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Wang Y, Wang C, Zhong R, Wang L, Sun L. Research progress of DNA methylation in colorectal cancer (Review). Mol Med Rep 2024; 30:154. [PMID: 38963030 PMCID: PMC11240861 DOI: 10.3892/mmr.2024.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
DNA methylation is one of the earliest and most significant epigenetic mechanisms discovered. DNA methylation refers, in general, to the addition of a methyl group to a specific base in the DNA sequence under the catalysis of DNA methyltransferase, with S‑adenosine methionine as the methyl donor, via covalent bonding and chemical modifications. DNA methylation is an important factor in inducing cancer. There are different types of DNA methylation, and methylation at different sites plays different roles. It is well known that the progression of colorectal cancer (CRC) is affected by the methylation of key genes. The present review did not only discuss the potential relationship between DNA methylation and CRC but also discussed how DNA methylation affects the development of CRC by affecting key genes. Furthermore, the clinical significance of DNA methylation in CRC was highlighted, including that of the therapeutic targets and biomarkers of methylation; and the importance of DNA methylation inhibitors was discussed as a novel strategy for treatment of CRC. The present review did not only focus upon the latest research findings, but earlier reviews were also cited as references to older literature.
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Affiliation(s)
- Yuxin Wang
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116027, P.R. China
| | - Chengcheng Wang
- Comparative Medicine Department of Researching and Teaching, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Ruiqi Zhong
- Comparative Medicine Department of Researching and Teaching, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Liang Wang
- Comparative Medicine Department of Researching and Teaching, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Lei Sun
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116027, P.R. China
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2
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Uzuner U, Akkus E, Kocak A, Çelik Uzuner S. Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study. J Biomol Struct Dyn 2024; 42:6892-6903. [PMID: 37458994 DOI: 10.1080/07391102.2023.2236714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2024]
Abstract
The COVID-19 pandemic has caused havoc around the globe since 2019 and is considered the largest global epidemic of the twentieth century. Although the first antiviral drug, Remdesivir, was initially introduced against COVID‑19, virtually no tangible therapeutic drugs exist to treat SARS-CoV-2 infection. FDA-approved Paxlovid (Nirmatrelvir supplemented by Ritonavir) was recently announced as a promising drug against the SARS-CoV-2 major protease (Mpro). Here we report for the first time the remarkable inhibitory potentials of lead epigenetic-targeting drugs (epi-drugs) against SARS-CoV-2 Mpro. Epi-drugs are promising compounds to be used in combination with cancer chemotherapeutics to regulate gene expression. The search for all known epi-drugs for the specific inhibition of SARS-CoV-2 Mpro was performed for the first time by consensus (three high-order program) molecular docking studies and end-state free energy calculations. Several epi-drugs were identified with highly comparable binding affinity to SARS-CoV-2 Mpro compared to Nirmatrelvir. In particular, potent histone methyltransferase inhibitor EPZ005687 and DNA methyltransferase inhibitor Guadecitabine were prominent as the most promising epi-drug inhibitors for SARS-CoV-2 Mpro. Long Molecular dynamics (MD) simulations (200 ns each) and corresponding MM-GBSA calculations confirmed the stability of the EPZ005687-Mpro complex with MM-GBSA binding free energy (ΔGbind) -48.2 kcal/mol (EPZ005687) compared to Nirmatrelvir (-44.7 kcal/mol). Taken together, the antiviral activities of the highlighted epi-drugs are reported beyond widespread use in combination with anti-cancer agents. The current findings therefore highlight as yet unexplored antiviral potential of epi-drugs suitable for use in patients struggling with chronic immunosuppressive disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ugur Uzuner
- Synthetic and Systems Biology Innovation Hub, Texas A&M University, College Station, TX, USA
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Ebru Akkus
- Department of Bioengineering, Faculty of Science, Gebze Technical University, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Faculty of Science, Gebze Technical University, Kocaeli, Turkey
| | - Selcen Çelik Uzuner
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
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Ding Y, Zhou G, Hu W. Epigenetic regulation of TGF-β pathway and its role in radiation response. Int J Radiat Biol 2024; 100:834-848. [PMID: 38506660 DOI: 10.1080/09553002.2024.2327395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
PURPOSE Transforming growth factor (TGF-β) plays a dual role in tumor progression as well as a pivotal role in radiation response. TGF-β-related epigenetic regulations, including DNA methylation, histone modifications (including methylation, acetylation, phosphorylation, ubiquitination), chromatin remodeling and non-coding RNA regulation, have been found to affect the occurrence and development of tumors as well as their radiation response in multiple dimensions. Due to the significance of radiotherapy in tumor treatment and the essential roles of TGF-β signaling in radiation response, it is important to better understand the role of epigenetic regulation mechanisms mediated by TGF-β signaling pathways in radiation-induced targeted and non-targeted effects. CONCLUSIONS By revealing the epigenetic mechanism related to TGF-β-mediated radiation response, summarizing the existing relevant adjuvant strategies for radiotherapy based on TGF-β signaling, and discovering potential therapeutic targets, we hope to provide a new perspective for improving clinical treatment.
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Affiliation(s)
- Yunan Ding
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
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4
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Gil-Martín E, Ramos E, López-Muñoz F, Egea J, Romero A. Potential of melatonin to reverse epigenetic aberrations in oral cancer: new findings. EXCLI JOURNAL 2023; 22:1280-1310. [PMID: 38234969 PMCID: PMC10792176 DOI: 10.17179/excli2023-6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
It is now an accepted principle that epigenetic alterations cause cellular dyshomeostasis and functional changes, both of which are essential for the initiation and completion of the tumor cycle. Oral carcinogenesis is no exception in this regard, as most of the tumors in the different subsites of the oral cavity arise from the cross-reaction between (epi)genetic inheritance and the huge challenge of environmental stressors. Currently, the biochemical machinery is put at the service of the tumor program, halting the cell cycle, triggering uncontrolled proliferation, driving angiogenesis and resistance to apoptosis, until the archetypes of the tumor phenotype are reached. Melatonin has the ability to dynamically affect the epigenetic code. It has become accepted that melatonin can reverse (epi)genetic aberrations present in oral and other cancers, suggesting the possibility of enhancing the oncostatic capacity of standard multimodal treatments by incorporating this indolamine as an adjuvant. First steps in this direction confirm the potential of melatonin as a countermeasure to mitigate the detrimental side effects of conventional first-line radiochemotherapy. This single effect could produce synergies of extraordinary clinical importance, allowing doses to be increased and treatments not to be interrupted, ultimately improving patients' quality of life and prognosis. Motivated by the urgency of improving the medical management of oral cancer, many authors advocate moving from in vitro and preclinical research, where the bulk of melatonin cancer research is concentrated, to systematic randomized clinical trials on large cohorts. Recognizing the challenge to improve the clinical management of cancer, our motivation is to encourage comprehensive and robust research to reveal the clinical potential of melatonin in oral cancer control. To improve the outcome and quality of life of patients with oral cancer, here we provide the latest evidence of the oncolytic activity that melatonin can achieve by manipulating epigenetic patterns in oronasopharyngeal tissue.
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Affiliation(s)
- Emilio Gil-Martín
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, 36310 Vigo, Spain
| | - Eva Ramos
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Francisco López-Muñoz
- Faculty of Health, Camilo José Cela University of Madrid (UCJC), 28692 Madrid, Spain
- Neuropsychopharmacology Unit, Hospital 12 de Octubre Research Institute, 28041 Madrid, Spain
| | - Javier Egea
- Unidad de Investigación, Hospital Santa Cristina, Instituto de Investigación Sanitaria Princesa (IIS-IP), 28006 Madrid, Spain
| | - Alejandro Romero
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
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An L, Li M, Jia Q. Mechanisms of radiotherapy resistance and radiosensitization strategies for esophageal squamous cell carcinoma. Mol Cancer 2023; 22:140. [PMID: 37598158 PMCID: PMC10439611 DOI: 10.1186/s12943-023-01839-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/02/2023] [Indexed: 08/21/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the sixth most common cause of cancer-related mortality worldwide, with more than half of them occurred in China. Radiotherapy (RT) has been widely used for treating ESCC. However, radiation-induced DNA damage response (DDR) can promote the release of cytokines and chemokines, and triggers inflammatory reactions and changes in the tumor microenvironment (TME), thereby inhibiting the immune function and causing the invasion and metastasis of ESCC. Radioresistance is the major cause of disease progression and mortality in cancer, and it is associated with heterogeneity. Therefore, a better understanding of the radioresistance mechanisms may generate more reversal strategies to improve the cure rates and survival periods of ESCC patients. We mainly summarized the possible mechanisms of radioresistance in order to reveal new targets for ESCC therapy. Then we summarized and compared the current strategies to reverse radioresistance.
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Affiliation(s)
- Lingbo An
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China
- College of Medical Technology, Xi'an Medical University, Xi'an, China
| | - Mingyang Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China.
| | - Qingge Jia
- Department of Reproductive Medicine, Xi'an International Medical Center Hospital, Northwest University, Xi'an, China.
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Zhang D, Sun Y, Lei M, Wang Y, Cai C. Deciphering the potential ability of RG108 in cisplatin-induced HEI-OC1 ototoxicity: a research based on RNA-seq and molecular biology experiment. Hereditas 2023; 160:18. [PMID: 37088824 PMCID: PMC10124021 DOI: 10.1186/s41065-023-00283-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/11/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Drug-induced hearing loss (DIHL) is very common, and seriously affects people's happiness in life. RG108 is a small molecule inhibitor. RG108 is protective against DIHL. Our purpose is to probe the incidence of RG108 on cisplatin-induced ototoxicity. MATERIALS AND METHODS In our research, the ototoxicity of RG108 was investigated in HEI-OC1. We observed under the microscope whether RG108 had an effect on cisplatin-induced cochlear hair cells. RNA-seq experiments were further performed to explore possible gene ontology (GO) and pathways. ROS assay was applied to supervisory the effect of RG108 on oxidative harm of auditory cells. In auditory cells, RG108 was tested for its effects on apoptosis-related proteins by Western blotting (WB). RESULTS GO analysis showed that RG108 associated with apoptosis. KEGG analysis shows RG108 may act on PI3K-AKT signaling pathway (PASP) in hearing loss. BIOCARTA analysis showed that RG108 may affect oxidative stress by activating NRF2 pathway. ROS ascerted that RG108 could rescue oxidative harm in HEI-OC1. RG108 rescued cisplatin-induced significant increase in Bax and significant decrease in BCL2. RG108 attenuates cisplatin-induced cochlear apoptosis through upregulated phosphorylated PI3K and phosphorylated AKT and down-regulated caspase3. MTT experiments showed that both PI3K and AKT inhibitors could significantly rescue the damage caused by cisplatin to HEI-OC1. RG108 significantly increases the level of NRF2/HO-1/NQO1 in cisplatin-induced cells. CONCLUSION Overall, these results provide evidence that NRF2/PI3K-AKT axis may mediate RG108 in the treatment of DIHL, which provide a broader outlook on drug-induced deafness treatment.
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Affiliation(s)
- Dongdong Zhang
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
- School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yixin Sun
- School of Medicine, Xiamen University, Xiamen, 361003, China
- Department of Surgery, The Second People's Hospital of Neijiang Affiliated to Southwest Medical University, Neijiang, 641000, China
- Department of Surgery, The Second People's Hospital of Neijiang, Neijiang, 641000, China
| | - Min Lei
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
- School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yue Wang
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
| | - Chengfu Cai
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China.
- School of Medicine, Xiamen University, Xiamen, 361003, China.
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Abstract
Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance of several types of chromatin changes. The abundance of DNA lesions (chemical perturbations to nucleotides) increases with age, as does the number of genomic mutations and transcriptional disruptions caused by replication or transcription of those lesions, respectively. At the epigenetic level, precise DNA methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, the tight regulation of histone modifications begins to unravel. The genomic instability caused by these mechanisms allows transposon element reactivation and remobilization, further mutations, gene dysregulation, and cytoplasmic chromatin fragments. This cumulative genomic instability promotes cell signaling events that drive cell fate decisions and extracellular communications known to disrupt tissue homeostasis and regeneration. In this Review, we focus on age-related epigenetic changes and their interactions with age-related genomic changes that instigate these events.
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Affiliation(s)
- Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Christopher D. Faulk
- Institute on the Biology of Aging and Metabolism
- Department of Animal Science, and
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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Enhanced Cytotoxic Effects in Human Oral Squamous Cell Carcinoma Cells Treated with Combined Methyltransferase Inhibitors and Histone Deacetylase Inhibitors. Biomedicines 2022; 10:biomedicines10040763. [PMID: 35453513 PMCID: PMC9029187 DOI: 10.3390/biomedicines10040763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022] Open
Abstract
Combined treatment of human oral squamous cell carcinoma (OSCCs) with DNA methyltransferase inhibitors (DNMTis), histone methyltransferase inhibitors (HMTis), and histone deacetylase inhibitors (HDACis), and the molecular mechanisms underlying their anticancer effects, have not been fully elucidated. Herein, we investigated the cytotoxic effects of combined DNMTis (5-Aza-deoxycytidine: 5-Aza-dC, RG108), HMTis (3-deazaneplanocin A: DZNep), and HDACis (trichostatin A: TSA) treatment on human OSCC cells and explored their molecular mechanisms. Combined 5-Aza-dC, or RG108, and TSA treatment significantly decreased HSC-2 and Ca9-22 cell viability. Combinatorial DZNep and TSA treatment also decreased Ca9-22 cell viability. Although caspase 3/7 activation was not observed in HSC-2 cells following combined treatment, caspase activity was significantly increased in Ca9-22 cells treated with DZNep and TSA. Moreover, combined treatment with 5-Aza-dC, RG108, and TSA increased the proportion of HSC-2 and Ca9-22 cells in the S and G2/M phases. Meanwhile, increased phosphorylation of the histone variant H2A.X, a marker of double-stranded DNA breaks, was observed in both cells after combination treatment. Hence, the decreased viability induced by combined treatment with epigenomic inhibitors results from apoptosis and cell cycle arrest in S and G2/M phases. Thus, epigenomic therapy comprising combined low concentrations of DNMTi, HMTi, and HDACi is effective against OSCC.
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Hu C, Liu X, Zeng Y, Liu J, Wu F. DNA methyltransferase inhibitors combination therapy for the treatment of solid tumor: mechanism and clinical application. Clin Epigenetics 2021; 13:166. [PMID: 34452630 PMCID: PMC8394595 DOI: 10.1186/s13148-021-01154-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, an epigenetic modification, regulates gene transcription and maintains genome stability. DNA methyltransferase (DNMT) inhibitors can activate silenced genes at low doses and cause cytotoxicity at high doses. The ability of DNMT inhibitors to reverse epimutations is the basis of their use in novel strategies for cancer therapy. In this review, we examined the literature on DNA methyltransferase inhibitors. We summarized the mechanisms underlying combination therapy using DNMT inhibitors and clinical trials based on combining hypomethylation agents with other chemotherapeutic drugs. We also discussed the efficacy of such compounds as antitumor agents, the need to optimize treatment schedules and the regimens for maximal biologic effectiveness. Notably, the combination of DNMT inhibitors and chemotherapy and/or immune checkpoint inhibitors may provide helpful insights into the development of efficient therapeutic approaches.
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Affiliation(s)
- Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China
| | - Xiaohan Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yue Zeng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Junqi Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Fang Wu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China.
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Deregulation of Transcriptional Enhancers in Cancer. Cancers (Basel) 2021; 13:cancers13143532. [PMID: 34298745 PMCID: PMC8303223 DOI: 10.3390/cancers13143532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary One of the major challenges in cancer treatments is the dynamic adaptation of tumor cells to cancer therapies. In this regard, tumor cells can modify their response to environmental cues without altering their DNA sequence. This cell plasticity enables cells to undergo morphological and functional changes, for example, during the process of tumour metastasis or when acquiring resistance to cancer therapies. Central to cell plasticity, are the dynamic changes in gene expression that are controlled by a set of molecular switches called enhancers. Enhancers are DNA elements that determine when, where and to what extent genes should be switched on and off. Thus, defects in enhancer function can disrupt the gene expression program and can lead to tumour formation. Here, we review how enhancers control the activity of cancer-associated genes and how defects in these regulatory elements contribute to cell plasticity in cancer. Understanding enhancer (de)regulation can provide new strategies for modulating cell plasticity in tumour cells and can open new research avenues for cancer therapy. Abstract Epigenetic regulations can shape a cell’s identity by reversible modifications of the chromatin that ultimately control gene expression in response to internal and external cues. In this review, we first discuss the concept of cell plasticity in cancer, a process that is directly controlled by epigenetic mechanisms, with a particular focus on transcriptional enhancers as the cornerstone of epigenetic regulation. In the second part, we discuss mechanisms of enhancer deregulation in adult stem cells and epithelial-to-mesenchymal transition (EMT), as two paradigms of cell plasticity that are dependent on epigenetic regulation and serve as major sources of tumour heterogeneity. Finally, we review how genetic variations at enhancers and their epigenetic modifiers contribute to tumourigenesis, and we highlight examples of cancer drugs that target epigenetic modifications at enhancers.
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Lodewijk I, Nunes SP, Henrique R, Jerónimo C, Dueñas M, Paramio JM. Tackling tumor microenvironment through epigenetic tools to improve cancer immunotherapy. Clin Epigenetics 2021; 13:63. [PMID: 33761971 PMCID: PMC7992805 DOI: 10.1186/s13148-021-01046-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic alterations are known contributors to cancer development and aggressiveness. Additional to alterations in cancer cells, aberrant epigenetic marks are present in cells of the tumor microenvironment, including lymphocytes and tumor-associated macrophages, which are often overlooked but known to be a contributing factor to a favorable environment for tumor growth. Therefore, the main aim of this review is to give an overview of the epigenetic alterations affecting immune cells in the tumor microenvironment to provoke an immunosuppressive function and contribute to cancer development. Moreover, immunotherapy is briefly discussed in the context of epigenetics, describing both its combination with epigenetic drugs and the need for epigenetic biomarkers to predict response to immune checkpoint blockage. MAIN BODY Combining both topics, epigenetic machinery plays a central role in generating an immunosuppressive environment for cancer growth, which creates a barrier for immunotherapy to be successful. Furthermore, epigenetic-directed compounds may not only affect cancer cells but also immune cells in the tumor microenvironment, which could be beneficial for the clinical response to immunotherapy. CONCLUSION Thus, modulating epigenetics in combination with immunotherapy might be a promising therapeutic option to improve the success of this therapy. Further studies are necessary to (1) understand in depth the impact of the epigenetic machinery in the tumor microenvironment; (2) how the epigenetic machinery can be modulated according to tumor type to increase response to immunotherapy and (3) find reliable biomarkers for a better selection of patients eligible to immunotherapy.
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Affiliation(s)
- Iris Lodewijk
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
| | - Sandra P. Nunes
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar – University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar – University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Marta Dueñas
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jesús M. Paramio
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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12
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A novel methylation signature predicts radiotherapy sensitivity in glioma. Sci Rep 2020; 10:20406. [PMID: 33230136 PMCID: PMC7683673 DOI: 10.1038/s41598-020-77259-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma (GBM) is the most common and malignant cancer of the central nervous system, and radiotherapy is widely applied in GBM treatment; however, the sensitivity to radiotherapy varies in different patients. To solve this clinical dilemma, a radiosensitivity prediction signature was constructed in the present study based on genomic methylation. In total, 1044 primary GBM samples with clinical and methylation microarray data were involved in this study. LASSO-COX, GSVA, Kaplan–Meier survival curve analysis, and COX regression were performed for the construction and verification of predictive models. The R programming language was used as the main tool for statistical analysis and graphical work. Via the integration analysis of methylation and the survival data of primary GBM, a novel prognostic and radiosensitivity prediction signature was constructed. This signature was found to be stable in prognosis prediction in the TCGA and CGGA databases. The possible mechanism was also explored, and it was found that this signature is closely related to DNA repair functions. Most importantly, this signature could predict whether GBM patients could benefit from radiotherapy. In summary, a radiosensitivity prediction signature for GBM patients based on five methylated probes was constructed, and presents great potential for clinical application.
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13
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Shafiee-Kermani F, Carney ST, Jima D, Utin UC, Farrar LB, Oputa MO, Hines MR, Kinyamu HK, Trotter KW, Archer TK, Hoyo C, Koller BH, Freedland SJ, Grant DJ. Expression of UDP Glucuronosyltransferases 2B15 and 2B17 is associated with methylation status in prostate cancer cells. Epigenetics 2020; 16:289-299. [PMID: 32660355 DOI: 10.1080/15592294.2020.1795601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Studies have suggested that abrogated expression of detoxification enzymes, UGT2B15 and UGT2B17, are associated with prostate tumour risk and progression. We investigated the role of EGF on the expression of these enzymes since it interacts with signalling pathways to also affect prostate tumour progression and is additionally associated with decreased DNA methylation. The expression of UGT2B15, UGT2B17, de novo methyltransferases, DNMT3A and DNMT3B was assessed in prostate cancer cells (LNCaP) treated with EGF, an EGFR inhibitor PD16893, and the methyltransferase inhibitor, 5-azacytidine, respectively. The results showed that EGF treatment decreased levels of expression of all four genes and that their expression was reversed by PD16893. Treatment with 5-azacytidine, markedly decreased expression of UGT2B15 and UGT2B17 over 85% as well as significantly decreased expression of DNMT3B, but not the expression of DNMT3A. DNMT3B siRNA treated LNCaP cells had decreased expression of UGT2B15 and UGT2B17, while DNMT3A siRNA treated cells had only moderately decreased UGT2B15 expression. Treatment with DNMT methyltransferase inhibitor, RG108, significantly decreased UGT2B17 expression. Additionally, methylation differences between prostate cancer samples and benign prostate samples from an Illumina 450K Methylation Array study were assessed. The results taken together suggest that hypomethylation of the UGT2B15 and UGT2B17 genes contributes to increased risk of prostate cancer and may provide a putative biomarker or epigenetic target for chemotherapeutics. Mechanistic studies are warranted to determine the role of the methylation marks in prostate cancer.
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Affiliation(s)
- Farideh Shafiee-Kermani
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - Skyla T Carney
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - Dereje Jima
- Bioinformatics Research Center, Ricks Hall, 1 Lampe Dr, North Carolina State University , Raleigh, NC, USA.,Center of Human Health and the Environment, North Carolina State University , Raleigh, NC, USA
| | - Utibe C Utin
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - LaNeisha B Farrar
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - Melvin O Oputa
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - Marcono R Hines
- Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
| | - H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC, USA
| | - Kevin W Trotter
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC, USA
| | - Cathrine Hoyo
- Center of Human Health and the Environment, North Carolina State University , Raleigh, NC, USA.,Epidemiology and Environmental Epigenomics Laboratory, Department of Biological Sciences, Center of Human Health and the Environment, North Carolina State University , Raleigh, NC, USA
| | - Beverly H Koller
- Department of Genetics UNC School of Medicine, University of North Carolina at Chapel Hill , NC, USA
| | - Stephen J Freedland
- Cedars-Sinai Health System Center for Integrated Research on Cancer and Lifestyles , Cancer Genetics and Prevention Program, Surgery, Los Angeles, CA, USA
| | - Delores J Grant
- Center of Human Health and the Environment, North Carolina State University , Raleigh, NC, USA.,Department of Biological and Biomedical Sciences, Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University , Durham, NC, USA
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Huertas CS, Calvo-Lozano O, Mitchell A, Lechuga LM. Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective. Front Chem 2019; 7:724. [PMID: 31709240 PMCID: PMC6823211 DOI: 10.3389/fchem.2019.00724] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.
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Affiliation(s)
- Cesar S. Huertas
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
| | - Arnan Mitchell
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
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