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Yu B, Geng C, Wu Z, Zhang Z, Zhang A, Yang Z, Huang J, Xiong Y, Yang H, Chen Z. A CIC-related-epigenetic factors-based model associated with prediction, the tumor microenvironment and drug sensitivity in osteosarcoma. Sci Rep 2024; 14:1308. [PMID: 38225273 PMCID: PMC10789798 DOI: 10.1038/s41598-023-49770-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024] Open
Abstract
Osteosarcoma is generally considered a cold tumor and is characterized by epigenetic alterations. Although tumor cells are surrounded by many immune cells such as macrophages, T cells may be suppressed, be inactivated, or not be presented due to various mechanisms, which usually results in poor prognosis and insensitivity to immunotherapy. Immunotherapy is considered a promising anti-cancer therapy in osteosarcoma but requires more research, but osteosarcoma does not currently respond well to this therapy. The cancer immunity cycle (CIC) is essential for anti-tumor immunity, and is epigenetically regulated. Therefore, it is possible to modulate the immune microenvironment of osteosarcoma by targeting epigenetic factors. In this study, we explored the correlation between epigenetic modulation and CIC in osteosarcoma through bioinformatic methods. Based on the RNA data from TARGET and GSE21257 cohorts, we identified epigenetic related subtypes by NMF clustering and constructed a clinical prognostic model by the LASSO algorithm. ESTIMATE, Cibersort, and xCell algorithms were applied to analyze the tumor microenvironment. Based on eight epigenetic biomarkers (SFMBT2, SP140, CBX5, HMGN2, SMARCA4, PSIP1, ACTR6, and CHD2), two subtypes were identified, and they are mainly distinguished by immune response and cell cycle regulation. After excluding ACTR6 by LASSO regression, the prognostic model was established and it exhibited good predictive efficacy. The risk score showed a strong correlation with the tumor microenvironment, drug sensitivity and many immune checkpoints. In summary, our study sheds a new light on the CIC-related epigenetic modulation mechanism of osteosarcoma and helps search for potential drugs for osteosarcoma treatment.
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Affiliation(s)
- Bin Yu
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Chengkui Geng
- Department of Orthopedics of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhongxiong Wu
- Department of Orthopedics of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhongzi Zhang
- Department of Orthopedics of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Aili Zhang
- Department of Orthopedics of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Ze Yang
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Jiazheng Huang
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Ying Xiong
- Department of Orthopedics of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Huiqin Yang
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China.
| | - Zhuoyuan Chen
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan Province, China.
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Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
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Ye D, Wang Y, Deng X, Zhou X, Liu D, Zhou B, Zheng W, Wang X, Fang L. DNMT3a-dermatopontin axis suppresses breast cancer malignancy via inactivating YAP. Cell Death Dis 2023; 14:106. [PMID: 36774339 PMCID: PMC9922281 DOI: 10.1038/s41419-023-05657-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023]
Abstract
Breast cancer (BC) is the most common malignant tumor in women worldwide, and its recurrence and metastasis negatively affect patient prognosis. However, the mechanisms underlying its tumorigenesis and progression remain unclear. Recently, the influence of dermatopontin (DPT), which is an extracellular matrix protein, has been proposed in the development of cancer. Here we found that DNMT3a-mediated DPT, promoter hypermethylation results in the downregulation of DPT expression in breast cancer and its low expression correlated with poor prognosis. Notably, DPT directly interacted with YAP to promote YAP Ser127 phosphorylation, and restricted the translocation of endogenous YAP from the cytoplasm to the nucleus, thereby suppressing malignant phenotypes in BC cells. In addition, Ectopic YAP overexpression reversed the inhibitory effects of DPT on BC growth and metastasis. Our study showed the critical role of DPT in regulating BC progression, making it easier to explore the clinical potential of modulating DPT/YAP activity in BC targeted therapies.
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Affiliation(s)
- Danrong Ye
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Yuying Wang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Xiaochong Deng
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Xiqian Zhou
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Diya Liu
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Baian Zhou
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Wenfang Zheng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Xuehui Wang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
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Dai E, Zhu Z, Wahed S, Qu Z, Storkus WJ, Guo ZS. Epigenetic modulation of antitumor immunity for improved cancer immunotherapy. Mol Cancer 2021; 20:171. [PMID: 34930302 PMCID: PMC8691037 DOI: 10.1186/s12943-021-01464-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
Epigenetic mechanisms play vital roles not only in cancer initiation and progression, but also in the activation, differentiation and effector function(s) of immune cells. In this review, we summarize current literature related to epigenomic dynamics in immune cells impacting immune cell fate and functionality, and the immunogenicity of cancer cells. Some important immune-associated genes, such as granzyme B, IFN-γ, IL-2, IL-12, FoxP3 and STING, are regulated via epigenetic mechanisms in immune or/and cancer cells, as are immune checkpoint molecules (PD-1, CTLA-4, TIM-3, LAG-3, TIGIT) expressed by immune cells and tumor-associated stromal cells. Thus, therapeutic strategies implementing epigenetic modulating drugs are expected to significantly impact the tumor microenvironment (TME) by promoting transcriptional and metabolic reprogramming in local immune cell populations, resulting in inhibition of immunosuppressive cells (MDSCs and Treg) and the activation of anti-tumor T effector cells, professional antigen presenting cells (APC), as well as cancer cells which can serve as non-professional APC. In the latter instance, epigenetic modulating agents may coordinately promote tumor immunogenicity by inducing de novo expression of transcriptionally repressed tumor-associated antigens, increasing expression of neoantigens and MHC processing/presentation machinery, and activating tumor immunogenic cell death (ICD). ICD provides a rich source of immunogens for anti-tumor T cell cross-priming and sensitizing cancer cells to interventional immunotherapy. In this way, epigenetic modulators may be envisioned as effective components in combination immunotherapy approaches capable of mediating superior therapeutic efficacy.
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Affiliation(s)
- Enyong Dai
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhi Zhu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Surgical Oncology, China Medical University, Shenyang, China
| | - Shudipto Wahed
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Zhaoxia Qu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Walter J Storkus
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Departments of Dermatology, Immunology, Pathology and Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY, USA.
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Guo ZS, Qu Z. PDLIM2: Signaling pathways and functions in cancer suppression and host immunity. Biochim Biophys Acta Rev Cancer 2021; 1876:188630. [PMID: 34571051 DOI: 10.1016/j.bbcan.2021.188630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
PDZ and LIM domains-containing proteins play pivotal functions in cell cytoskeleton organization, cell polarization and differentiation. As a key member of the family, PDLIM2 regulates stability and activity of transcription factors such as NF-κB, STATs and β-catenin, and thus exert it functions in inflammation, immunity, and cancer. PDLIM2 functions as a tumor suppressor in multiple tissues and it is often genetically mutated or epigenetically silenced in human cancers derived from lung, breast, ovarian and other histologies. However, in certain types of cancers, PDLIM2 may promote cancer cell proliferation and metastases. Therefore, PDLIM2 is added to a long list of genes that can function as tumor suppressor or oncogenic protein. During tumorigenesis induced by oncogenic viruses, PDLIM2 is a key target. Through promotion of NF-κB/RelA and STAT3 degradation, PDLIM2 enhances expression of proteins involved in antigen presentation and promotes T-cell activation while repressing multidrug resistance genes, thereby rendering mutated cells susceptible to immune surveillance and cytotoxicity mediated by immune cells and chemotherapeutic drugs. Intriguingly, PDLIM2 in alveolar macrophages (AMs) plays key roles in monitoring lung tumorigenesis, as its selective genetic deletion leads to constitutive activation of STAT3, driving monocyte differentiation to AMs with pro-tumorigenic polarization and activation. PDLIM2 has also been explored as a therapeutic target for cancer therapy. At the end of this review, we provide perspectives on this important molecule and discuss the future directions of both basic and translational studies.
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Affiliation(s)
- Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Zhaoxia Qu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Montes-Grajales D, Morelos-Cortes X, Olivero-Verbel J. Discovery of New Protein Targets of BPA Analogs and Derivatives Associated with Noncommunicable Diseases: A Virtual High-Throughput Screening. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:37009. [PMID: 33769846 PMCID: PMC7997610 DOI: 10.1289/ehp7466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND Bisphenol A analogs and derivatives (BPs) have emerged as new contaminants with little or no information about their toxicity. These have been found in numerous everyday products, from thermal paper receipts to plastic containers, and measured in human samples. OBJECTIVES The objectives of this research were to identify in silico new protein targets of BPs associated with seven noncommunicable diseases (NCDs), and to study their protein-ligand interactions using computer-aided tools. METHODS Fifty BPs were identified by a literature search and submitted to a virtual high-throughput screening (vHTS) with 328 proteins associated with NCDs. Protein-protein interactions between predicted targets were examined using STRING, and the protocol was validated in terms of binding site recognition and correlation between in silico affinities and in vitro data. RESULTS According to the vHTS, several BPs may target proteins associated with NCDs, some of them with stronger affinities than bisphenol A (BPA). The best affinity score (the highest in silico affinity absolute value) was obtained after docking 4,4'-bis(N-carbamoyl-4-methylbenzensulfonamide)diphenylmethane (BTUM) on estradiol 17-beta-dehydrogenase 1 (-13.7 kcal/mol). However, other molecules, such as bisphenol A bis(diphenyl phosphate) (BDP), bisphenol PH (BPPH), and Pergafast 201 also exhibited great affinities (top 10 affinity scores for each disease) with proteins related to NCDs. DISCUSSION Molecules such as BTUM, BDP, BPPH, and Pergafast 201 could be targeting key signaling pathways related to NCDs. These BPs should be prioritized for in vitro and in vivo toxicity testing and to further assess their possible role in the development of these diseases. https://doi.org/10.1289/EHP7466.
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Affiliation(s)
- Diana Montes-Grajales
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Xiomara Morelos-Cortes
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
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He H, Chen D, Cui S, Wu G, Piao H, Wang X, Ye P, Jin S. HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma. BMC Med Genomics 2020; 13:118. [PMID: 32831081 PMCID: PMC7447581 DOI: 10.1186/s12920-020-00770-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC). Methods In this bioinformatics analysis, 348 liver cancer samples were collected from the Cancer Genome Atlas (TCGA) database to analyse specific DNA methylation sites that affect the prognosis of HCC patients. Results 10,699 CpG sites (CpGs) that were significantly related to the prognosis of patients were clustered into 7 subgroups, and the samples of each subgroup were significantly different in various clinical pathological data. In addition, by calculating the level of methylation sites in each subgroup, 119 methylation sites (corresponding to 105 genes) were selected as specific methylation sites within the subgroups. Moreover, genes in the corresponding promoter regions in which the above specific methylation sites were located were subjected to signalling pathway enrichment analysis, and it was discovered that these genes were enriched in the biological pathways that were reported to be closely correlated with HCC. Additionally, the transcription factor enrichment analysis revealed that these genes were mainly enriched in the transcription factor KROX. A naive Bayesian classification model was used to construct a prognostic model for HCC, and the training and test data sets were used for independent verification and testing. Conclusion This classification method can well reflect the heterogeneity of HCC samples and help to develop personalized treatment and accurately predict the prognosis of patients.
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Affiliation(s)
- Hui He
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Di Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd, Dalian, 116023, China
| | - Shimeng Cui
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Gang Wu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of China Medical University, Shenyang, 110042, Liaoning Province, China
| | - Hailong Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd, Dalian, 116023, China
| | - Xun Wang
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Peng Ye
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning Province, China
| | - Shi Jin
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China.
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Singh VK, Arora D, Ansari MI, Sharma PK. Phytochemicals based chemopreventive and chemotherapeutic strategies and modern technologies to overcome limitations for better clinical applications. Phytother Res 2019; 33:3064-3089. [DOI: 10.1002/ptr.6508] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Vipendra Kumar Singh
- Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology GroupCSIR‐Indian Institute of Toxicology Research Lucknow India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad‐ 201002 India
| | - Deepika Arora
- Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology GroupCSIR‐Indian Institute of Toxicology Research Lucknow India
- Material and Measurement LaboratoryNational Institute of Standards and Technology Gaithersburg 20899 Maryland USA
| | - Mohammad Imran Ansari
- Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology GroupCSIR‐Indian Institute of Toxicology Research Lucknow India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad‐ 201002 India
| | - Pradeep Kumar Sharma
- Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology GroupCSIR‐Indian Institute of Toxicology Research Lucknow India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad‐ 201002 India
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Murugan K, Sangeetha S, Ranjitha S, Vimala A, Al-Sohaibani S, Rameshkumar G. HDACiDB: a database for histone deacetylase inhibitors. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:2257-64. [PMID: 25945037 PMCID: PMC4408954 DOI: 10.2147/dddt.s78276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/website.
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Affiliation(s)
- Kasi Murugan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shanmugasamy Sangeetha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Shanmugasamy Ranjitha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Antony Vimala
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Saleh Al-Sohaibani
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gopal Rameshkumar
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
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Bartlett DL, Liu Z, Sathaiah M, Ravindranathan R, Guo Z, He Y, Guo ZS. Oncolytic viruses as therapeutic cancer vaccines. Mol Cancer 2013; 12:103. [PMID: 24020520 PMCID: PMC3847443 DOI: 10.1186/1476-4598-12-103] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/06/2013] [Indexed: 12/24/2022] Open
Abstract
Oncolytic viruses (OVs) are tumor-selective, multi-mechanistic antitumor agents. They kill infected cancer and associated endothelial cells via direct oncolysis, and uninfected cells via tumor vasculature targeting and bystander effect. Multimodal immunogenic cell death (ICD) together with autophagy often induced by OVs not only presents potent danger signals to dendritic cells but also efficiently cross-present tumor-associated antigens from cancer cells to dendritic cells to T cells to induce adaptive antitumor immunity. With this favorable immune backdrop, genetic engineering of OVs and rational combinations further potentiate OVs as cancer vaccines. OVs armed with GM-CSF (such as T-VEC and Pexa-Vec) or other immunostimulatory genes, induce potent anti-tumor immunity in both animal models and human patients. Combination with other immunotherapy regimens improve overall therapeutic efficacy. Coadministration with a HDAC inhibitor inhibits innate immunity transiently to promote infection and spread of OVs, and significantly enhances anti-tumor immunity and improves the therapeutic index. Local administration or OV mediated-expression of ligands for Toll-like receptors can rescue the function of tumor-infiltrating CD8+ T cells inhibited by the immunosuppressive tumor microenvironment and thus enhances the antitumor effect. Combination with cyclophosphamide further induces ICD, depletes Treg, and thus potentiates antitumor immunity. In summary, OVs properly armed or in rational combinations are potent therapeutic cancer vaccines.
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Affiliation(s)
- David L Bartlett
- University of Pittsburgh Cancer Institute and Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Bozkurt E, Atmaca H, Kisim A, Uzunoglu S, Uslu R, Karaca B. Effects of Thymus serpyllum extract on cell proliferation, apoptosis and epigenetic events in human breast cancer cells. Nutr Cancer 2013; 64:1245-50. [PMID: 23163852 DOI: 10.1080/01635581.2012.719658] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thymus (T.) serpyllum (wild thyme) is an aromatic medicinal plant due to its several biological properties, including anticancer activity. Breast cancer is one of the most common malignancies and increasing evidence supports that it is not only a genetic but also an epigenetic disease. Epigenetics investigates changes in gene expression caused by mechanisms that do not involve alterations in DNA sequence. DNA methylation and histone acetylation are the most widely studied epigenetic changes in cancer cells. This study evaluated the effects of T. serpyllum on apoptosis and epigenetic events in breast cancer cells. XTT cell viability assay was used to determine cytotoxicity. DNA fragmentation and caspase 3/7 activity assays were used in the assesment of apoptosis. DNA methyltransferase (DNMT) and histone deacetylase (HDAC) activities were evaluated by ELISA and verified by qRT-PCR. T. serpyllum extract induced significant cytotoxicity in breast cancer cells (MCF-7 and MDA-MB-231) but not in normal cells. It also induced apoptosis and inhibited the DNMT and HDAC activities in MDA-MB-231 cells. In the present study, the first preliminary data on the effects of the methanolic extract of T. serpyllum in normal and breast cancer cells were obtained and suggest that T. serpyllum may be a promising candidate in the development of novel therapeutic drugs for breast cancer treatment.
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Affiliation(s)
- Emir Bozkurt
- Department of Biology, Faculty of Science and Arts, Celal Bayar University, Manisa, Turkey
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Li Q, O'Malley ME, Bartlett DL, Guo ZS. Homeobox gene Rhox5 is regulated by epigenetic mechanisms in cancer and stem cells and promotes cancer growth. Mol Cancer 2011; 10:63. [PMID: 21609483 PMCID: PMC3125390 DOI: 10.1186/1476-4598-10-63] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 05/24/2011] [Indexed: 12/29/2022] Open
Abstract
Background Homeobox genes murine Rhox5 and human RHOXF1 are expressed in early embryonic stages and then mostly restricted to germline tissues in normal adult, yet they are aberrantly expressed in cancer cells in vitro and in vivo . Here we study the epigenetic regulation and potential functions of Rhox5 gene. Findings In Rhox5 -silenced or extremely low expresser cells, we observed low levels of active histone epigenetic marks (H3ac, H4ac and H3K4me2) and high levels of repressive mark H3K9me2 along with DNA hypermethylation in the promoter. In Rhox5 low expresser cells, we typically observed modest levels of both active and repressive histone marks along with moderate DNA methylation. In Rhox5 highly expressed CT26 cancer cells, we observed DNA hypomethylation along with high levels of both active and repressive histone marks. Epigenetic drugs (retinoic acid and MS-275) induced F9 cell differentiation with enhanced Rhox5 expression and dynamic changes of epigenetic marks. Finally, Rhox5 knockdown by small hairpin RNA (shRNA) in CT26 colon cancer decreased cell proliferation and migration in vitro and tumor growth in vivo . Conclusions Both DNA methylation and histone methylation/acetylation play key roles in modulating Rhox5 expression in various cell types. The stem cell-like "bivalent domain", an epigenetic feature originally identified in key differentiation genes within stem cells, exists in the Rhox5 gene promoter in not only embryonic stem cells but also cancer cells, cancer stem cells, and differentiated Sertoli cells. As Ras signaling-dependent Rhox5 expression promotes tumor growth, Rhox5 may be an ideal target for therapeutic intervention in cancer.
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Affiliation(s)
- Qiang Li
- The University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania 15213, USA
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