrence
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Lanjing Zhang
- Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA
- Department of Chemical Biology, Earnest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Sumimasa Arimura
- Department of Medicine and Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA.
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MAYLINA L, KAMBAYASHI S, BABA K, IGASE M, MIZUNO T, OKUDA M. Decreased sensitivity of cyclin-dependent kinase 4/6 inhibitors, palbociclib and abemaciclib to canine lymphoma cells with high p16 protein expression and low retinoblastoma protein phosphorylation. J Vet Med Sci 2023; 85:99-104. [PMID: 36450591 PMCID: PMC9887221 DOI: 10.1292/jvms.22-0498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Canine lymphoma/leukemia cell lines with p16 protein expressions: high (17-71 and GL-1) and low (CLBL-1, CLC, Nody-1, and UL-1) were treated in vitro with cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors, palbociclib or abemaciclib. Cell proliferation decreased as a result, with higher IC50 levels observed in the high p16 (17-71 and GL-1) and one low p16 (UL-1) cell lines compared with the low p16 cells (CLBL-1, CLC, and Nody-1). As expected, palbociclib and abemaciclib treatment reduced pRb phosphorylation in a dose-dependent manner, especially in cells with low p16. These results suggest that CDK4/6 inhibitors have potential as new chemotherapeutic agents for canine lymphoma and high p16 protein expression may be used as a biomarker for resistance to CDK4/6 inhibitor therapy.
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Affiliation(s)
- Leni MAYLINA
- Laboratory of Veterinary Internal Medicine, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Division of Veterinary Internal Medicine, Department of Clinic, Reproduction and Pathology, School of Veterinary Medicine and Biomedical Sciences, IPB
University, Bogor, Indonesia
| | - Satoshi KAMBAYASHI
- Laboratory of Veterinary Internal Medicine, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Laboratory of Veterinary Internal Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Kenji BABA
- Laboratory of Veterinary Internal Medicine, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Laboratory of Veterinary Internal Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masaya IGASE
- Laboratory of Molecular Diagnosis and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Laboratory of Molecular Diagnosis and Therapeutics, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Takuya MIZUNO
- Laboratory of Molecular Diagnosis and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Laboratory of Molecular Diagnosis and Therapeutics, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masaru OKUDA
- Laboratory of Veterinary Internal Medicine, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Laboratory of Veterinary Internal Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan,Correspondence to: Okuda M: , Laboratory of Veterinary Internal Medicine,
Joint Faculty of Veterinary Medicine, Yamaguchi University, Yoshida 1677-1, Yamaguchi 753-8515, Japan
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Horii T, Morita S, Kimura M, Hatada I. Efficient generation of epigenetic disease model mice by epigenome editing using the piggyBac transposon system. Epigenetics Chromatin 2022; 15:40. [PMID: 36522780 PMCID: PMC9756621 DOI: 10.1186/s13072-022-00474-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Epigenome-edited animal models enable direct demonstration of disease causing epigenetic mutations. Transgenic (TG) mice stably expressing epigenome-editing factors exhibit dramatic and stable changes in target epigenome modifications. Successful germline transmission of a transgene from founder mice to offspring will yield a sufficient number of epigenome-edited mice for phenotypic analysis; however, if the epigenetic mutation has a detrimental phenotypic effect, it can become difficult to obtain the next generation of animals. In this case, the phenotype of founder mice must be analyzed directly. Unfortunately, current TG mouse production efficiency (TG founders per pups born) is relatively low, and improvements would increase the versatility of this technology. RESULTS In the current study, we describe an approach to generate epigenome-edited TG mice using a combination of both the dCas9-SunTag and piggyBac (PB) transposon systems. Using this system, we successfully generated mice with demethylation of the differential methylated region of the H19 gene (H19-DMR), as a model for Silver-Russell syndrome (SRS). SRS is a disorder leading to growth retardation, resulting from low insulin-like growth factor 2 (IGF2) gene expression, often caused by epimutations at the H19-IGF2 locus. Under optimized conditions, the efficiency of TG mice production using the PB system was approximately threefold higher than that using the conventional method. TG mice generated by this system showed demethylation of the targeted DNA region and associated changes in gene expression. In addition, these mice exhibited some features of SRS, including intrauterine and postnatal growth retardation, due to demethylation of H19-DMR. CONCLUSIONS The dCas9-SunTag and PB systems serve as a simple and reliable platform for conducting direct experiments using epigenome-edited founder mice.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-Machi, Maebashi, Gunma, 371-8512, Japan.
| | - Sumiyo Morita
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-Machi, Maebashi, Gunma 371-8512 Japan
| | - Mika Kimura
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-Machi, Maebashi, Gunma 371-8512 Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-Machi, Maebashi, Gunma, 371-8512, Japan. .,Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), 3-39-22 Showa-Machi, Maebashi, Gunma, 371-8511, Japan.
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Tian Y, Zhou J, Qiao J, Liu Z, Gu L, Zhang B, Lu Y, Xing R, Deng D. Detection of somatic copy number deletion of the CDKN2A gene by quantitative multiplex PCR for clinical practice. Front Oncol 2022; 12:1038380. [DOI: 10.3389/fonc.2022.1038380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
BackgroundA feasible method to detect somatic copy number deletion (SCND) of genes is still absent to date.MethodsInterstitial base-resolution deletion/fusion coordinates for CDKN2A were extracted from published articles and our whole genome sequencing (WGS) datasets. The copy number of the CDKN2A gene was measured with a quantitative multiplex PCR assay P16-Light and confirmed with whole genome sequencing (WGS).ResultsEstimated common deletion regions (CDRs) were observed in many tumor suppressor genes, such as ATM, CDKN2A, FAT1, miR31HG, PTEN, and RB1, in the SNP array-based COSMIC datasets. A 5.1 kb base-resolution CDR could be identified in >90% of cancer samples with CDKN2A deletion by sequencing. The CDKN2A CDR covers exon-2, which is essential for P16INK4A and P14ARF synthesis. Using the true CDKN2A CDR as a PCR target, a quantitative multiplex PCR assay P16-Light was programmed to detect CDKN2A gene copy number. P16-Light was further confirmed with WGS as the gold standard among cancer tissue samples from 139 patients.ConclusionThe 5.1 kb CDKN2A CDR was found in >90% of cancers containing CDKN2A deletion. The CDKN2A CDR was used as a potential target for developing the P16-Light assay to detect CDKN2A SCND and amplification for routine clinical practices.
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Sapozhnikov DM, Szyf M. Enzyme-free targeted DNA demethylation using CRISPR-dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Nat Protoc 2022; 17:2840-2881. [PMID: 36207463 DOI: 10.1038/s41596-022-00741-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
DNA methylation involves the enzymatic addition of a methyl group primarily to cytosine residues in DNA. This protocol describes how to produce complete and minimally confounded DNA demethylation of specific sites in the genome of cultured cells by clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and without the involvement of an epigenetic-modifying enzyme, the purpose of which is the evaluation of the functional (i.e., gene expression or phenotypic) consequences of DNA demethylation of specific sites that have been previously implicated in particular pathological or physiological contexts. This protocol maximizes the ability of the easily reprogrammable CRISPR-dCas9 system to assess the impact of DNA methylation from a causal rather than correlational perspective: alternative protocols for CRISPR-dCas9-based site-specific DNA methylation or demethylation rely on the recruitment of epigenetic enzymes that exhibit additional nonspecific activities at both the targeted site and throughout the genome, confounding conclusions of causality of DNA methylation. Inhibition or loss of DNA methylation is accomplished by three consecutive lentiviral transductions. The first two lentiviruses establish stable expression of dCas9 and a guide RNA, which will physically obstruct either maintenance or de novo DNA methyltransferase activity at the guide RNA target site. A third lentivirus introduces Cre recombinase to delete the dCas9 transgene, which leads to loss of dCas9 from the target site, allowing transcription factors and/or the transcription machinery to interact with the demethylated target site. This protocol requires 3-8 months to complete owing to prolonged cell passaging times, but there is little hands-on time, and no specific skills beyond basic molecular biology techniques are necessary.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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10
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Tian W, Yuan H, Qin S, Liu W, Zhang B, Gu L, Zhou J, Deng D. Kaiso phosphorylation at threonine 606 leads to its accumulation in the cytoplasm, reducing its transcriptional repression of the tumor suppressor
CDH1
. Mol Oncol 2022; 16:3192-3209. [PMID: 35851744 PMCID: PMC9441001 DOI: 10.1002/1878-0261.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/09/2022] [Accepted: 07/18/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Wei Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Hongfan Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Sisi Qin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Wensu Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
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11
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Shi J, Sun J, Liu L, Shan T, Meng H, Yang T, Wang S, Wei T, Chen B, Ma Y, Wang Q, Wang H, Liu J, Wang L. P16ink4a overexpression ameliorates cardiac remodeling of mouse following myocardial infarction via CDK4/pRb pathway. Biochem Biophys Res Commun 2022; 595:62-68. [PMID: 35093641 DOI: 10.1016/j.bbrc.2022.01.077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/19/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND P16ink4a can accumulate in senescent cells and can be induced by different oncogenic stimulations. These functions make p16ink4a a biomarker of senescence and cancer. However, the exact role of p16ink4a remains unclear in cardiovascular disease. This study was aimed to investigate the role of p16ink4a in cardiac remodeling after myocardial infarction (MI). METHODS In vivo, gain and loss of function experiments using p16ink4a overexpression and knockdown adenovirus were induced to determine the effect of p16ink4a on cardiac structure and function after MI. The in vitro effects of p16ink4a were evaluated by overexpression and knockdown adenovirus of p16ink4a on isolated neonatal mouse cardiac myocytes (NMCMs) and neonatal mouse cardiac fibroblasts (NMCFs). RESULTS Expression level of p16ink4a was increased after MI and enriched in the infarction area. In vivo, overexpression of p16ink4a protected, while knockdown of p16ink4a worsened cardiac function. In vitro, p16ink4a did not influence the hypertrophy of NMCMs. Overexpression of p16ink4a inhibited the proliferation and migration of NMCFs and reduced the level of collagen I and α-SMA. Consistently, knockdown of p16ink4a in vitro displayed the opposite effects. Further mechanism studies revealed that p16ink4a affected the expression level of cyclin-dependent kinase 4 (CDK4) and phosphorylation of retinoblastoma (pRb), which could be a potential pathway in regulating cardiac remodeling after MI. CONCLUSION Overexpression of 16ink4a in cardiac fibroblasts can ameliorate cardiac dysfunction and attenuate pathological cardiac remodeling in mice after MI by regulating the p16ink4a/CDK4/pRb pathway.
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Affiliation(s)
- Jianzhou Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiateng Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Liu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Tiankai Shan
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Haoyu Meng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Tongtong Yang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Sibo Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Tianwen Wei
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Bingrui Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yao Ma
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Qiming Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiabao Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Liansheng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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12
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Qiao J, Tian Y, Cheng X, Liu Z, Zhou J, Gu L, Zhang B, Zhang L, Ji J, Xing R, Deng D. CDKN2A Deletion Leading to Hematogenous Metastasis of Human Gastric Carcinoma. Front Oncol 2022; 11:801219. [PMID: 35004325 PMCID: PMC8733704 DOI: 10.3389/fonc.2021.801219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Somatic copy number deletion (SCND) of CDKN2A gene is the most frequent event in cancer genomes. Whether CDKN2A SCND drives human cancer metastasis is far from clear. Hematogenous metastasis is the main reason of human gastric carcinoma (GC) death. Thus, prediction GC metastasis is eagerly awaited. Method GC patients (n=408) enrolled in both a cross-sectional and a prospective cohorts were analysed. CDKN2A SCND was detected with a quantitative PCR assay (P16-Light). Association of CDKN2A SCND and GC metastasis was evaluated. Effect of CDKN2A SCND by CRISPR/Cas9 on biological behaviors of cancer cells was also studied. Results CDKN2A SCND was detected in 38.9% of GCs from patients (n=234) enrolled in the cross-sectional cohort. Association analysis showed that more CDKN2A SCND was recognized in GCs with hematogenous metastasis than those without (66.7% vs. 35.7%, p=0.014). CDKN2A SCND was detected in 36.8% of baseline pN0M0 GCs from patients (n=174) enrolled in the prospective study, the relationship between CDKN2A SCND and hematogenous metastasis throughout the follow-up period (62.7 months in median) was also significant (66.7% vs. 34.6%, p=0.016). Using CDKN2A SCND as a biomarker for predicting hematogenous metastasis of GCs, the prediction sensitivity and specificity were 66.7% and 65.4%. The results of functional experiments indicated that CDKN2A SCND could obviously downregulate P53 expression that consequently inhibited the apoptosis of MGC803 GC and HEK293T cells. This may account for hematogenous metastasis of GCs by CDKN2A SCND. Conclusion CDKN2A SCND may drive GC metastasis and could be used as a predictor for hematogenous metastasis of GCs.
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Affiliation(s)
- Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuan Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xiaojing Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Rui Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Tumor Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
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13
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Cortés-Mancera FM, Sarno F, Goubert D, Rots MG. Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:515-533. [DOI: 10.1007/978-3-031-11454-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Kramar B, Šuput D, Milisav I. Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines. PeerJ 2021; 9:e12358. [PMID: 34760375 PMCID: PMC8570159 DOI: 10.7717/peerj.12358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background One of the most frequently deleted genes in cancer is CDKN2A encoding p16. This protein is often overexpressed in senescent cells, while its suppression can bypass the oncogene-induced senescence to enable transformation and tumorigenesis. The roles of the protein p16 are recently being expanded from the cell cycle progression regulator to the cellular regulator interacting in several different pathways. Yet data on its liver and liver cells' expression are inconclusive. Methods The expression of the p16 gene in liver and liver cells was determined by RT-qPCR and compared to its protein amounts by western blotting. Results p16 is expressed at low levels in the liver and rat hepatocytes. Its expression varies from none to the considerable levels in the examined hepatocellular carcinoma cell lines (FaO and HepG2) and in immortalized mouse hepatocytes. Such significant expression differences of an important cellular regulator warrant the need to closely examine the differences in biochemical pathways correlated with the p16 expression when using hepatocytes and hepatoma liver models.
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Affiliation(s)
- Barbara Kramar
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology, Zaloska 4, Ljubljana, Slovenia
| | - Dušan Šuput
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology, Zaloska 4, Ljubljana, Slovenia
| | - Irina Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology, Zaloska 4, Ljubljana, Slovenia.,University of Ljubljana, Laboratory of oxidative stress research, Faculty of Health Sciences, Zdravstvena pot 5, Ljubljana, Slovenia
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15
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Montano E, Pollice A, Lucci V, Falco G, Affinito O, La Mantia G, Vivo M, Angrisano T. Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression. Biomolecules 2021; 11:biom11081124. [PMID: 34439790 PMCID: PMC8392192 DOI: 10.3390/biom11081124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/06/2023] Open
Abstract
The identification of the molecular mechanisms controlling early cell fate decisions in mammals is of paramount importance as the ability to determine specific lineage differentiation represents a significant opportunity for new therapies. Pancreatic Progenitor Cells (PPCs) constitute a regenerative reserve essential for the maintenance and regeneration of the pancreas. Besides, PPCs represent an excellent model for understanding pathological pancreatic cellular remodeling. Given the lack of valid markers of early endoderm, the identification of new ones is of fundamental importance. Both products of the Ink4a/Arf locus, in addition to being critical cell-cycle regulators, appear to be involved in several disease pathologies. Moreover, the locus' expression is epigenetically regulated in ES reprogramming processes, thus constituting the ideal candidates to modulate PPCs homeostasis. In this study, starting from mouse embryonic stem cells (mESCs), we analyzed the early stages of pancreatic commitment. By inducing mESCs commitment to the pancreatic lineage, we observed that both products of the Cdkn2a locus, Ink4a and Arf, mark a naïve pancreatic cellular state that resembled PPC-like specification. Treatment with epi-drugs suggests a role for chromatin remodeling in the CDKN2a (Cycline Dependent Kinase Inhibitor 2A) locus regulation in line with previous observations in other cellular systems. Our data considerably improve the comprehension of pancreatic cellular ontogeny, which could be critical for implementing pluripotent stem cells programming and reprogramming toward pancreatic lineage commitment.
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Affiliation(s)
- Elena Montano
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
| | - Alessandra Pollice
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
| | - Valeria Lucci
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
- Department of Nuclear Medicine, IRCCS—Referral Cancer Center of Basilicata (CROB), 85028 Rionero in Vulture, Italy
| | - Geppino Falco
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
- Department of Nuclear Medicine, IRCCS—Referral Cancer Center of Basilicata (CROB), 85028 Rionero in Vulture, Italy
- Biogem Scarl, Istituto di Ricerche Genetiche “Gaetano Salvatore”, 83031 Ariano Irpino, Italy
| | | | - Girolama La Mantia
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
| | - Maria Vivo
- Department of Chemistry and Biology, University of Salerno, 84084 Fisciano, Italy
- Correspondence: (M.V.); (T.A.); Tel.: +39-081-679721 (T.A.)
| | - Tiziana Angrisano
- Department of Biology, University of Naples “Federico II”, 80147 Naples, Italy; (E.M.); (A.P.); (V.L.); (G.F.); (G.L.M.)
- Correspondence: (M.V.); (T.A.); Tel.: +39-081-679721 (T.A.)
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16
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A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma. Biosci Rep 2021; 41:227938. [PMID: 33634306 PMCID: PMC7955104 DOI: 10.1042/bsr20203945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To build a novel predictive model for hepatocellular carcinoma (HCC) patients based on DNA methylation data. METHODS Four independent DNA methylation datasets for HCC were used to screen for common differentially methylated genes (CDMGs). Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to explore the biological roles of CDMGs in HCC. Univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox analysis were performed to identify survival-related CDMGs (SR-CDMGs) and to build a predictive model. The importance of this model was assessed using Cox regression analysis, propensity score-matched (PSM) analysis and stratification analysis. A validation group from the Cancer Genome Atlas (TCGA) was constructed to further validate the model. RESULTS Four SR-CDMGs were identified and used to build the predictive model. The risk score of this model was calculated as follows: risk score = (0.01489826 × methylation level of WDR69) + (0.15868618 × methylation level of HOXB4) + (0.16674959 × methylation level of CDKL2) + (0.16689301 × methylation level of HOXA10). Kaplan-Meier analysis demonstrated that patients in the low-risk group had a significantly longer overall survival (OS; log-rank P-value =0.00071). The Cox model multivariate analysis and PSM analysis identified the risk score as an independent prognostic factor (P<0.05). Stratified analysis results further confirmed this model performed well. By analyzing the validation group, the results of receiver operating characteristic (ROC) curve analysis and survival analysis further validated this model. CONCLUSION Our DNA methylation-based prognosis predictive model is effective and reliable in predicting prognosis for patients with HCC.
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17
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Yusuf AP, Abubakar MB, Malami I, Ibrahim KG, Abubakar B, Bello MB, Qusty N, Elazab ST, Imam MU, Alexiou A, Batiha GES. Zinc Metalloproteins in Epigenetics and Their Crosstalk. Life (Basel) 2021; 11:186. [PMID: 33652690 PMCID: PMC7996840 DOI: 10.3390/life11030186] [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: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these classes of proteins engage in crosstalk that fundamentally maintains the epigenome's modus operandi. Changes in the expression or function of these proteins induced by zinc deficiency or loss of function mutations in their ZBDs may lead to aberrant epigenetic reprogramming, which may worsen the risk of non-communicable chronic diseases. This review attempts to address zinc's role and its proteins in natural epigenetic programming and artificial reprogramming and briefly discusses how the ZBDs in these proteins interact with the chromatin.
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Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Naeem Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Mecca 21955, Saudi Arabia;
| | - Sara T. Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Dakahlia 35516, Egypt;
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
- AFNP Med, Haidingergasse 29, 1030 Vienna, Austria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt
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18
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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19
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Li Y, Zhang T, Zhang H, Wang X, Liu X, Huang Q, Li L. Clinical Significance of P16 Gene Methylation in Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:133-142. [PMID: 32949396 DOI: 10.1007/978-981-15-4494-1_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of death from cancer in China. The lack of early screening technologies makes most patients to be diagnosed at advanced stages with a poor prognosis which often miss the best treatment opportunities. Thus, identifying biomarkers for minimally invasive detection and prognosis of early stage disease is urgently needed. Genetic and epigenetic alterations that promote tumorigenesis and metastasis exist in multiple cancers. These aberrant alterations usually represent early events in cancer progression suggesting their potential applications as a biomarker for cancer prediction. Studies have shown that DNA methylation is one of the key factors in progression of lung cancer. P16 promoter methylation is one of the most common epigenetic change plays a key role in lung cancer. In this review, we highlight the p16 gene methylation and its clinical significance in lung cancer.
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Affiliation(s)
- Yanjun Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Tingting Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Hui Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Xiangdong Wang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Xiaozhuan Liu
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Qihong Huang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Li Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Zhengzhou University People's Hospital, Zhengzhou, Henan, China. .,Henan University People's Hospital, Zhengzhou, Henan, China. .,Department of Scientific Research and Discipline Construction, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
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20
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Matsushita J, Suzuki T, Okamura K, Ichihara G, Nohara K. Identification by TCGA database search of five genes that are aberrantly expressed and involved in hepatocellular carcinoma potentially via DNA methylation changes. Environ Health Prev Med 2020; 25:31. [PMID: 32703154 PMCID: PMC7376645 DOI: 10.1186/s12199-020-00871-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/05/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Various treatments for hepatocellular carcinoma (HCC) are utilized in clinical practice; however, the prognosis is still poor on account of high recurrence rates. DNA methylation levels of CpG islands around promoters (promoter CpGis) inversely regulate gene expression and closely involved in carcinogenesis. As a new strategy, several chemicals globally inhibiting DNA methylation have been developed aiming at reducing DNA methylation levels and maintaining the expression of tumor suppressor genes. On the other hand, since these drugs nonspecifically modify DNA methylation, they can cause serious adverse effects. In order to ameliorate the methods by targeting specific CpGs, information of cancer-related genes that are regulated by DNA methylation is required. METHODS We searched candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and which are involved in HCC cases. To do so, we first identified genes whose expression were changed in HCC by comparing gene expressions of 371 HCC tissues and 41 non-tumor tissues using the Cancer Genome Atlas (TCGA) database. The genes were further selected for poor prognosis by log-rank test of Kaplan-Meier plot and for cancer relevance by Pubmed search. Expression profiles of upregulated genes in HCC tissues were assessed by Gene Ontology (GO) analysis. Finally, using DNA methylation data of TCGA database, we selected genes whose promoter DNA methylation levels were inversely correlated with gene expression. RESULTS We found 115 genes which were significantly up- or downregulated in HCC tissues and were associated with poor prognosis and cancer relevance. The upregulated genes were significantly enriched in cell division, cell cycle, and cell proliferation. Among the upregulated genes in HCC, we identified hypomethylation of CpGis around promoters of FANCB, KIF15, KIF4A, ERCC6L, and UBE2C. In addition, TCGA data showed that the tumor suppressor gene P16 is unexpectedly overexpressed in many types of cancers. CONCLUSIONS We identified five candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and associate with cancer cases and poor prognosis in HCC. Modification of site-specific DNA methylation of these genes enables a different approach for HCC treatment with higher selectivity and lower adverse effects.
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Affiliation(s)
- Junya Matsushita
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.,Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Takehiro Suzuki
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kazuyuki Okamura
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Gaku Ichihara
- Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Keiko Nohara
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.
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21
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Zhang S, Zeng T, Hu B, Zhang YH, Feng K, Chen L, Niu Z, Li J, Huang T, Cai YD. Discriminating Origin Tissues of Tumor Cell Lines by Methylation Signatures and Dys-Methylated Rules. Front Bioeng Biotechnol 2020; 8:507. [PMID: 32528944 PMCID: PMC7264161 DOI: 10.3389/fbioe.2020.00507] [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] [Received: 03/07/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for multiple biological processes. DNA methylation in mammals acts as an epigenetic mark of transcriptional repression. Aberrant levels of DNA methylation can be observed in various types of tumor cells. Thus, DNA methylation has attracted considerable attention among researchers to provide new and feasible tumor therapies. Conventional studies considered single-gene methylation or specific loci as biomarkers for tumorigenesis. However, genome-scale methylated modification has not been completely investigated. Thus, we proposed and compared two novel computational approaches based on multiple machine learning algorithms for the qualitative and quantitative analyses of methylation-associated genes and their dys-methylated patterns. This study contributes to the identification of novel effective genes and the establishment of optimal quantitative rules for aberrant methylation distinguishing tumor cells with different origin tissues.
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Affiliation(s)
- Shiqi Zhang
- School of Life Sciences, Shanghai University, Shanghai, China.,Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Tao Zeng
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China
| | - Bin Hu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic, Guangzhou, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Zhibin Niu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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22
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Horii T, Morita S, Hino S, Kimura M, Hino Y, Kogo H, Nakao M, Hatada I. Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome. Genome Biol 2020; 21:77. [PMID: 32234052 PMCID: PMC7110793 DOI: 10.1186/s13059-020-01991-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/08/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetic modifications, including DNA methylation, play an important role in gene silencing and genome stability. Consequently, epigenetic dysregulation can cause several diseases, such as cancer, obesity, diabetes, autism, and imprinting disorders. RESULTS We validate three methods for the generation of epigenome-edited mice using the dCas9-SunTag and single-chain variable fragment-TET1 catalytic domain. We generate model mice for Silver-Russell syndrome (SRS), an imprinting disorder, by target-specific DNA demethylation in the H19 differentially methylated region. Like SRS patients, these mice show H19 upregulation and Igf2 downregulation, leading to severe intrauterine and postnatal growth retardation. CONCLUSION This is the first report of an imprinting disease model animal generated by targeted demethylation of specific loci of the epigenome in fertilized eggs. Epigenome-edited animals are also useful for exploring the causative epimutations in epigenetic diseases.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Hiroshi Kogo
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan.
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23
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Wu C, Yang P, Liu B, Tang Y. Is there a CDKN2A-centric network in pancreatic ductal adenocarcinoma? Onco Targets Ther 2020; 13:2551-2562. [PMID: 32273725 PMCID: PMC7108878 DOI: 10.2147/ott.s232464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/19/2020] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer has a high mortality rate and its incidence has risen rapidly in recent years. Meanwhile, the diagnosis and treatment of this cancer remain challenging. Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, but, currently, no sufficiently effective modalities for its treatment exist. The early diagnosis rate of pancreatic cancer is low and most patients have reached an advanced stage at the time of diagnosis. PDAC evolves from precancerous lesions and is highly aggressive and metastatic. It is essential to understand how the disease progresses and metastasizes. CDKN2A mutations are very common in PDAC. Therefore, here, we have performed a literature review and discuss the role of CDKN2A and some related genes in the development of PDAC, as well as the basis of gene targeting with a correlation coefficient of CDKN2A above 0.9 on the STRING website. It is noteworthy that the interaction of CDKN2A with each gene has been reported in the literature. The role of these genes and CDKN2A in PDAC may provide new directions that will advance the current knowledge base and treatment options since cancer progression is realized through interactions among cells. Our findings provide new insights into the treatment of PADC that can, to some extent, improve the diagnosis rate and quality of life of patients.
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Affiliation(s)
- Chu Wu
- Cancer Research Institute, Key Laboratory of Tumor Cellular & Molecular Pathology, Medical College of Hengyang, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Ping Yang
- Cancer Research Institute, Key Laboratory of Tumor Cellular & Molecular Pathology, Medical College of Hengyang, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Bingxue Liu
- Cancer Research Institute, Key Laboratory of Tumor Cellular & Molecular Pathology, Medical College of Hengyang, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Yunlian Tang
- Cancer Research Institute, Key Laboratory of Tumor Cellular & Molecular Pathology, Medical College of Hengyang, University of South China, Hengyang, Hunan 421001, People's Republic of China
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24
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Ma W, Qiao J, Zhou J, Gu L, Deng D. Characterization of novel LncRNA P14AS as a protector of ANRIL through AUF1 binding in human cells. Mol Cancer 2020; 19:42. [PMID: 32106863 PMCID: PMC7045492 DOI: 10.1186/s12943-020-01150-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/06/2020] [Indexed: 12/14/2022] Open
Abstract
Background The CDKN2A/B locus contains crucial tumor suppressors and a lncRNA gene ANRIL. However, the mechanisms that coordinately regulate their expression levels are not clear. Methods Novel RNAs transcribed from the CDKN2A gene were screened by CDKN2A-specific RNA capture deep-sequencing and confirmed by Northern blotting and clone-sequencing. Long non-coding RNA (lncRNA) binding proteins were characterized by RNA pull-down combined with mass spectrometry and RNA immunoprecipitation. LncRNA functions in human cells were studied using a set of biological assays in vitro and in vivo. Results We characterized a novel lncRNA, P14AS with its promoter in the antisense strand of the fragment near CDKN2A exon 1b in human cells. The mature P14AS is a three-exon linear cytoplasmic lncRNA (1043-nt), including an AU-rich element (ARE) in exon 1. P14AS decreases AUF1-ANRIL/P16 RNA interaction and then increases ANRIL/P16 expression by competitively binding to AUF1 P37 and P40 isoforms. Interestingly, P14AS significantly promoted the proliferation of cancer cells and tumor formation in NOD-SCID mice in a P16-independent pattern. Moreover, in human colon cancer tissues, the expression levels of P14AS and ANRIL lncRNAs were significantly upregulated compared with the paired normal tissues. Conclusion A novel lncRNA, P14AS, transcribed from the antisense strand of the CDKN2A/P14 gene, promotes colon cancer development by cis upregulating the expression of oncogenic ANRIL.
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Affiliation(s)
| | | | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing, 100142, China.
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25
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Jinesh GG, Brohl AS. The genetic script of metastasis. Biol Rev Camb Philos Soc 2020; 95:244-266. [PMID: 31663259 DOI: 10.1111/brv.12562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/24/2023]
Abstract
Metastasis is a pivotal event that changes the course of cancers from benign and treatable to malignant and difficult to treat, resulting in the demise of patients. Understanding the genetic control of metastasis is thus crucial to develop efficient and sustainable targeted therapies. Here we discuss the alterations in epigenetic mechanisms, transcription, chromosomal instability, chromosome imprinting, non-coding RNAs, coding RNAs, mutant RNAs, enhancers, G-quadruplexes, and copy number variation to dissect the genetic control of metastasis. We conclude that the genetic control of metastasis is predominantly executed through epithelial to mesenchymal transition and evasion of cell death. We discuss how genetic regulatory mechanisms can be harnessed for therapeutic purposes to achieve sustainable control over cancer metastasis.
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Affiliation(s)
- Goodwin G Jinesh
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
| | - Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
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26
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Total Panax notoginseng saponin inhibits vascular smooth muscle cell proliferation and migration and intimal hyperplasia by regulating WTAP/p16 signals via m 6A modulation. Biomed Pharmacother 2020; 124:109935. [PMID: 31986407 DOI: 10.1016/j.biopha.2020.109935] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/14/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Intimal hyperplasia, the key event of arterial restenosis, is a result of vascular smooth muscle cell (VSMC) proliferation and migration. Previous studies have demonstrated that total Panax notoginseng saponin (TPNS) represses intimal hyperplasia and inhibits the proliferation of VSMCs following balloon injury. However, the underlying roles of TPNS in intimal hyperplasia remain unclear. In this study, we first found that TPNS inhibited the intimal hyperplasia and reversed the reduced m6A quantity in balloon catheter-injured rat carotid artery. Then, we measured the expression profiles of m6A "writers" (i.e., methyltransferase like 3 (METTL3), methyltransferase like 14 (METTL14), and WT1 associated protein (WTAP)) and "erasers" (i.e., FTO alpha-ketoglutarate dependent dioxygenase (FTO) and alkB homolog 5, RNA demethylase (ALKBH5)) in vivo and found that TPNS up-regulated the reduced the WTAP expression in balloon catheter-injured rat carotid artery. Furthermore, we illustrated that TPNS inhibited the viability, proliferation, and migration potential of VSMCs via promotion of WTAP expression and suppression of WTAP restored the TPNS-induced inhibition of cell viability, proliferation and migration potential of VSMCs. In addition, we found that p16 was up-regulated in VSMCs treated with TPNS and repression of p16 restored the TPNS-induced inhibition of cell viability, proliferation and migration potential of VSMCs. Finally, we elucidated that, mechanistically, WTAP exerted its role by regulating p16 via m6A modification. Collectively, our results reveal the WTAP-p16 signaling axis and highlight the critical roles of m6A modification in intimal hyperplasia. Thus, this study provided a potential biomarker for the assessment of intimal hyperplasia risk following angioplasty as well as a novel therapeutic target for this disease.
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27
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Editing DNA Methylation in Mammalian Embryos. Int J Mol Sci 2020; 21:ijms21020637. [PMID: 31963664 PMCID: PMC7014263 DOI: 10.3390/ijms21020637] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 01/08/2023] Open
Abstract
DNA methylation in mammals is essential for numerous biological functions, such as ensuring chromosomal stability, genomic imprinting, and X-chromosome inactivation through transcriptional regulation. Gene knockout of DNA methyltransferases and demethylation enzymes has made significant contributions to analyzing the functions of DNA methylation in development. By applying epigenome editing, it is now possible to manipulate DNA methylation in specific genomic regions and to understand the functions of these modifications. In this review, we first describe recent DNA methylation editing technology. We then focused on changes in DNA methylation status during mammalian gametogenesis and preimplantation development, and have discussed the implications of applying this technology to early embryos.
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28
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Li P, Gan Y, Qin S, Han X, Cui C, Liu Z, Zhou J, Gu L, Lu ZM, Zhang B, Deng D. DNA hydroxymethylation increases the susceptibility of reactivation of methylated P16 alleles in cancer cells. Epigenetics 2019; 15:618-631. [PMID: 31790633 DOI: 10.1080/15592294.2019.1700004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is well established that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidation steps, a certain proportion of 5hmCs remain in the genome. Although 5hmCs contribute to the flexibility of chromatin and protect bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In this present study, we have engineered a zinc-finger protein-based P16-specific DNA dioxygenase (P16-TET) to induce P16 hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that although the hydroxymethylated P16 alleles retain transcriptionally inactive, hydroxymethylation could increase the susceptibility of reactivation of methylated P16 alleles.
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Affiliation(s)
- Paiyun Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Ying Gan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Sisi Qin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Xiao Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Chenghua Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Zhe-Ming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute , Beijing, China
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29
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Li P, Zhang X, Gu L, Zhou J, Deng D. P16 methylation increases the sensitivity of cancer cells to the CDK4/6 inhibitor palbociclib. PLoS One 2019; 14:e0223084. [PMID: 31652270 PMCID: PMC6814222 DOI: 10.1371/journal.pone.0223084] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
The P16 (CDKN2Aink4a) gene is an endogenous CDK4/6 inhibitor. Palbociclib (PD0332991) is an anti-CDK4/6 chemical for cancer treatment. P16 is most frequently inactivated by copy number deletion and DNA methylation in cancers. It is well known that cancer cells with P16 deletion are more sensitive to palbociclib than those without. However, whether P16 methylation is related to palbociclib sensitivity is not known. By analyzing public pharmacogenomic datasets, we found that the IC50 of palbociclib in cancer cell lines (n = 522) was positively correlated with both the P16 expression level and P16 gene copy number. Our experimental results further showed that cancer cell lines with P16 methylation were more sensitive to palbociclib than those without. To determine whether P16 methylation directly increased the sensitivity of cancer cells to palbociclib, we induced P16 methylation in the lung cancer cell lines H661 and HCC827 and the gastric cancer cell line BGC823 via an engineered P16-specific DNA methyltransferase (P16-Dnmt) and found that the sensitivity of these cells to palbociclib was significantly increased. The survival rate of P16-Dnmt cells was significantly lower than that of vector control cells 48 hrs post treatment with palbociclib (10 μM). Notably, palbociclib treatment also selectively inhibited the proliferation of the P16-methylated subpopulation of P16-Dnmt cells, further indicating that P16 methylation can increase the sensitivity of cells to this CDK4/6 inhibitor. These results were confirmed in an animal experiment. In conclusion, inactivation of the P16 gene by DNA methylation can increase the sensitivity of cancer cells to palbociclib.
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Affiliation(s)
- Paiyun Li
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xuehong Zhang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
- * E-mail:
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30
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Liu Z, Cheng X, Zhang L, Zhou J, Deng D, Ji J. A panel of DNA methylated markers predicts metastasis of pN 0M 0 gastric carcinoma: a prospective cohort study. Br J Cancer 2019; 121:529-536. [PMID: 31431673 PMCID: PMC6889426 DOI: 10.1038/s41416-019-0552-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The aim of this prospective study was to evaluate the feasibility of predicting GC metastasis using CDH1, GFRA1, P16 and ZNF382 DNA methylation as biomarkers. METHODS 198 GC patients without metastasis at the time of surgery resection were recruited into the double-blind cohort (NCT02159339). Gene methylation was analysed using MethyLight assays. GC metastasis and survival data were obtained from 178 patients with 94.7% compliance during follow-up. RESULTS Twenty six cases of metastasis and 5 cases of recurrence were observed in 178 cases (17.4%) during the follow-up (median, 62.7 months). The GC metastasis rate for GFRA1 methylation-positive patients was significantly reduced compared with GFRA1 methylation-negative patients (odds ratio [OR]: 0.23, 95% confidence interval [CI] 0.08-0.66). Similar results were also observed using ZNF382 methylation as a predictor (OR: 0.17, 95% CI 0.06-0.47). A risk score including methylation of GFRA1 and ZNF382 was generated. The metastasis rate was significantly increased in high-risk GC patients (OR: 4.71, 95% CI: 1.85-12.00). GC patients with high risk had a shorter overall survival, especially for patients with stage I GC (P = 0.024). CONCLUSIONS The combination of GFRA1 and ZNF382 methylation is a biomarker panel for the prediction of GC metastasis.
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Affiliation(s)
- Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Xiaojing Cheng
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Lianhai Zhang
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China.
| | - Jiafu Ji
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China.
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Li R, Yang YE, Yin YH, Zhang MY, Li H, Qu YQ. Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers. J Transl Med 2019; 17:324. [PMID: 31558162 PMCID: PMC6764142 DOI: 10.1186/s12967-019-2068-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Background DNA methylation can regulate the role of long noncoding RNAs (lncRNAs) in the development of lung adenocarcinoma (LUAD). The present study aimed to identify methylation-driven lncRNAs and mRNAs as biomarkers in the prognosis of LUAD using bioinformatics analysis. Methods Differentially expressed RNAs were obtained using the edge R package from 535 LUAD tissues and 59 adjacent non-LUAD tissues. Differentially methylated genes were obtained using the limma R package from 475 LUAD tissues and 32 adjacent non-LUAD tissues. Methylation-driven mRNA and lncRNA were obtained using the MethylMix R package from 465 LUAD tissues with matched DNA methylation and RNA expression and 32 non-LUAD tissues with DNA methylation. Gene ontology and ConsensusPathDB pathway analysis were performed to identify functional enrichment of methylation-driven mRNAs. Univariate and multivariate Cox regression analyses were performed to identify the independent effect of each variable for predicting the prognosis of LUAD. Kaplan–Meier curve analysis of DNA methylation and gene expression might provide potential prognostic biomarkers for LUAD patients. Results A total of 99 methylation-driven mRNAs and 17 methylation-driven lncRNAs were obtained. Univariate and multivariate Cox regression analysis showed that 6 lncRNAs (FOXE1, HOXB13-AS1_2, VMO1, HIST1H3F, AJ003147.8, ASXL3) were retrieved to construct a predictive model associated with overall survival in LUAD patients. Combined DNA methylation and gene expression survival analysis revealed that 4 lncRNAs (AC023824.1, AF186192.1, LINC01354 and WASIR2) and 8 mRNAs (S1PR1, CCDC181, F2RL1, EFS, KLHDC9, MPV17L, GKN2, ITPRIPL1) might act as independent biomarkers for the prognosis of LUAD. Conclusions Methylation-driven lncRNA and mRNA contribute to the survival of LUAD, and 4 lncRNAs and 8 mRNAs might be potential biomarkers for the prognosis of LUAD.
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Affiliation(s)
- Rui Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yi-E Yang
- Department of Clinical Laboratory, Qianfoshan Hospital of Shandong Province, Jinan, 250014, China
| | - Yun-Hong Yin
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Meng-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Hao Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Yi-Qing Qu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
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32
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Liu Z, Lin H, Gan Y, Cui C, Zhang B, Gu L, Zhou J, Zhu G, Deng D. P16 Methylation Leads to Paclitaxel Resistance of Advanced Non-Small Cell Lung Cancer. J Cancer 2019; 10:1726-1733. [PMID: 31205528 PMCID: PMC6547999 DOI: 10.7150/jca.26482] [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: 04/04/2018] [Accepted: 01/12/2019] [Indexed: 01/07/2023] Open
Abstract
Paclitaxel-based chemotherapy is widely used as the first-line treatment for non-small cell lung cancer (NSCLC). However, only 20%-40% of patients have shown sensitivity to paclitaxel. This study aimed to investigate whether P16 methylation could be used to predict paclitaxel chemosensitivity of NSCLC. Advanced NSCLC (N=45) were obtained from patients who were enrolled in a phase-III randomized paclitaxel-based clinical trial. Genomic DNA samples were extracted from the biopsies prior to chemotherapy. P16 methylation was detected using MethyLight. The association between P16 methylation and the sensitivity of paclitaxel in cell lines was determined by in vitro assay using a P16-specific DNA demethylase (P16-TET) and methyltransferase (P16-Dnmt). The total response rate of the low-dose paclitaxel-based chemo-radiotherapy was significantly lower in P16 methylation-positive NSCLCs than that in the P16 methylation-negative NSCLCs (2/15 vs. 16/30: adjusted OR=0.085; 95%CI, 0.012-0.579). Results revealed that P16 demethylation significantly decreased paclitaxel resistance of lung cancer H1299 cells (IC50 values decreased from 2.15 to 1.13 µg/ml, P<0.001). In contrast, P16-specific methylation by P16-Dnmt significantly increased paclitaxel resistance of lung cancer HCC827 cells and gastric cancer BGC823 cells (IC50 values increased from 18.2 to 24.0 ng/ml and 0.18 to 0.81 µg/ml, respectively; P=0.049 and <0.001, respectively). The present results suggest that P16 methylation may lead to paclitaxel resistance and be a predictor of paclitaxel chemosensitivity of NSCLC.
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Affiliation(s)
- Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Hongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research, Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142
- National Clinical Research Center for Respiratory Diseases, Department of Radiation Oncology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Ying Gan
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Chenghua Cui
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
| | - Guangying Zhu
- Key Laboratory of Carcinogenesis and Translational Research, Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142
- National Clinical Research Center for Respiratory Diseases, Department of Radiation Oncology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, Division of Etiology
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33
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Jiao Y, Feng Y, Wang X. Regulation of Tumor Suppressor Gene CDKN2A and Encoded p16-INK4a Protein by Covalent Modifications. BIOCHEMISTRY (MOSCOW) 2018; 83:1289-1298. [PMID: 30482142 DOI: 10.1134/s0006297918110019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
CDKN2A is one of the most studied tumor suppressor genes. It encodes the p16-INK4a protein that plays a critical role in the cell cycle progression, differentiation, senescence, and apoptosis. Mutations in CDKN2A or dysregulation of its functional activity are frequently associated with various types of human cancer. As a cyclin-dependent kinase inhibitor, p16-INK4a forms a complex with cyclin-dependent kinases 4/6 (CDK4/6) thereby competing with cyclin D. It is believed that the helix-turn-helix structures in the content of tandem ankyrin repeats in p16-INK4a are required for the protein interaction with CDK4. Until recently, the mechanisms considered to be involved in the regulation of p16-INK4a functions and cancer development have been mutations in DNA, homozygous or heterozygous gene loss, and methylation of CDKN2A promoter region. In this review, we discuss recent findings on the regulation of p16-INK4a by covalent modifications at both transcriptional and post-translational levels.
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Affiliation(s)
- Yang Jiao
- School of Physical Education, Northeast Normal University, Changchun, Jilin, 130024, P. R. China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal University, Changchun, Jilin, 130024, P. R. China
| | - Xiuli Wang
- Central Laboratory of General Biology, School of Life Sciences, Northeast Normal University, Changchun, Jilin, 130024, P. R. China.
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Abstract
DNA methylation plays important roles in determining cellular identity, disease, and environmental responses, but little is known about the mechanisms that drive methylation changes during cellular differentiation and tumorigenesis. Meanwhile, the causal relationship between DNA methylation and transcription remains incompletely understood. Recently developed targeted DNA methylation manipulation tools can address these gaps in knowledge, leading to new insights into how methylation governs gene expression. Here, we summarize technological developments in the DNA methylation editing field and discuss the remaining challenges facing current tools, as well as potential future directions.
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Affiliation(s)
- Yong Lei
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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35
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Liu H, Liu Z, Liu XW, Xu S, Wang L, Liu Y, Zhou J, Gu L, Gao Y, Liu XY, Shi H, Sun Z, Deng D. A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral epithelial dysplasia: observation from a prospective study. BMC Cancer 2018; 18:918. [PMID: 30249192 PMCID: PMC6154879 DOI: 10.1186/s12885-018-4787-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/31/2018] [Indexed: 01/18/2023] Open
Abstract
Background Total P16 methylation (P16M), including P16 hydroxymethylation (P16H) and true-P16M, correlates with malignant transformation of oral epithelial dysplasia (OED). Both true-P16M and P16H are early events in carcinogenesis. The aim of this study is to prospectively determine if discrimination of true-P16M from P16H is necessary for prediction of cancer development from OEDs. Methods Patients (n = 265) with mild or moderate OED were recruited into the double blind two-center cohort. Total-P16M and P16H were analyzed using the 115-bp MethyLight, TET-assisted bisulfite (TAB) methylation-specific PCR (MSP), and TAB-sequencing. Total-P16M-positive and P16H-negative samples were defined as true-P16M-positive. Progression of OEDs was monitored for a minimum 24 months follow-up period. Results P16H was detected in 23 of 73 (31.5%) total-P16M-positive OEDs. Follow-up information was obtained from 247 patients with an ultimate compliance rate of 93.2%. OED-derived squamous cell carcinomas were observed in 13.0% (32/247) patients during follow-up (median, 41.0 months). The cancer progression rate for total-P16M-positive patients was significantly increased when compared to total-P16M-negative patients [23.3% vs 8.6%; adjusted odds ratio = 2.67 (95% CI: 1.19–5.99)]. However, the cancer progression rates were similar between P16H- and true-P16M-positive OEDs [26.1% (6/23) vs 22.0% (11/50); odds ratio = 0.80 (95% CI: 0.22–2.92)]. The cancer-free survival was also similar for these patients. Conclusion P16H and true-P16M are similar biomarkers for determining malignant potential of OEDs. Discrimination of P16H from true-P16M, at least in OED, may be not necessary in clinical applications. Trial registration This study is registered prospectively in the U.S. National Institutes of Health Clinical Trials Protocol Registration System (trial number NCT02967120, available at https://ClinicalTrials.gov/ct2/show/NCT02967120). Electronic supplementary material The online version of this article (10.1186/s12885-018-4787-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University School of Stomatology, Beijing, 100081, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Aetiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Xue-Wei Liu
- Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Si Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University School of Stomatology, Beijing, 100081, China
| | - Lei Wang
- Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Yang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University School of Stomatology, Beijing, 100081, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Aetiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Aetiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yan Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University School of Stomatology, Beijing, 100081, China
| | - Xiao-Yong Liu
- Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Huidong Shi
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zheng Sun
- Capital Medical University School of Stomatology, Beijing, 100050, China.
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Aetiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Tong Y, Sun J, Wong CF, Kang Q, Ru B, Wong CN, Chan AS, Leung SY, Zhang J. MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. Genome Biol 2018; 19:73. [PMID: 29871649 PMCID: PMC5989391 DOI: 10.1186/s13059-018-1442-0] [Citation(s) in RCA: 16] [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: 10/27/2017] [Accepted: 05/03/2018] [Indexed: 12/11/2022] Open
Abstract
Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumorigenesis called MICMIC. Many predictions are directly validated by dCas9-based epigenetic editing to support the accuracy and efficiency of our tool. Oncogenic and lineage-specific transcription factors are shown to aberrantly shape the methylation landscape by modifying tumor-subtype core regulatory circuitry. Notably, the gene regulatory networks orchestrated by enhancer methylation across different cancer types are seen to converge on a common architecture. MICMIC is available on https://github.com/ZhangJlab/MICMIC .
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Affiliation(s)
- Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chi Fat Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Qingzheng Kang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - April Sheila Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong.
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37
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Bao L, Qian Z, Lyng MB, Wang L, Yu Y, Wang T, Zhang X, Yang H, Brünner N, Wang J, Ditzel HJ. Coexisting genomic aberrations associated with lymph node metastasis in breast cancer. J Clin Invest 2018; 128:2310-2324. [PMID: 29558370 DOI: 10.1172/jci97449] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/06/2018] [Indexed: 01/04/2023] Open
Abstract
Single cancer cell-sequencing studies currently use randomly selected cells, limiting correlations among genomic aberrations, morphology, and spatial localization. We laser-captured microdissected single cells from morphologically distinct areas of primary breast cancer and corresponding lymph node metastasis and performed whole-exome or deep-target sequencing of more than 100 such cells. Two major subclones coexisted in different areas of the primary tumor, and the lymph node metastasis originated from a minor subclone in the invasive front of the primary tumor, with additional copy number changes, including chr8q gain, but no additional point mutations in driver genes. Lack of metastasis-specific driver events led us to assess whether other clonal and subclonal genomic aberrations preexisting in primary tumors contribute to lymph node metastasis. Gene mutations and copy number variations analyzed in 5 breast cancer tissue sample sets revealed that copy number variations in several genomic regions, including areas within chr1p, chr8q, chr9p, chr12q, and chr20q, harboring several metastasis-associated genes, were consistently associated with lymph node metastasis. Moreover, clonal expansion was observed in an area of morphologically normal breast epithelia, likely driven by a driver mutation and a subsequent amplification in chr1q. Our study illuminates the molecular evolution of breast cancer and genomic aberrations contributing to metastases.
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Affiliation(s)
- Li Bao
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,BGI-Shenzhen, Shenzhen, China.,Sino-Danish Breast Cancer Research Center, and.,Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Maria B Lyng
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Sino-Danish Breast Cancer Research Center, and
| | - Ling Wang
- Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuan Yu
- BGI-Shenzhen, Shenzhen, China
| | - Ting Wang
- Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,Sino-Danish Breast Cancer Research Center, and
| | - Nils Brünner
- Sino-Danish Breast Cancer Research Center, and.,Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,Sino-Danish Breast Cancer Research Center, and
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Sino-Danish Breast Cancer Research Center, and.,Department of Oncology, and.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
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Lu F, Xu H, Wang Q, Li M, Meng J, Kuang Y. Inhibition of enhancer of zeste homolog 2 increases the expression of p16 and suppresses the proliferation and migration of ovarian carcinoma cells in vitro and in vivo. Oncol Lett 2018; 15:3233-3239. [PMID: 29435063 DOI: 10.3892/ol.2017.7712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase, which targets histone H3 lysine 27. Studies have reported that EZH2 is involved in the development of several types of tumor, including ovarian cancer. p16, a well-known cell cycle regulator, has been demonstrated to be a tumor suppressor gene in a variety of malignant cells. However, the regulatory association between EZH2 and p16 in ovarian cancer remains to be fully elucidated. The present study aimed to determine whether EZH2 is involved in the development of ovarian cancer by regulating the expression of p16. An EZH2 short hairpin RNA (shRNA) lentiviral vector was constructed and used for transducing A2780 and SKOV3 ovarian cancer cell lines. The expression levels of EZH2 and p16 in the ovarian cancer cells were detected using a reverse transcription-quantitative polymerase chain reaction and western blot analyses, respectively. The function of the inhibition of EZH2 in cell proliferation and migration were determined using a CCK-8 assay and Transwell assay. In addition, a nude mouse xenograft model was used to determine the function of EZH2 and p16 in the formation of ovarian cancer in vivo. The results revealed that the inhibition of EZH2 increased the expression of p16, and suppressed the proliferation and migration capabilities of ovarian cancer in vitro. The downregulated expression of EZH2 suppressed ovarian tumor formation in vivo. The results of the study revealed that p16 was negatively regulated by EZH2 in ovarian cancer, and that p16 and EZH2 are important in the tumorigenesis of ovarian cancer. EZH2 and p16 represent potential biomarkers for the diagnosis of ovarian cancer and as targets for ovarian cancer gene therapy.
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Affiliation(s)
- Fangfang Lu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Hong Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Qi Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Meiyi Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jiahua Meng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yan Kuang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Gan Y, Ma W, Wang X, Qiao J, Zhang B, Cui C, Liu Z, Deng D. Coordinated transcription of ANRIL and P16 genes is silenced by P16 DNA methylation. Chin J Cancer Res 2018; 30:93-103. [PMID: 29545723 DOI: 10.21147/j.issn.1000-9604.2018.01.10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Objective To investigate the relationship between the transcription of ANRIL, P15, P14 and P16 at the same locus and the regulation mechanism of ANRIL. Methods Publicly available database of Cancer Cell Line Encyclopedia (CCLE) was used in bioinformatic analyses. Methylation of CpG islands was detected by denaturing high performance liquid chromatography (DHPLC). Gene transcript levels were determined using quantitative real-time polymerase chain reaction (qRT-PCR) assays. An engineered P16-specific transcription factor and DNA methyltransferase were used to induce P16-specific DNA demethylation and methylation. Results The expression level of ANRIL was positively and significantly correlated with that of P16 but not with that of P15 in the CCLE database. This was confirmed in human cell lines and patient colon tissue samples. In addition, ANRIL was significantly upregulated in colon cancer tissues. Transcription of ANRIL and P16 was observed only in cell lines in which the P16 alleles were unmethylated and not in cell lines with fully methylated P16 alleles. Notably, P16-specific methylation significantly decreased transcription of P16 and ANRIL in BGC823 and GES1 cells. In contrast, P16-specific demethylation re-activated transcription of ANRIL and P16 in H1299 cells (P<0.001). Alteration ofANRIL expression was not induced by P16 expression changes. Conclusions ANRIL and P16 are coordinately transcribed in human cells and regulated by the methylation status of the P16 CpG islands around the transcription start site.
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Affiliation(s)
- Ying Gan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wanru Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiuhong Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Chenghua Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Pei YF, Zhang YJ, Lei Y, Wu WD, Ma TH, Liu XQ. Hypermethylation of the CHRDL1 promoter induces proliferation and metastasis by activating Akt and Erk in gastric cancer. Oncotarget 2017; 8:23155-23166. [PMID: 28423564 PMCID: PMC5410293 DOI: 10.18632/oncotarget.15513] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/07/2017] [Indexed: 12/13/2022] Open
Abstract
CHRDL1 (Chordin-like 1) is a secreted protein that acts as an antagonist of bone morphogenetic protein (BMP). BMP plays a role as an activator of BMP receptor II (BMPR II), which mediates extracellular to intracellular signal transmission and is involved in carcinogenesis and metastasis. Herein, we report that CHRDL1 expression was significantly down-regulated in gastric cancer tissues and associated with poor survival. Clinic-pathological parameters demonstrated a close relationship between low CHRDL1 expression and metastasis. In vitro, CHRDL1 knockdown promoted tumor cell proliferation and migration through BMPR II by activating Akt, Erk and β-catenin. Furthermore, we observed the hypermethylation of the CHRDL1 promoter in gastric cancer, which induced low expression of CHRDL1 and decreased its secretion to the supernatant. Finally, in vivo experiments confirmed that CHRDL1 acted as a tumor suppressor gene in suppressing tumor growth and metastasis.
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Affiliation(s)
- Yao-Fei Pei
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang Province 310014, PR China
| | - Ya-Jing Zhang
- Department of General Surgery, Bejing Anzhen Hospital, Capital Medical University, Beijing 100000, PR China
| | - Yao Lei
- Department of Interventional Therapy and Vascular Surgery, Hunan Provincial People's Hospital, Changsha, Hunan Province 410005, PR China
| | - Wei-ding Wu
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang Province 310014, PR China
| | - Tong-Hui Ma
- Genetron Health (Beijing) Technology, Co. Ltd., Changping, Beijing 100000, PR China
| | - Xi-Qiang Liu
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang Province 310014, PR China
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Zhou X, Zhao M, Duan X, Guo B, Cheng W, Ding S, Ju H. Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity. ACS APPLIED MATERIALS & INTERFACES 2017; 9:40087-40093. [PMID: 29111659 DOI: 10.1021/acsami.7b13551] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL-1 with a detection limit of 0.045 U mL-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.
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Affiliation(s)
- Xiaoyan Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- Department of Clinical Laboratory, The Affiliated Hospital of Medical College, Qingdao University , Qingdao 266101, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Xiaolei Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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42
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Saunderson EA, Stepper P, Gomm JJ, Hoa L, Morgan A, Allen MD, Jones JL, Gribben JG, Jurkowski TP, Ficz G. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Nat Commun 2017; 8:1450. [PMID: 29133799 PMCID: PMC5684409 DOI: 10.1038/s41467-017-01078-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/16/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this is sufficient to drive cellular transformation is not clear. To investigate this question, we use a CRISPR-dCas9 epigenetic editing tool, where an inactive form of Cas9 is fused to DNA methyltransferase effectors. Using this system, here we show simultaneous de novo DNA methylation of genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN in primary breast cells isolated from healthy human breast tissue. We find that promoter methylation is maintained in this system, even in the absence of the fusion construct, and this prevents cells from engaging senescence arrest. Our data show that the key driver of this phenotype is repression of CDKN2A transcript p16 where myoepithelial cells harbour cancer-like gene expression but do not exhibit anchorage-independent growth. This work demonstrates that hit-and-run epigenetic events can prevent senescence entry, which may facilitate tumour initiation. “Although aberrant promoter DNA hypermethylation is a hallmark of cancer, it is not clear whether it is sufficient to drive transformation. Here, the authors use CRISPR-dCas9 to perform hit-and-run epigenetic editing, which prevents senescence entry in primary breast cells from healthy donors.”
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Affiliation(s)
- Emily A Saunderson
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Peter Stepper
- Institute for Biochemistry and Technical Biochemistry, Department of Biochemistry, Faculty of Chemistry, University of Stuttgart, D-70569, Stuttgart, Germany
| | - Jennifer J Gomm
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Lily Hoa
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Adrienne Morgan
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael D Allen
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J Louise Jones
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - John G Gribben
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Tomasz P Jurkowski
- Institute for Biochemistry and Technical Biochemistry, Department of Biochemistry, Faculty of Chemistry, University of Stuttgart, D-70569, Stuttgart, Germany.
| | - Gabriella Ficz
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK.
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43
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Bai J, Li Y, Zhang G. Cell cycle regulation and anticancer drug discovery. Cancer Biol Med 2017; 14:348-362. [PMID: 29372101 PMCID: PMC5785171 DOI: 10.20892/j.issn.2095-3941.2017.0033] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/13/2017] [Indexed: 02/05/2023] Open
Abstract
Cellular growth, development, and differentiation are tightly controlled by a conserved biological mechanism: the cell cycle. This cycle is primarily regulated by cyclin-dependent kinase (CDK)-cyclin complexes, checkpoint kinases, and CDK inhibitors. Deregulation of the cell cycle is a hallmark of the transformation of normal cells into tumor cells. Given its importance in tumorigenesis, several cell cycle inhibitors have emerged as potential therapeutic drugs for the treatment of cancers-both as single-agent therapy and in combination with traditional cytotoxic or molecular targeting agents. In this review, we discuss the mechanisms underlying cell cycle regulation and present small-molecule anticancer drugs that are under development, including both pan-CDK inhibitors and CDK4/6-selective inhibitors. In addition, we provide an outline of some promising CDK inhibitors currently in preclinical and clinical trials that target cell cycle abnormalities in various cancers.
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Affiliation(s)
- Jingwen Bai
- Department of Oncology, Xiang’an Hospital of Xiamen University, Xiamen 361005, China
- Changjiang Scholar’s Laboratory of Shantou University Medical College (SUMC), Shantou 515041, China
| | - Yaochen Li
- Department of Oncology, Xiang’an Hospital of Xiamen University, Xiamen 361005, China
| | - Guojun Zhang
- Department of Oncology, Xiang’an Hospital of Xiamen University, Xiamen 361005, China
- Changjiang Scholar’s Laboratory of Shantou University Medical College (SUMC), Shantou 515041, China
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44
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Lei Y, Zhang X, Su J, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W, Goodell MA. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat Commun 2017; 8:16026. [PMID: 28695892 PMCID: PMC5508226 DOI: 10.1038/ncomms16026] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/18/2017] [Indexed: 12/19/2022] Open
Abstract
Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, ageing and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1. Our study presents a rapid and efficient strategy to achieve locus-specific cytosine modifications in the genome without obvious impact on global methylation in 24 h. Finally, we demonstrate our tool can induce targeted CpG methylation in mice by zygote microinjection, thereby demonstrating its potential utility in early development. Understanding how DNA methylation regulates gene expression requires the capacity to deploy it to regions of interest. The authors generate a highly rapid and locus-specific CpG methylation tool by fusing dCas9 to MQ1 DNA methyltransferase and show efficacy at multiple sites in vitro and in vivo.
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Affiliation(s)
- Yong Lei
- Department of Molecular and Human Genetics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaotian Zhang
- Department of Molecular and Human Genetics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jianzhong Su
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mira Jeong
- Department of Molecular and Human Genetics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael C Gundry
- Department of Molecular and Human Genetics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University, Houston, Texas 77030, USA
| | - Wei Li
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Margaret A Goodell
- Department of Molecular and Human Genetics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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45
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Rathnam C, Chueng STD, Yang L, Lee KB. Advanced Gene Manipulation Methods for Stem Cell Theranostics. Theranostics 2017; 7:2775-2793. [PMID: 28824715 PMCID: PMC5562215 DOI: 10.7150/thno.19443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022] Open
Abstract
In the field of tissue engineering, autologous cell sources are ideal to prevent adverse immune responses; however, stable and reliable cell sources are limited. To acquire more reliable cell sources, the harvesting and differentiation of stem cells from patients is becoming more and more common. To this end, the need to control the fate of these stem cells before transplantation for therapeutic purposes is urgent. Since transcription factors orchestrate all of the gene activities inside of a cell, researchers have developed engineered and synthetic transcription factors to precisely control the fate of stem cells allowing for safer and more effective cell sources. Engineered transcription factors, mutant fusion proteins of naturally occurring proteins, comprise the three main domains of natural transcription factors including DNA binding domains, transcriptional activation domains, and a linker domain. Several key advancements of engineered zinc finger proteins, transcriptional activator-like effectors, and deficient cas9 proteins have revolutionized the field of engineered transcription factors allowing for precise control of gene regulation. Synthetic transcription factors are chemically made transcription factor mimics that use small molecule based moieties to replicate the main functions of natural transcription factors. These include hairpin polyamides, triple helix forming oligonucleotides, and nanoparticle-based methods. Synthetic transcription factors allow for non-viral delivery and greater spatiotemporal control of gene expression. The developments in engineered and synthetic transcription factors have lowered the risk of tumorigenicity and improved differentiation capability of stem cells, as well as facilitated many key discoveries in the fields of cancer and stem cell biology, thus providing a stepping stone to advance regenerative medicine in the clinic for cell replacement therapies.
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46
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A Tox21 Approach to Altered Epigenetic Landscapes: Assessing Epigenetic Toxicity Pathways Leading to Altered Gene Expression and Oncogenic Transformation In Vitro. Int J Mol Sci 2017; 18:ijms18061179. [PMID: 28587163 PMCID: PMC5486002 DOI: 10.3390/ijms18061179] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
An emerging vision for toxicity testing in the 21st century foresees in vitro assays assuming the leading role in testing for chemical hazards, including testing for carcinogenicity. Toxicity will be determined by monitoring key steps in functionally validated molecular pathways, using tests designed to reveal chemically-induced perturbations that lead to adverse phenotypic endpoints in cultured human cells. Risk assessments would subsequently be derived from the causal in vitro endpoints and concentration vs. effect data extrapolated to human in vivo concentrations. Much direct experimental evidence now shows that disruption of epigenetic processes by chemicals is a carcinogenic mode of action that leads to altered gene functions playing causal roles in cancer initiation and progression. In assessing chemical safety, it would therefore be advantageous to consider an emerging class of carcinogens, the epigenotoxicants, with the ability to change chromatin and/or DNA marks by direct or indirect effects on the activities of enzymes (writers, erasers/editors, remodelers and readers) that convey the epigenetic information. Evidence is reviewed supporting a strategy for in vitro hazard identification of carcinogens that induce toxicity through disturbance of functional epigenetic pathways in human somatic cells, leading to inactivated tumour suppressor genes and carcinogenesis. In the context of human cell transformation models, these in vitro pathway measurements ensure high biological relevance to the apical endpoint of cancer. Four causal mechanisms participating in pathways to persistent epigenetic gene silencing were considered: covalent histone modification, nucleosome remodeling, non-coding RNA interaction and DNA methylation. Within these four interacting mechanisms, 25 epigenetic toxicity pathway components (SET1, MLL1, KDM5, G9A, SUV39H1, SETDB1, EZH2, JMJD3, CBX7, CBX8, BMI, SUZ12, HP1, MPP8, DNMT1, DNMT3A, DNMT3B, TET1, MeCP2, SETDB2, BAZ2A, UHRF1, CTCF, HOTAIR and ANRIL) were found to have experimental evidence showing that functional perturbations played “driver” roles in human cellular transformation. Measurement of epigenotoxicants presents challenges for short-term carcinogenicity testing, especially in the high-throughput modes emphasized in the Tox21 chemicals testing approach. There is need to develop and validate in vitro tests to detect both, locus-specific, and genome-wide, epigenetic alterations with causal links to oncogenic cellular phenotypes. Some recent examples of cell-based high throughput chemical screening assays are presented that have been applied or have shown potential for application to epigenetic endpoints.
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47
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Zhu B, Gong Y, Yan G, Wang D, Wang Q, Qiao Y, Hou J, Liu B, Tang C. Atorvastatin treatment modulates
p16
promoter methylation to regulate
p16
expression. FEBS J 2017; 284:1868-1881. [PMID: 28425161 DOI: 10.1111/febs.14087] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/02/2017] [Accepted: 04/18/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Boqian Zhu
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Yaoyao Gong
- Department of Gastroenterology The First Affiliated Hospital of Nanjing Medical University China
| | - Gaoliang Yan
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Dong Wang
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Qingjie Wang
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Yong Qiao
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Jiantong Hou
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Bo Liu
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
| | - Chengchun Tang
- Department of Cardiology Zhongda Hospital of Southeast University Medical School Nanjing China
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48
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Liu Z, Zhou J, Gu L, Deng D. Significant impact of amount of PCR input templates on various PCR-based DNA methylation analysis and countermeasure. Oncotarget 2016; 7:56447-56455. [PMID: 27487147 PMCID: PMC5302926 DOI: 10.18632/oncotarget.10906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/20/2016] [Indexed: 12/21/2022] Open
Abstract
Methylation changes of CpG islands can be determined using PCR-based assays. However, the exact impact of the amount of input templates (TAIT) on DNA methylation analysis has not been previously recognized. Using COL2A1 gene as an input reference, TAIT difference between human tissues with methylation-positive and -negative detection was calculated for two representative genes GFRA1 and P16. Results revealed that TAIT in GFRA1 methylation-positive frozen samples (n = 332) was significantly higher than the methylation-negative ones (n = 44) (P < 0.001). Similar difference was found in P16 methylation analysis. The TAIT-related effect was also observed in methylation-specific PCR (MSP) and denatured high performance liquid chromatography (DHPLC) analysis. Further study showed that the minimum TAIT for a successful MethyLight PCR reaction should be ≥ 9.4 ng (CtCOL2A1 ≤ 29.3), when the cutoff value of the methylated-GFRA1 proportion for methylation-positive detection was set at 1.6%. After TAIT of the methylation non-informative frozen samples (n = 94; CtCOL2A1 > 29.3) was increased above the minimum TAIT, the methylation-positive rate increased from 72.3% to 95.7% for GFRA1 and 26.6% to 54.3% for P16, respectively (Ps < 0.001). Similar results were observed in the FFPE samples. In conclusion, TAIT critically affects results of various PCR-based DNA methylation analyses. Characterization of the minimum TAIT for target CpG islands is essential to avoid false-negative results.
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Affiliation(s)
- Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
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Zeng L, Ma H, Pan S, You J, Zhang G, Yu Z, Sheng G, Fu J. LINE-1 gene hypomethylation and p16 gene hypermethylation in HepG2 cells induced by low-dose and long-term triclosan exposure: The role of hydroxyl group. Toxicol In Vitro 2016; 34:35-44. [DOI: 10.1016/j.tiv.2016.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/20/2016] [Accepted: 03/06/2016] [Indexed: 12/18/2022]
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50
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McDonald JI, Celik H, Rois LE, Fishberger G, Fowler T, Rees R, Kramer A, Martens A, Edwards JR, Challen GA. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation. Biol Open 2016; 5:866-74. [PMID: 27170255 PMCID: PMC4920199 DOI: 10.1242/bio.019067] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Advances in sequencing technology allow researchers to map genome-wide changes in DNA methylation in development and disease. However, there is a lack of experimental tools to site-specifically manipulate DNA methylation to discern the functional consequences. We developed a CRISPR/Cas9 DNA methyltransferase 3A (DNMT3A) fusion to induce DNA methylation at specific loci in the genome. We induced DNA methylation at up to 50% of alleles for targeted CpG dinucleotides. DNA methylation levels peaked within 50 bp of the short guide RNA (sgRNA) binding site and between pairs of sgRNAs. We used our approach to target methylation across the entire CpG island at the CDKN2A promoter, three CpG dinucleotides at the ARF promoter, and the CpG island within the Cdkn1a promoter to decrease expression of the target gene. These tools permit mechanistic studies of DNA methylation and its role in guiding molecular processes that determine cellular fate. Summary: We developed a CRISPR/dCas9-DNMT3A fusion protein to repress the expression of endogenous genes in combination with multiple guide RNAs. This tool can help us elucidate the role of DNA methylation in normal development and disease.
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Affiliation(s)
- James I McDonald
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Hamza Celik
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Lisa E Rois
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gregory Fishberger
- College of Arts and Science, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tolison Fowler
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Ryan Rees
- College of Arts and Science, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ashley Kramer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Andrew Martens
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - John R Edwards
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Grant A Challen
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA Developmental, Regenerative and Stem Cell Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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