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Garg P, Krishna M, Subbalakshmi AR, Ramisetty S, Mohanty A, Kulkarni P, Horne D, Salgia R, Singhal SS. Emerging biomarkers and molecular targets for precision medicine in cervical cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189106. [PMID: 38701936 DOI: 10.1016/j.bbcan.2024.189106] [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: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cervical cancer remains a significant global health burden, necessitating innovative approaches for improved diagnostics and personalized treatment strategies. Precision medicine has emerged as a promising paradigm, leveraging biomarkers and molecular targets to tailor therapy to individual patients. This review explores the landscape of emerging biomarkers and molecular targets in cervical cancer, highlighting their potential implications for precision medicine. By integrating these biomarkers into comprehensive diagnostic algorithms, clinicians can identify high-risk patients at an earlier stage, enabling timely intervention and improved patient outcomes. Furthermore, the identification of specific molecular targets has paved the way for the development of targeted therapies aimed at disrupting key pathways implicated in cervical carcinogenesis. In conclusion, the evolving landscape of biomarkers and molecular targets presents exciting opportunities for advancing precision medicine in cervical cancer. By harnessing these insights, clinicians can optimize treatment selection, enhance patient outcomes, and ultimately transform the management of this devastating disease.
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Affiliation(s)
- Pankaj Garg
- Department of Chemistry, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Madhu Krishna
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ayalur Raghu Subbalakshmi
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sravani Ramisetty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Departments of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
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Hawkins-Hooker A, Visonà G, Narendra T, Rojas-Carulla M, Schölkopf B, Schweikert G. Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning. Nat Commun 2023; 14:4750. [PMID: 37550323 PMCID: PMC10406842 DOI: 10.1038/s41467-023-40211-2] [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: 03/09/2022] [Accepted: 07/18/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic modifications are dynamic mechanisms involved in the regulation of gene expression. Unlike the DNA sequence, epigenetic patterns vary not only between individuals, but also between different cell types within an individual. Environmental factors, somatic mutations and ageing contribute to epigenetic changes that may constitute early hallmarks or causal factors of disease. Epigenetic modifications are reversible and thus promising therapeutic targets for precision medicine. However, mapping efforts to determine an individual's cell-type-specific epigenome are constrained by experimental costs and tissue accessibility. To address these challenges, we developed eDICE, an attention-based deep learning model that is trained to impute missing epigenomic tracks by conditioning on observed tracks. Using a recently published set of epigenomes from four individual donors, we show that transfer learning across individuals allows eDICE to successfully predict individual-specific epigenetic variation even in tissues that are unmapped in a given donor. These results highlight the potential of machine learning-based imputation methods to advance personalized epigenomics.
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Affiliation(s)
- Alex Hawkins-Hooker
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany.
- Centre for Artificial Intelligence, University College London, London, UK.
| | - Giovanni Visonà
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Tanmayee Narendra
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Interfaculty Institute for Biomedical Informatics, University of Tübingen, Sand 13, Tübingen, 72076, Germany
| | - Mateo Rojas-Carulla
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Bernhard Schölkopf
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Gabriele Schweikert
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
- Interfaculty Institute for Biomedical Informatics, University of Tübingen, Sand 13, Tübingen, 72076, Germany.
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Ma Z, Zuo Y, Wang W. Ginsenoside Rg3 inhibits renal cell carcinoma cell migration, invasion, colony formation, and tube formation and enhances apoptosis through promoting the DNA demethylation and histone acetylation. J Pharm Pharmacol 2023; 75:76-86. [PMID: 36264186 DOI: 10.1093/jpp/rgac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/06/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVES This study explored the effect and mechanism of Rg3 on renal cell carcinoma (RCC) progression. METHODS RCC cells were treated with different concentrations of Rg3, 5-Aza-dc (a methyltransferase inhibitor) or TSA (a deacetylase inhibitor). Rg3-induced cytotoxicity, migration, invasion, colony formation, tube formation and apoptosis of RCC cells were evaluated by CCK-8, wound healing, Transwell, colony formation, tube formation and flow cytometry assays, respectively. Methylation and expressions of p53, p21 and p16, and expressions of methylation-related genes and histone deacetylases and histone acetylation-related genes (H3 (acetyl K14), H3 (acetyl K9), H4 (acetyl K12), H4 (acetyl K5) and H4 (acetyl K16)) were analysed by qRT-PCR and western blot. KEY FINDINGS Rg3 dose-dependently decreased the viability, inhibited migration, invasion, colony formation and tube formation, and enhanced apoptosis of RCC cells. Rg3 enhanced the demethylation levels and expressions of p53, p21 and p16 as well as the expressions of histone acetylation-related genes, but repressed the expressions of methylation-related genes and histone deacetylases. Rg3 had the same effect as 5-Aza-dc and TSA did on the above-mentioned cellular changes. CONCLUSION Rg3 restrains RCC cell migration, invasion, colony formation and tube formation, yet enhances apoptosis through promoting demethylation of p53, p21 and p16, and histone acetylation.
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Affiliation(s)
- Zhiqiang Ma
- Urinary Surgery Department, Shijiazhuang Third Hospital, Shijiazhuang, China
| | - Yan Zuo
- Urinary Surgery Department, Shijiazhuang Third Hospital, Shijiazhuang, China
| | - Wei Wang
- Urinary Surgery Department, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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Epigenetics of Thymic Epithelial Tumors. Cancers (Basel) 2023; 15:cancers15020360. [PMID: 36672310 PMCID: PMC9856807 DOI: 10.3390/cancers15020360] [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: 12/06/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/08/2023] Open
Abstract
Thymic epithelial tumors (TETs) arise from the epithelial cells of the thymus and consist in the 1% of all adult malignancies, despite the fact that they are the most common lesions of the anterior mediastinum. TETs can be divided mainly into thymomas, thymic carcinomas, and the rarest ad aggressive neuroendocrine forms. Despite the surgical resection is quite resolving, the diagnosis of TETs is complicated by the absence of symptoms and the clinical presentation aggravated by several paraneoplastic disorders, including myasthenia gravis. Thus, the heterogeneity of TETs prompts the search for molecular biomarkers that could be helpful for tumor characterization and clinical outcomes prediction. With these aims, several researchers investigated the epigenetic profiles of TETs. In this manuscript, we narratively review the works investigating the deregulation of epigenetic mechanisms in TETs, highlighting the need for further studies combining genetic, epigenetic, and expression data to better characterize the different molecular subtypes and identify, for each of them, the most relevant epigenetic biomarkers of clinical utility.
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Yu X, Wang Y, Shi X, Wang Z, Wen P, He Y, Guo W. Dysfunctional epigenetic protein-coding gene-related signature is associated with the prognosis of pancreatic cancer based on histone modification and transcriptome analysis. Sci Rep 2023; 13:146. [PMID: 36599884 PMCID: PMC9813002 DOI: 10.1038/s41598-022-27316-2] [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: 04/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Emerging evidence suggests that epigenetic alterations are responsible for the oncogenesis and progression of cancer. However, the role of epigenetic reprogramming in pancreatic cancer is still not clear. In this study, we used the limma R package to identify differentially expressed protein-coding genes (PCGs) between pancreatic cancer tissues and normal control tissues. The cell-type identification by the estimating relative subsets of RNA transcripts (CIBERSORT) package was used to quantify relative cell fractions in tumors. Prognostic molecular clusters were constructed using ConsensusClusterPlus analysis. Furthermore, the least absolute shrinkage and selection operator and stepAIC methods were used to construct a risk model. We identified 2351 differentially expressed PCGs between pancreatic cancer and normal control tissues in The cancer genome atlas dataset. Combined with histone modification data, we identified 363 epigenetic PCGs (epi-PCGs) and 19,010 non-epi-PCGs. Based on the epi-PCGs, we constructed three molecular clusters characterized by different expression levels of chemokines and immune checkpoint genes and distinct abundances of various immune cells. Furthermore, we generated a 9-gene model based on dysfunctional epi-PCGs. Additionally, we found that patients with high risk scores showed poorer prognoses than patients with low risk scores (p < 0.0001). Further analysis showed that the risk score was significantly related to survival and was an independent risk factor for pancreatic cancer patients. In conclusion, we constructed a 9-gene prognostic risk model based on epi-PCGs that might serve as an effective classifier to predict overall survival and the response to immunotherapy in pancreatic cancer patients.
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Affiliation(s)
- Xiao Yu
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Yun Wang
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Xiaoyi Shi
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Zhihui Wang
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Peihao Wen
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Yuting He
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Wenzhi Guo
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
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Bradic M, Taleb S, Thomas B, Chidiac O, Robay A, Hassan N, Malek J, Ait Hssain A, Abi Khalil C. DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome. J Transl Med 2022; 20:526. [PMID: 36371196 PMCID: PMC9652914 DOI: 10.1186/s12967-022-03737-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/30/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND COVID-19 infections could be complicated by acute respiratory distress syndrome (ARDS), increasing mortality risk. We sought to assess the methylome of peripheral blood mononuclear cells in COVID-19 with ARDS. METHODS We recruited 100 COVID-19 patients with ARDS under mechanical ventilation and 33 non-COVID-19 controls between April and July 2020. COVID-19 patients were followed at four time points for 60 days. DNA methylation and immune cell populations were measured at each time point. A multivariate cox proportional risk regression analysis was conducted to identify predictive signatures according to survival. RESULTS The comparison of COVID-19 to controls at inclusion revealed the presence of a 14.4% difference in promoter-associated CpGs in genes that control immune-related pathways such as interferon-gamma and interferon-alpha responses. On day 60, 24% of patients died. The inter-comparison of baseline DNA methylation to the last recorded time point in both COVID-19 groups or the intra-comparison between inclusion and the end of follow-up in every group showed that most changes occurred as the disease progressed, mainly in the AIM gene, which is associated with an intensified immune response in those who recovered. The multivariate Cox proportional risk regression analysis showed that higher methylation of the "Apoptotic execution Pathway" genes (ROC1, ZNF789, and H1F0) at inclusion increases mortality risk by over twofold. CONCLUSION We observed an epigenetic signature of immune-related genes in COVID-19 patients with ARDS. Further, Hypermethylation of the apoptotic execution pathway genes predicts the outcome. TRIAL REGISTRATION IMRPOVIE study, NCT04473131.
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Affiliation(s)
- Martina Bradic
- grid.5386.8000000041936877XDepartment of Genetic Medicine, Weill Cornell Medicine, New York, USA ,grid.51462.340000 0001 2171 9952Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah Taleb
- grid.452146.00000 0004 1789 3191Division of Genomics and Translational Biomedicine, College of Health and Life Sciences- HBKU, Doha, Qatar
| | - Binitha Thomas
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Omar Chidiac
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Amal Robay
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Nessiya Hassan
- grid.413548.f0000 0004 0571 546XNursery and midwifery research department, Hamad Medical Corporation., Doha, Qatar
| | - Joel Malek
- grid.416973.e0000 0004 0582 4340Genomics Core. Weill Cornell Medicine-Qatar., Doha, Qatar
| | - Ali Ait Hssain
- grid.413548.f0000 0004 0571 546XMedical Intensive Care Unit, Hamad Medical Corporation., Doha, Qatar
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA. .,Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar. .,Joan and Sanford I. Weill Department of Medicine., Weill Cornell Medicine, New York, USA.
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Cabral N, de Figueiredo V, Gandini M, de Souza CF, Medeiros RA, Lery LMS, Lara FA, de Macedo CS, Pessolani MCV, Pereira GMB. Modulation of the Response to Mycobacterium leprae and Pathogenesis of Leprosy. Front Microbiol 2022; 13:918009. [PMID: 35722339 PMCID: PMC9201476 DOI: 10.3389/fmicb.2022.918009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/16/2022] [Indexed: 12/20/2022] Open
Abstract
The initial infection by the obligate intracellular bacillus Mycobacterium leprae evolves to leprosy in a small subset of the infected individuals. Transmission is believed to occur mainly by exposure to bacilli present in aerosols expelled by infected individuals with high bacillary load. Mycobacterium leprae-specific DNA has been detected in the blood of asymptomatic household contacts of leprosy patients years before active disease onset, suggesting that, following infection, the bacterium reaches the lymphatic drainage and the blood of at least some individuals. The lower temperature and availability of protected microenvironments may provide the initial conditions for the survival of the bacillus in the airways and skin. A subset of skin-resident macrophages and the Schwann cells of peripheral nerves, two M. leprae permissive cells, may protect M. leprae from effector cells in the initial phase of the infection. The interaction of M. leprae with these cells induces metabolic changes, including the formation of lipid droplets, that are associated with macrophage M2 phenotype and the production of mediators that facilitate the differentiation of specific T cells for M. leprae-expressed antigens to a memory regulatory phenotype. Here, we discuss the possible initials steps of M. leprae infection that may lead to active disease onset, mainly focusing on events prior to the manifestation of the established clinical forms of leprosy. We hypothesize that the progressive differentiation of T cells to the Tregs phenotype inhibits effector function against the bacillus, allowing an increase in the bacillary load and evolution of the infection to active disease. Epigenetic and metabolic mechanisms described in other chronic inflammatory diseases are evaluated for potential application to the understanding of leprosy pathogenesis. A potential role for post-exposure prophylaxis of leprosy in reducing M. leprae-induced anti-inflammatory mediators and, in consequence, Treg/T effector ratios is proposed.
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Affiliation(s)
- Natasha Cabral
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Vilma de Figueiredo
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Mariana Gandini
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Cíntia Fernandes de Souza
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Rychelle Affonso Medeiros
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Letícia Miranda Santos Lery
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Flávio Alves Lara
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Cristiana Santos de Macedo
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | | | - Geraldo Moura Batista Pereira
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
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Chu LH, Liao CC, Liew PL, Chen CW, Su PH, Wen KC, Lai HC, Huang RL, Chen LY. Epigenomic Analysis Reveals the KCNK9 Potassium Channel as a Potential Therapeutic Target for Adenomyosis. Int J Mol Sci 2022; 23:ijms23115973. [PMID: 35682653 PMCID: PMC9180761 DOI: 10.3390/ijms23115973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/28/2022] Open
Abstract
Adenomyosis is linked to dysmenorrhea and infertility. The pathogenesis of adenomyosis remains unclear, and little is known of the genetic and epigenetic changes in the eutopic endometrium in adenomyosis, which may predispose patients to the invasion and migration of endometrial tissues into the myometrium. Transcriptome studies have identified genes related to various cell behaviors but no targets for therapeutic intervention. The epigenetics of the eutopic endometrium in adenomyosis have rarely been investigated. Endometrial tissue was obtained from premenopausal women with (n = 32) or without adenomyosis (n = 17) who underwent hysterectomy aged 34–57 years at a tertiary hospital. The methylome and transcriptome were assessed by using a Methylation 450 K BeadChip array and Affymetrix expression microarray. Protein expression was examined by immunohistochemistry. Differential methylation analysis revealed 53 lowly methylated genes and 176 highly methylated genes with consistent gene expression in adenomyosis, including three genes encoding potassium ion channels. High expression of KCNK9 in the eutopic and ectopic endometria in patients with adenomyosis but not in normal controls was observed. Hormone-free, antibody-based KCNK9 targeting is a potential therapeutic strategy for adenomyosis-related dysmenorrhea, menorrhagia, and infertility.
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Affiliation(s)
- Ling-Hui Chu
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
| | - Chi-Chun Liao
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Nuwa Fertility Center, Taipei 106467, Taiwan
| | - Phui-Ly Liew
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan;
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chien-Wen Chen
- Dr Wang Reproductive Fertility Center, Taipei 110007, Taiwan;
| | - Po-Hsuan Su
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Kuo-Chang Wen
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, National Defense Medical Center, Taipei 11490, Taiwan
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Lin-Yu Chen
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (L.-H.C.); (C.-C.L.); (P.-H.S.); (K.-C.W.); (H.-C.L.); (R.-L.H.)
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Correspondence: ; Tel.: +886-2-2249-0088 (ext. 8740)
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9
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On the Cutting Edge of Oral Cancer Prevention: Finding Risk-Predictive Markers in Precancerous Lesions by Longitudinal Studies. Cells 2022; 11:cells11061033. [PMID: 35326482 PMCID: PMC8947091 DOI: 10.3390/cells11061033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 02/06/2023] Open
Abstract
Early identification and management of precancerous lesions at high risk of developing cancers is the most effective and economical way to reduce the incidence, mortality, and morbidity of cancers as well as minimizing treatment-related complications, including pain, impaired functions, and disfiguration. Reliable cancer-risk-predictive markers play an important role in enabling evidence-based decision making as well as providing mechanistic insight into the malignant conversion of precancerous lesions. The focus of this article is to review updates on markers that may predict the risk of oral premalignant lesions (OPLs) in developing into oral squamous cell carcinomas (OSCCs), which can logically be discovered only by prospective or retrospective longitudinal studies that analyze pre-progression OPL samples with long-term follow-up outcomes. These risk-predictive markers are different from those that prognosticate the survival outcome of cancers after they have been diagnosed and treated, or those that differentiate between different lesion types and stages. Up-to-date knowledge on cancer-risk-predictive markers discovered by longitudinally followed studies will be reviewed. The goal of this endeavor is to use this information as a starting point to address some key challenges limiting our progress in this area in the hope of achieving effective translation of research discoveries into new clinical interventions.
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10
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Holubekova V, Kolkova Z, Kasubova I, Samec M, Mazurakova A, Koklesova L, Kubatka P, Rokos T, Kozubik E, Biringer K, Kudela E. Interaction of cervical microbiome with epigenome of epithelial cells: Significance of inflammation to primary healthcare. Biomol Concepts 2022; 13:61-80. [PMID: 35245973 DOI: 10.1515/bmc-2022-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
One pillar of the predictive, preventive, and personalized medicine framework strategies is the female health. The evaluation of women's lifestyle and dietary habits in context with genetic and modifiable risk factors may reflect the prevention of cervical cancer before the occurrence of clinical symptoms and prediction of cervical lesion behavior. The main aim of this review is to analyze publications in the field of precision medicine that allow the use of research knowledge of cervical microbiome, epigenetic modifications, and inflammation in potential application in clinical practice. Personalized approach in evaluating patient's risk of future development of cervical abnormality should consider the biomarkers of the local microenvironment characterized by the microbial composition, epigenetic pattern of cervical epithelium, and presence of chronic inflammation. Novel sequencing techniques enable a more detailed characterization of actual state in cervical epithelium. Better understanding of all changes in multiomics level enables a better assessment of disease prognosis and selects the eligible targeted therapy in personalized medicine. Restoring of healthy vaginal microflora and reversing the outbreak of cervical abnormality can be also achieved by dietary habits as well as uptake of prebiotics, probiotics, synbiotics, microbial transplantation, and others.
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Affiliation(s)
- Veronika Holubekova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Zuzana Kolkova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Ivana Kasubova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Marek Samec
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Alena Mazurakova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Tomas Rokos
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kozubik
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kudela
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
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11
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Zhou S, Zhang S, Zhang H, Ma J, Dai H, Qu L, Zhou M. Clinical Potential of lncRNA PPP1R26-AS1 in Breast Cancer and Its Contribution to Cancer Progression. Mol Biotechnol 2022; 64:660-669. [PMID: 35064892 DOI: 10.1007/s12033-022-00452-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Breast cancer has become the most leading diagnosed tumor worldwide in 2020. In this study, the biomarker potential and influence on the cellular function of lncRNA PPP1R26-AS1 was investigated in breast cancer. Expression levels of lncRNA PPP1R26-AS1 in breast tissues and cells were detected by RT-qPCR. Association between lncRNA PPP1R26-AS1 level and clinical parameters was investigated by Chi-square analysis. The prognostic potential was assessed by Kaplan-Meier and multivariate Cox regression analysis. Knockdown of lncRNA PPP1R26-AS1 was subjected to study the effect on cell proliferation, invasion, and migration by CCK-8 and transwell assay. The bind between PPP1R26-AS1 and miR-1226-3p was investigated. LncRNA PPP1R26-AS1 was highly expressed in breast tissues and cell lines. This upregulation was correlated with pTNM, positive ER status, luminal B subtype, positive nodal status, and shorter overall survival in breast cancer patients. Significant decreases in proliferation, migration, and invasion activity were observed upon knockdown of lncRNA PPP1R26-AS1. lncRNA PPP1R26-AS1 could act as ceRNA to bind with miR-1226-3p in breast cancer. LncRNA PPP1R26-AS1, as oncogenic lncRNA, could provide a new perspective on the development of prognostic biomarkers and a new approach in tailoring the treatment personalized in breast cancer.
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Affiliation(s)
- Shuping Zhou
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China
| | - Shaoli Zhang
- Department of Geriatrics, Shanghai Sixth People's Hospital, Shanghai, 201306, China
| | - Hui Zhang
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China
| | - Junxia Ma
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China
| | - Huangzhen Dai
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China
| | - Lili Qu
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China
| | - Meixiang Zhou
- Department of Medical Oncology, Shanghai Sixth People's Hospital, No. 222, Huanhuxi Third Road, Shanghai, 201306, China.
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12
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Samanta S, Mahata R, Santra MK. The Cross-Talk between Epigenetic Gene Regulation and Signaling Pathways Regulates Cancer Pathogenesis. Subcell Biochem 2022; 100:427-472. [PMID: 36301502 DOI: 10.1007/978-3-031-07634-3_13] [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] [Indexed: 06/16/2023]
Abstract
Cancer begins due to uncontrolled cell division. Cancer cells are insensitive to the signals that control normal cell proliferation. This uncontrolled cell division is due to the accumulation of abnormalities in different factors associated with the cell division, including different cyclins, cell cycle checkpoint inhibitors, and cellular signaling. Cellular signaling pathways are aberrantly activated in cancer mainly due to epigenetic regulation and post-translational regulation. In this chapter, the role of epigenetic regulation in aberrant activation of PI3K/AKT, Ras, Wnt, Hedgehog, Notch, JAK/STAT, and mTOR signaling pathways in cancer progression is discussed. The role of epigenetic regulators in controlling the upstream regulatory proteins and downstream effector proteins responsible for abnormal cellular signaling-mediated cancer progression is covered in this chapter. Similarly, the role of signaling pathways in controlling epigenetic gene regulation-mediated cancer progression is also discussed. We have tried to ascertain the current status of potential epigenetic drugs targeting several epigenetic regulators to prevent different cancers.
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Affiliation(s)
- Snigdha Samanta
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rumpa Mahata
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Manas Kumar Santra
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India.
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13
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Tan Y, Liu L, Zhang X, Xue Y, Gao J, Zhao J, Chi N, Zhu Y. THUMPD3-AS1 is correlated with gastric cancer and regulates cell function through miR-1252-3p and CXCL17. Crit Rev Eukaryot Gene Expr 2022; 32:69-80. [DOI: 10.1615/critreveukaryotgeneexpr.2022042848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Wang Y, Qiao L, Yang J, Li X, Duan Y, Liu J, Chen S, Li H, Liu D, Fang T, Ma J, Li X, Ye F, Wan J, Wei J, Xu Q, Guo E, Jin P, Wu M, Zhang L, Xia Y, Wu Y, Shao J, Feng Y, Zhang Q, Yang Z, Chen G, Zhang Q, Li X, Wang S, Hu J, Wang X, Tan MP, Takabe K, Kong B, Yang Q, Ma D, Gao Q. Serum semaphorin 4C as a diagnostic biomarker in breast cancer: A multicenter retrospective study. Cancer Commun (Lond) 2021; 41:1373-1386. [PMID: 34738326 PMCID: PMC8696225 DOI: 10.1002/cac2.12233] [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: 03/10/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Background To date, there is no approved blood‐based biomarker for breast cancer detection. Herein, we aimed to assess semaphorin 4C (SEMA4C), a pivotal protein involved in breast cancer progression, as a serum diagnostic biomarker. Methods We included 6,213 consecutive inpatients from Tongji Hospital, Qilu Hospital, and Hubei Cancer Hospital. Training cohort and two validation cohorts were introduced for diagnostic exploration and validation. A pan‐cancer cohort was used to independently explore the diagnostic potential of SEMA4C among solid tumors. Breast cancer patients who underwent mass excision prior to modified radical mastectomy were also analyzed. We hypothesized that increased pre‐treatment serum SEMA4C levels, measured using optimized in‐house enzyme‐linked immunosorbent assay kits, could detect breast cancer. The endpoints were diagnostic performance, including area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. Post‐surgery pathological diagnosis was the reference standard and breast cancer staging followed the TNM classification. There was no restriction on disease stage for eligibilities. Results We included 2667 inpatients with breast lesions, 2378 patients with other solid tumors, and 1168 healthy participants. Specifically, 118 patients with breast cancer were diagnosed with stage 0 (5.71%), 620 with stage I (30.00%), 966 with stage II (46.73%), 217 with stage III (10.50%), and 8 with stage IV (0.39%). Patients with breast cancer had significantly higher serum SEMA4C levels than benign breast tumor patients and normal controls (P < 0.001). Elevated serum SEMA4C levels had AUC of 0.920 (95% confidence interval [CI]: 0.900–0.941) and 0.932 (95%CI: 0.911–0.953) for breast cancer detection in the two validation cohorts. The AUCs for detecting early‐stage breast cancer (n = 366) and ductal carcinoma in situ (n = 85) were 0.931 (95%CI: 0.916–0.946) and 0.879 (95%CI: 0.832–0.925), respectively. Serum SEMA4C levels significantly decreased after surgery, and the reduction was more striking after modified radical mastectomy, compared with mass excision (P < 0.001). The positive rate of enhanced serum SEMA4C levels was 84.77% for breast cancer and below 20.75% for the other 14 solid tumors. Conclusions Serum SEMA4C demonstrated promising potential as a candidate biomarker for breast cancer diagnosis. However, validation in prospective settings and by other study groups is warranted.
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Affiliation(s)
- Ya Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Long Qiao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, P. R. China
| | - Jie Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Xiong Li
- Department of Gynecology and Obstetrics, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, P. R. China
| | - Yaqi Duan
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Jiahao Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Shaoqi Chen
- Department of Obstetrics and Gynecology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
| | - Huayi Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Dan Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Tian Fang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Jingjing Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Xiaoting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Fei Ye
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, 90001, USA
| | - Juncheng Wei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Qin Xu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Ping Jin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Mingfu Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Lin Zhang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Yun Xia
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Yaqun Wu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Jun Shao
- Department of Breast Surgery, Hubei Cancer Hospital, Wuhan, Hubei, 430079, P. R. China
| | - Yaojun Feng
- Department of Breast Surgery, Hubei Cancer Hospital, Wuhan, Hubei, 430079, P. R. China
| | - Qing Zhang
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Zongyuan Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Qinghua Zhang
- Department of Gynecology and Obstetrics, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, P. R. China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Junbo Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Xiaoyun Wang
- Yidu Cloud (Beijing) Technology Co., Beijing, 100000, P. R. China
| | - Mona P Tan
- MammoCare, The Breast Clinic & Surgery, Singapore, 329563, Singapore
| | - Kazuaki Takabe
- Department of Surgery and the Massey Cancer Centre, Virginia Commonwealth University School of Medicine, Richmond, Virginia, 23298, USA
| | - Beihua Kong
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Qifeng Yang
- Department of Breast Surgery, Qilu Hospital of Shandong University, No.107, Jinan Culture Road, Jinan, Shandong, 250012, P. R. China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China.,Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P. R. China
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15
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Giambò F, Leone GM, Gattuso G, Rizzo R, Cosentino A, Cinà D, Teodoro M, Costa C, Tsatsakis A, Fenga C, Falzone L. Genetic and Epigenetic Alterations Induced by Pesticide Exposure: Integrated Analysis of Gene Expression, microRNA Expression, and DNA Methylation Datasets. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168697. [PMID: 34444445 PMCID: PMC8394939 DOI: 10.3390/ijerph18168697] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023]
Abstract
Environmental or occupational exposure to pesticides is considered one of the main risk factors for the development of various diseases. Behind the development of pesticide-associated pathologies, there are both genetic and epigenetic alterations, where these latter are mainly represented by the alteration in the expression levels of microRNAs and by the change in the methylation status of the DNA. At present, no studies have comprehensively evaluated the genetic and epigenetic alterations induced by pesticides; therefore, the aim of the present study was to identify modifications in gene miRNA expression and DNA methylation useful for the prediction of pesticide exposure. For this purpose, an integrated analysis of gene expression, microRNA expression, and DNA methylation datasets obtained from the GEO DataSets database was performed to identify putative genes, microRNAs, and DNA methylation hotspots associated with pesticide exposure and responsible for the development of different diseases. In addition, DIANA-miRPath, STRING, and GO Panther prediction tools were used to establish the functional role of the putative biomarkers identified. The results obtained demonstrated that pesticides can modulate the expression levels of different genes and induce different epigenetic alterations in the expression levels of miRNAs and in the modulation of DNA methylation status.
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Affiliation(s)
- Federica Giambò
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy;
| | - Gian Marco Leone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.M.L.); (G.G.); (R.R.); (A.C.)
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.M.L.); (G.G.); (R.R.); (A.C.)
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.M.L.); (G.G.); (R.R.); (A.C.)
| | - Alessia Cosentino
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.M.L.); (G.G.); (R.R.); (A.C.)
| | - Diana Cinà
- Health Management of the “Cannizzaro” Emergency Hospital of Catania, 95126 Catania, Italy;
- Clinical Pathology and Clinical Molecular Biology Unit, “Garibaldi Centro” Hospital, ARNAS Garibaldi, 95123 Catania, Italy
| | - Michele Teodoro
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Occupational Medicine Section, University of Messina, 98125 Messina, Italy; (M.T.); (C.F.)
| | - Chiara Costa
- Clinical and Experimental Medicine Department, University of Messina, 98125 Messina, Italy;
| | - Aristides Tsatsakis
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece;
| | - Concettina Fenga
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Occupational Medicine Section, University of Messina, 98125 Messina, Italy; (M.T.); (C.F.)
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute-IRCCS ‘Fondazione G. Pascale’, 80131 Naples, Italy
- Correspondence: ; Tel.: +39-095-478-1278
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16
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Wang SC, Liao LM, Ansar M, Lin SY, Hsu WW, Su CM, Chung YM, Liu CC, Hung CS, Lin RK. Automatic Detection of the Circulating Cell-Free Methylated DNA Pattern of GCM2, ITPRIPL1 and CCDC181 for Detection of Early Breast Cancer and Surgical Treatment Response. Cancers (Basel) 2021; 13:cancers13061375. [PMID: 33803633 PMCID: PMC8002961 DOI: 10.3390/cancers13061375] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
The early detection of cancer can reduce cancer-related mortality. There is no clinically useful noninvasive biomarker for early detection of breast cancer. The aim of this study was to develop accurate and precise early detection biomarkers and a dynamic monitoring system following treatment. We analyzed a genome-wide methylation array in Taiwanese and The Cancer Genome Atlas (TCGA) breast cancer (BC) patients. Most breast cancer-specific circulating methylated CCDC181, GCM2 and ITPRIPL1 biomarkers were found in the plasma. An automatic analysis process of methylated ccfDNA was established. A combined analysis of CCDC181, GCM2 and ITPRIPL1 (CGIm) was performed in R using Recursive Partitioning and Regression Trees to establish a new prediction model. Combined analysis of CCDC181, GCM2 and ITPRIPL1 (CGIm) was found to have a sensitivity level of 97% and an area under the curve (AUC) of 0.955 in the training set, and a sensitivity level of 100% and an AUC of 0.961 in the test set. The circulating methylated CCDC181, GCM2 and ITPRIPL1 was also significantly decreased after surgery (all p < 0.001). The aberrant methylation patterns of the CCDC181, GCM2 and ITPRIPL1 genes means that they are potential biomarkers for the detection of early BC and can be combined with breast imaging data to achieve higher accuracy, sensitivity and specificity, facilitating breast cancer detection. They may also be applied to monitor the surgical treatment response.
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Affiliation(s)
- Sheng-Chao Wang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan;
| | - Li-Min Liao
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Shih-Yun Lin
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Wei-Wen Hsu
- Department of Statistics, College of Arts and Sciences, Kansas State University, 101 Dickens Hall, 1116 Mid-Campus Drive N, Manhattan, KS 66506-0802, USA;
| | - Chih-Ming Su
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan
| | - Yu-Mei Chung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Cai-Cing Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Chin-Sheng Hung
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan
- Correspondence: (C.-S.H.); (R.-K.L.); Tel.: +886-970-405-127 (C.-S.H.); +886-2-2736-1661 (ext. 6162) (R.-K.L.)
| | - Ruo-Kai Lin
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan;
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Clinical trial center, Taipei Medical University Hospital, 252 Wu-Hsing Street, Taipei 110, Taiwan
- Correspondence: (C.-S.H.); (R.-K.L.); Tel.: +886-970-405-127 (C.-S.H.); +886-2-2736-1661 (ext. 6162) (R.-K.L.)
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Ahmadi M, Mohammadi Z, Azad M, Foroughi F, Khojastehpour S, Gheibi N, Samiee-Rad F, Maali A. Evaluation of expression level and methylation profile of CXX1 gene in breast cancer tissue blocks. J Cancer Res Ther 2021; 17:1328-1334. [DOI: 10.4103/jcrt.jcrt_27_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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18
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Jensen ET, Langefeld CD, Zimmerman KD, Howard TD, Dellon ES. Epigenetic methylation in Eosinophilic Esophagitis: Molecular ageing and novel biomarkers for treatment response. Clin Exp Allergy 2020; 50:1372-1380. [PMID: 32986922 DOI: 10.1111/cea.13748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/09/2020] [Accepted: 09/20/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND Treatment failure in eosinophilic esophagitis (EoE) is common. We hypothesize that DNA methylation differs between patients by treatment response to topical steroids (oral viscous budesonide), thus offering the potential to inform targeting therapies. OBJECTIVE We sought to identify differentially methylated sites and affiliated genes in pre-treatment oesophageal cells between responders and non-responders and test for accelerated epigenetic ageing in oesophageal cells of EoE patients. METHODS DNA was extracted from prospectively collected and biobanked oesophageal biopsies from 36 Caucasian treatment naïve EoE patients at diagnosis. Methylation assays were completed using the Infinium HumanMethylation450 BeadChip. Normalized β values for each CpG site were tested (t test) for differential methylation. Further, 353 CpG probes were used to estimate epigenetic age for each patient and a linear regression model tested whether chronologic age and epigenetic age differed. Epigenetic age results were confirmed in an independent cohort of healthy controls. RESULTS Eighteen CpG sites were differentially methylated by treatment response (P < .00001). The mean epigenetic age and chronological age were 56.1 ± 11.1 and 36.7 ± 12.3 years, a mean age difference of 19.3 ± 5.2 years (P < .0001); accelerated ageing was not observed in the oesophageal cells of healthy controls. CONCLUSIONS AND CLINICAL RELEVANCE EoE patients that respond versus do not respond to treatment have differences in their methylation profile, including enrichment of genes in pathways consistent with cellular injury and repair due to environmental stress and cell adhesion and barrier integrity. EoE also appears to accelerate cellular ageing. Whether treatment can arrest or reverse accelerated epigenetic ageing and the implications for long-term disease progression is important areas for future research.
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Affiliation(s)
- Elizabeth T Jensen
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Internal Medicine, Section on Gastroenterology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Evan S Dellon
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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Bandera-Merchan B, Boughanem H, Crujeiras AB, Macias-Gonzalez M, Tinahones FJ. Ketotherapy as an epigenetic modifier in cancer. Rev Endocr Metab Disord 2020; 21:509-519. [PMID: 32514818 DOI: 10.1007/s11154-020-09567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic alterations in cancer play a variety of roles. Aberrant DNA methylation, as one of the epigenetic mechanisms, has been widely studied in both tumor and liquid biopsies and provide a useful bench mark for treatment response in cancer. Recently, several studies have reported an association between the type of diet and epigenetic modifications. Whereby there is a growing interest in finding the "anti-cancer diet formula", if such a thing exists. In this sense, ketogenic diets (KD) have reported potentially beneficial effects, which were able to prevent malignancies and decrease tumor growth. Some studies have even shown increased survival in cancer patients, reduced side effects of cytotoxic treatments, and intensified efficacy of cancer therapies. Although the biological mechanisms of KD are not well understood, it has been reported that KD may affect DNA methylation by modulating the expression of crucial genes involved in tumor survival and proliferation. However, there are many considerations to take into account to use ketotherapy in cancer, such as epigenetic mark, type of cancer, immunological and metabolic state or microbiota profile. In this review, we argue about ketotherapy as a potential strategy to consider as coadjuvant of cancer therapy. We will focus on mainly epigenetic mechanisms and dietary approach that could be included in the current clinical practice guidelines.
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Affiliation(s)
- Borja Bandera-Merchan
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
| | - Hatim Boughanem
- Biomedical Research Institute of Malaga (IBIMA). Faculty of Science, University of Malaga, 29010, Málaga, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain.
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
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20
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Jurdziński KT, Potempa J, Grabiec AM. Epigenetic regulation of inflammation in periodontitis: cellular mechanisms and therapeutic potential. Clin Epigenetics 2020; 12:186. [PMID: 33256844 PMCID: PMC7706209 DOI: 10.1186/s13148-020-00982-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetic mechanisms, namely DNA and histone modifications, are critical regulators of immunity and inflammation which have emerged as potential targets for immunomodulating therapies. The prevalence and significant morbidity of periodontitis, in combination with accumulating evidence that genetic, environmental and lifestyle factors cannot fully explain the susceptibility of individuals to disease development, have driven interest in epigenetic regulation as an important factor in periodontitis pathogenesis. Aberrant promoter methylation profiles of genes involved in inflammatory activation, including TLR2, PTGS2, IFNG, IL6, IL8, and TNF, have been observed in the gingival tissue, peripheral blood or buccal mucosa from patients with periodontitis, correlating with changes in expression and disease severity. The expression of enzymes that regulate histone acetylation, in particular histone deacetylases (HDACs), is also dysregulated in periodontitis-affected gingival tissue. Infection of gingival epithelial cells, gingival fibroblasts and periodontal ligament cells with the oral pathogens Porphyromonas gingivalis or Treponema denticola induces alterations in expression and activity of chromatin-modifying enzymes, as well as site-specific and global changes in DNA methylation profiles and in histone acetylation and methylation marks. These epigenetic changes are associated with excessive production of inflammatory cytokines, chemokines, and matrix-degrading enzymes that can be suppressed by small molecule inhibitors of HDACs (HDACi) or DNA methyltransferases. HDACi and inhibitors of bromodomain-containing BET proteins ameliorate inflammation, osteoclastogenesis, and alveolar bone resorption in animal models of periodontitis, suggesting their clinical potential as host modulation therapeutic agents. However, broader application of epigenomic methods will be required to create a comprehensive map of epigenetic changes in periodontitis. The integration of functional studies with global analyses of the epigenetic landscape will provide critical information on the therapeutic and diagnostic potential of epigenetics in periodontal disease.
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Affiliation(s)
- Krzysztof T Jurdziński
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA
| | - Aleksander M Grabiec
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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21
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Porcu M, Solinas C, Mannelli L, Micheletti G, Lambertini M, Willard-Gallo K, Neri E, Flanders AE, Saba L. Radiomics and "radi-…omics" in cancer immunotherapy: a guide for clinicians. Crit Rev Oncol Hematol 2020; 154:103068. [PMID: 32805498 DOI: 10.1016/j.critrevonc.2020.103068] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years the concept of precision medicine has become a popular topic particularly in medical oncology. Besides the identification of new molecular prognostic and predictive biomarkers and the development of new targeted and immunotherapeutic drugs, imaging has started to play a central role in this new era. Terms such as "radiomics", "radiogenomics" or "radi…-omics" are becoming increasingly common in the literature and soon they will represent an integral part of clinical practice. The use of artificial intelligence, imaging and "-omics" data can be used to develop models able to predict, for example, the features of the tumor immune microenvironment through imaging, and to monitor the therapeutic response beyond the standard radiological criteria. The aims of this narrative review are to provide a simplified guide for clinicians to these concepts, and to summarize the existing evidence on radiomics and "radi…-omics" in cancer immunotherapy.
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Affiliation(s)
- Michele Porcu
- Department of Radiology, AOU of Cagliari, University of Cagliari, Italy.
| | - Cinzia Solinas
- Medical Oncology, Azienda Tutela Salute Sardegna, Hospital Antonio Segni, Ozieri, SS, Italy
| | | | - Giulio Micheletti
- Department of Radiology, AOU of Cagliari, University of Cagliari, Italy
| | - Matteo Lambertini
- Department of Medical Oncology, U.O.C. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova, Italy
| | | | | | - Adam E Flanders
- Department of Radiology, Division of Neuroradiology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - Luca Saba
- Department of Radiology, AOU of Cagliari, University of Cagliari, Italy
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22
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Duforestel M, Briand J, Bougras-Cartron G, Heymann D, Frenel JS, Vallette FM, Cartron PF. Cell-free circulating epimarks in cancer monitoring. Epigenomics 2020; 12:145-155. [DOI: 10.2217/epi-2019-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but also have intercellular communication roles, being released in extracellular environment and in different body fluids. Here, we reviewed current literature on the use of these blood circulating epimarks in cancer monitoring. What stands out is that epimarkers must be considered as ‘real time’ images of the tumor, and can be isolated without invasive methods. In the future, the real challenge lies in the development of specific, sensitive, fast and clinically applicable detection and analysis methods of epimarkers.
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Affiliation(s)
- Manon Duforestel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - Jean-Sébastien Frenel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest Site René Gauducheau, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
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Abstract
Cells are constantly subjected to cytotoxic and genotoxic insults resulting in the accumulation of unrepaired damaged DNA, which leads to neuronal death. In this way, DNA damage has been implicated in the pathogenesis of neurological disorders, cancer, and aging. Lifestyle factors, such as physical exercise, are neuroprotective and increase brain function by improving cognition, learning, and memory, in addition to regulating the cellular redox milieu. Several mechanisms are associated with the effects of exercise in the brain, such as reduced production of oxidants, up-regulation of antioxidant capacity, and a consequent decrease in nuclear DNA damage. Furthermore, physical exercise is a potential strategy for further DNA damage repair. However, the neuroplasticity molecules that respond to different aspects of physical exercise remain unknown. In this review, we discuss the influence of exercise on DNA damage and adjacent mechanisms in the brain. We discuss the results of several studies that focus on the effects of physical exercise on brain DNA damage.
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Affiliation(s)
- Thais Ceresér Vilela
- Laboratory of Translational Biomedicine, Graduate Program of Health Sciences, University of Southern Santa Catarina - UNESC, Criciúma, SC, Brazil
| | - Vanessa Moraes de Andrade
- Laboratory of Translational Biomedicine, Graduate Program of Health Sciences, University of Southern Santa Catarina - UNESC, Criciúma, SC, Brazil
| | - Zsolt Radak
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Ricardo Aurino de Pinho
- Laboratory of Exercise Biochemistry in Health, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
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Postprandial Circulating miRNAs in Response to a Dietary Fat Challenge. Nutrients 2019; 11:nu11061326. [PMID: 31200481 PMCID: PMC6627817 DOI: 10.3390/nu11061326] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/19/2022] Open
Abstract
Postprandial lipemia has many physiopathological effects, some of which increase the risk of cardiovascular disease. MicroRNAs (miRNAs) can be found in almost all biological fluids, but their postprandial kinetics are poorly described. We aimed to profile circulating miRNAs in response to a fat challenge. In total, 641 circulating miRNAs were assessed by real-time PCR in plasmas from mice two hours after lipid gavage. Mice with intestine-specific loss of Dicer were screened to identify potential miRNAs released by the intestine. A total of 68 miRNAs were selected for further validation. Ten circulating miRNAs were finally validated as responsive to postprandial lipemia, including miR-206-3p, miR-543-3p, miR-466c-5p, miR-27b-5p, miR-409-3p, miR-340-3p, miR-1941-3p, miR-10a-3p, miR-125a-3p, and miR-468-3p. Analysis of their possible tissues of origin/target showed an enrichment of selected miRNAs in liver, intestine, brain, or skeletal muscle. miR-206, miR-27b-5p, and miR-409-3p were validated in healthy humans. Analysis of their predicted target genes revealed their potential involvement in insulin/insulin like growth factor (insulin/IGF), angiogenesis, cholecystokinin B receptor signaling pathway (CCKR), inflammation or Wnt pathways for mice, and in platelet derived growth factor (PDGF) and CCKR signaling pathways for humans. Therefore, the current study shows that certain miRNAs are released in the circulation in response to fatty meals, proposing them as potential novel therapeutic targets of lipid metabolism.
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