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Eftekhar Z, Aghaei M, Saki N. DNA damage repair in megakaryopoiesis: molecular and clinical aspects. Expert Rev Hematol 2024; 17:705-712. [PMID: 39117495 DOI: 10.1080/17474086.2024.2391102] [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: 04/18/2024] [Revised: 07/09/2024] [Accepted: 08/07/2024] [Indexed: 08/10/2024]
Abstract
INTRODUCTION Endogenous DNA damage is a significant factor in the damage of hematopoietic cells. Megakaryopoiesis is one of the pathways of hematopoiesis that ends with the production of platelets and plays the most crucial role in hemostasis. Despite the presence of efficient DNA repair mechanisms, some endogenous lesions can lead to mutagenic alterations, disruption of pathways of hematopoiesis including megakaryopoiesis and potentially result in human diseases. AREAS COVERED The complex regulation of DNA repair mechanisms plays a central role in maintaining genomic integrity during megakaryopoiesis and influences platelet production efficiency and quality. Moreover, anomalies in DNA repair processes are involved in several diseases associated with megakaryopoiesis, including myeloproliferative disorders and thrombocytopenia. EXPERT OPINION In the era of personalized medicine, diagnosing diseases related to megakaryopoiesis can only be made with a complete assessment of their molecular aspects to provide physicians with critical molecular data for patient management and to identify the subset of patients who could benefit from targeted therapy.
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Affiliation(s)
- Zeinab Eftekhar
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mojtaba Aghaei
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Jiang J, Xu J, Ji S, Yu X, Chen J. Unraveling the mysteries of MGMT: Implications for neuroendocrine tumors. Biochim Biophys Acta Rev Cancer 2024; 1879:189184. [PMID: 39303858 DOI: 10.1016/j.bbcan.2024.189184] [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: 01/28/2024] [Revised: 07/15/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Neuroendocrine tumors (NETs) are a diverse group of tumors that arise from neuroendocrine cells and are commonly found in various organs. A considerable proportion of NET patients were diagnosed at an advanced or metastatic stage. Alkylating agents are the primary treatment for NET, and O6-methylguanine methyltransferase (MGMT) remains the first-line of defense against DNA damage caused by these agents. Clinical trials have indicated that MGMT promoter methylation or its low/lacked expression can predict a favorable outcome with Temozolomide in NETs. Its status could help select NET patients who can benefit from alkylating agents. Therefore, MGMT status serves as a biomarker to guide decisions on the efficacy of Temozolomide as a personalized treatment option. Additionally, delving into the regulatory mechanisms of MGMT status can lead to the development of MGMT-targeted therapies, benefiting individuals with high levels of MGMT expression. This review aims to explore the polymorphism of MGMT regulation and summarize its clinical implications in NETs, which would help establish the role of MGMT as a biomarker and its potential as a therapeutic target in NETs. Additionally, we explore the benefits of combining Temozolomide and immunotherapy in MGMT hypermethylated subgroups. Future studies can focus on optimizing Temozolomide administration to induce specific immunomodulatory changes.
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Affiliation(s)
- Jianyun Jiang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Junfeng Xu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Shunrong Ji
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Xianjun Yu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Jie Chen
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Crisafulli G. Mutational Signatures in Colorectal Cancer: Translational Insights, Clinical Applications, and Limitations. Cancers (Basel) 2024; 16:2956. [PMID: 39272814 PMCID: PMC11393898 DOI: 10.3390/cancers16172956] [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: 08/12/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
A multitude of exogenous and endogenous processes have the potential to result in DNA damage. While the repair mechanisms are typically capable of correcting this damage, errors in the repair process can result in mutations. The findings of research conducted in 2012 indicate that mutations do not occur randomly but rather follow specific patterns that can be attributed to known or inferred mutational processes. The process of mutational signature analysis allows for the inference of the predominant mutational process for a given cancer sample, with significant potential for clinical applications. A deeper comprehension of these mutational signatures in CRC could facilitate enhanced prevention strategies, facilitate the comprehension of genotoxic drug activity, predict responses to personalized treatments, and, in the future, inform the development of targeted therapies in the context of precision oncology. The efforts of numerous researchers have led to the identification of several mutational signatures, which can be categorized into different mutational signature references. In CRC, distinct mutational signatures are identified as correlating with mismatch repair deficiency, polymerase mutations, and chemotherapy treatment. In this context, a mutational signature analysis offers considerable potential for enhancing minimal residual disease (MRD) tests in stage II (high-risk) and stage III CRC post-surgery, stratifying CRC based on the impacts of genetic and epigenetic alterations for precision oncology, identifying potential therapeutic vulnerabilities, and evaluating drug efficacy and guiding therapy, as illustrated in a proof-of-concept clinical trial.
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Jia W, Li N, Wang J, Gong X, Ouedraogo SY, Wang Y, Zhao J, Grech G, Chen L, Zhan X. Immune-related gene methylation prognostic instrument for stratification and targeted treatment of ovarian cancer patients toward advanced 3PM approach. EPMA J 2024; 15:375-404. [PMID: 38841623 PMCID: PMC11148001 DOI: 10.1007/s13167-024-00359-3] [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: 02/03/2024] [Accepted: 04/07/2024] [Indexed: 06/07/2024]
Abstract
Background DNA methylation is an important mechanism in epigenetics, which can change the transcription ability of genes and is closely related to the pathogenesis of ovarian cancer (OC). We hypothesize that DNA methylation is significantly different in OCs compared to controls. Specific DNA methylation status can be used as a biomarker of OC, and targeted drugs targeting these methylation patterns and DNA methyltransferase may have better therapeutic effects. Studying the key DNA methylation sites of immune-related genes (IRGs) in OC patients and studying the effects of these methylation sites on the immune microenvironment may provide a new method for further exploring the pathogenesis of OC, realizing early detection and effective monitoring of OC, identifying effective biomarkers of DNA methylation subtypes and drug targets, improving the efficacy of targeted drugs or overcoming drug resistance, and better applying it to predictive diagnosis, prevention, and personalized medicine (PPPM; 3PM) of OC. Method Hypermethylated subtypes (cluster 1) and hypomethylated subtypes (cluster 2) were established in OCs based on the abundance of different methylation sites in IRGs. The differences in immune score, immune checkpoints, immune cells, and overall survival were analyzed between different methylation subtypes in OC samples. The significant pathways, gene ontology (GO), and protein-protein interaction (PPI) network of the identified methylation sites in IRGs were enriched. In addition, the immune-related methylation signature was constructed with multiple regression analysis. A methylation site model based on IRGs was constructed and verified. Results A total of 120 IRGs with 142 differentially methylated sites (DMSs) were identified. The DMSs were clustered into a high-level methylation group (cluster 1) and a low-level methylation group (cluster 2). The significant pathways and GO analysis showed many immune-related and cancer-associated enrichments. A methylation site signature based on IRGs was constructed, including RORC|cg25112191, S100A13|cg14467840, TNF|cg04425624, RLN2|cg03679581, and IL1RL2|cg22797169. The methylation sites of all five genes showed hypomethylation in OC, and there were statistically significant differences among RORC|cg25112191, S100A13|cg14467840, and TNF|cg04425624 (p < 0.05). This prognostic model based on low-level methylation and high-level methylation groups was significantly linked to the immune microenvironment as well as overall survival in OC. Conclusions This study provided different methylation subtypes for OC patients according to the methylation sites of IRGs. In addition, it helps establish a relationship between methylation and the immune microenvironment, which showed specific differences in biological signaling pathways, genomic changes, and immune mechanisms within the two subgroups. These data provide ones to deeply understand the mechanism of immune-related methylation genes on the occurrence and development of OC. The methylation-site signature is also to establish new possibilities for OC therapy. These data are a precious resource for stratification and targeted treatment of OC patients toward an advanced 3PM approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00359-3.
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Affiliation(s)
- Wenshuang Jia
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Jingjing Wang
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xiaoxia Gong
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Yan Wang
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Junkai Zhao
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Godfrey Grech
- Department of Pathology, University of Malta, Msida, Malta
| | - Liang Chen
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
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Gowtham P, Girigoswami K, Thirumalai A, Harini K, Pallavi P, Girigoswami A. Association of TIMP2 418 G/C and MMP Gene Polymorphism with Risk of Urinary Cancers: Systematic Review and Meta-analysis. Genet Test Mol Biomarkers 2024; 28:83-90. [PMID: 38478803 DOI: 10.1089/gtmb.2023.0457] [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: 04/10/2024] Open
Abstract
Aim: The matrix metalloproteinases (MMPs) inhibit tissue inhibitors of metalloproteinases (TIMPs), playing a notable role in various biological processes, and mutations in TIMP2 genes impact a variety of urinary cancers. In this study, we analyze and evaluate the potential involvement of the TIMP2 418 G/C and MMP gene polymorphism in the etiology of urinary cancer. Methodology: For suitable case-control studies, a literature search was undertaken from various database sources such as PubMed, EMBASE, and Google Scholar. Incorporated into the analysis were case-control or cohort studies that documented the correlation between TIMP2 418 G/C and urological cancers. MetaGenyo served as the tool for conducting the meta-analysis, employing a fixed-effects model. The collective odds ratios, along with their corresponding 95% confidence intervals, were calculated and presented to assess the robustness of the observed associations. Results: A total of seven studies involving controls and cases out of recorded 1265 controls and 1154 cases were analyzed to ascertain the significant association of the TIMP2 gene with urologic cancer. No statistically significant correlation was observed between allelic, recessive, dominant, and overdominant models for the genetic variant under investigation. A 95% confidence interval (CI) and odds ratio (OR) were computed for each model, considering p-values <0.05. The OR and 95% CI for the allelic model were 0.99 and 0.77-1.27, respectively, whereas the respective values were 1.00 and 0.76-1.32 for the recessive model. In the dominant contrast model, OR and 95% CI were 1.09 and 0.62-1.90, while the same were 0.93 and 0.77-1.12 for the overdominant model. A funnel plot was used to reanalyze and detect the results as statically satisfactory. Conclusions: As a result of the data obtained, the TIMP2 gene polymorphism does not correlate statistically with cancer risk. The significance of this finding can only be confirmed using a large population, extensive epidemiological research, a comprehensive survey, and a better understanding of the molecular pathways associated.
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Affiliation(s)
- Pemula Gowtham
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
| | - Koyeli Girigoswami
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
| | - Anbazhagan Thirumalai
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
| | - Karthick Harini
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
| | - Pragya Pallavi
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
| | - Agnishwar Girigoswami
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, India
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Shapiro BD, Battle A. Bayesian Multi-View Clustering given complex inter-view structure. F1000Res 2024; 11:1460. [PMID: 38495778 PMCID: PMC10940850 DOI: 10.12688/f1000research.126215.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 03/19/2024] Open
Abstract
Multi-view datasets are becoming increasingly prevalent. These datasets consist of different modalities that provide complementary characterizations of the same underlying system. They can include heterogeneous types of information with complex relationships, varying degrees of missingness, and assorted sample sizes, as is often the case in multi-omic biological studies. Clustering multi-view data allows us to leverage different modalities to infer underlying systematic structure, but most existing approaches are limited to contexts in which entities are the same across views or have clear one-to-one relationships across data types with a common sample size. Many methods also make strong assumptions about the similarities of clusterings across views. We propose a Bayesian multi-view clustering approach (BMVC) which can handle the realities of multi-view datasets that often have complex relationships and diverse structure. BMVC incorporates known and complex many-to-many relationships between entities via a probabilistic graphical model that enables the joint inference of clusterings specific to each view, but where each view informs the others. Additionally, BMVC estimates the strength of the relationships between each pair of views, thus moderating the degree to which it imposes dependence constraints. We benchmarked BMVC on simulated data to show that it accurately estimates varying degrees of inter-view dependence when inter-view relationships are not limited to one-to-one correspondence. Next, we demonstrated its ability to capture visually interpretable inter-view structure in a public health survey of individuals and households in Puerto Rico following Hurricane Maria. Finally, we showed that BMVC clusters integrate the complex relationships between multi-omic profiles of breast cancer patient data, improving the biological homogeneity of clusters and elucidating hypotheses for functional biological mechanisms. We found that BMVC leverages complex inter-view structure to produce higher quality clusters than those generated by standard approaches. We also showed that BMVC is a valuable tool for real-world discovery and hypothesis generation.
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Affiliation(s)
- Benjamin D. Shapiro
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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Hong WF, Zhu DX, Chen YJ, Shen XZ, Cui YH, Du SS, Liu TS, Liang L. Coiled-coil domain-containing 154 promotes colorectal cancer proliferation and metastasis via interacting with minichromosome maintenance complex component 2. Cancer Lett 2023; 578:216460. [PMID: 37863352 DOI: 10.1016/j.canlet.2023.216460] [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: 08/21/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Coiled-Coil Domain-Containing (CCDC) is a large class of structural proteins containing left-handed supercoiled structure. The clinical value and the functional implication of CCDC in colorectal cancer (CRC) remain unknown. Based on the genetic, transcriptional, and clinical data from The Cancer Genome Atlas, five of thirty-six CCDC proteins were differentially expressed in the CRC and associated with the survival of patients with CRC. A CCDC-score model was established to evaluate the prognosis of patients. The potential function of Coiled-Coil Domain-Containing 154 (CCDC154) was investigated using bioinformatical methods, which unveiled that high expression of CCDC154 indicates poor survival for patients with CRC and correlates with low infiltration of CD8+ T cells and high infiltration of neutrophils, indicating that CCDC154 enhances tumor growth and metastasis. CCDC154 interacts with Minichromosome Maintenance Complex Component 2 (MCM2) protein and promotes malignant phenotype via MCM2. We validated the expression level and survival prediction value of CCDC154 in clinical samples, and analyzed its co-expression of MCM2, Ki-67 and p53. This work discloses the role of CCDC in clinical setting and CCDC154 functions in CRC.
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Affiliation(s)
- Wei-Feng Hong
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China
| | - De-Xiang Zhu
- Department of Colorectal Surgery, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China
| | - Yan-Jie Chen
- Department of Gastroenterology, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China
| | - Xi-Zhong Shen
- Department of Gastroenterology, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China
| | - Yue-Hong Cui
- Department of Medical Oncology, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China; Cancer Center, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China
| | - Shi-Suo Du
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China.
| | - Tian-Shu Liu
- Department of Medical Oncology, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China; Cancer Center, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China; Evidence-Based Medicine Center, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai 200032, People's Republic of China; Department of Cancer Screening and Prevention, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai 200032, People's Republic of China.
| | - Li Liang
- Department of Medical Oncology, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China; Cancer Center, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People's Republic of China; Evidence-Based Medicine Center, Zhongshan Hospital Fudan University, NO. 180, Fenglin Road, Xuhui District, Shanghai 200032, People's Republic of China.
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Gupta MK, Kushwah AS, Singh R, Srivastava K, Banerjee M. Genetic and epigenetic alterations in MGMT gene and correlation with concomitant chemoradiotherapy (CRT) in cervical cancer. J Cancer Res Clin Oncol 2023; 149:15159-15170. [PMID: 37634205 DOI: 10.1007/s00432-023-05305-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
PURPOSE The MGMT (O6-methylguanine-DNA methyltransferase) gene plays a crucial role in repairing DNA damage caused by alkylating agents, including those used in chemotherapy. Genetic and epigenetic alterations can influence the regulation of MGMT gene, which in turn may impact the response to concomitant chemoradiotherapy (CRT) in cervical cancer. The present study was undertaken to evaluate the correlation of such variations in MGMT gene with the treatment outcome of concomitant chemoradiotherapy (CRT) in cervical cancer. METHODS A total of 460 study subjects (240 controls and 220 patients) were subjected to genotypic analysis of MGMT gene variants rs12917(T/C) and rs2308327(A/G) by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). Out of them, 48 each of controls and patients were analyzed for promoter methylation and expression by methylation-specific PCR and real-time PCR, respectively. Patients (n = 48) were followed up and evaluated for treatment (CRT) outcome. Statistical analyses were done using GraphPad (9.0) and SPSS version 18.0. RESULTS Individuals with GG genotype, G allele of rs2308327, and haplotype 'TA' of both variants showed a significant increase in the development of cervical cancer (P ≤ 0.05). In epigenetic regulation, there was a significant hypermethylation of MGMT gene and down-regulation of their expression in patients compared to control individuals. In treatment outcome of CRT, GG genotype of rs2308327(A/G) gene variant showed better response and GG + AG was significantly associated with vital status (alive). Unmethylated MGMT gene showed better median overall survival up to 25 months significant in comparison to methylated MGMT promoter. CONCLUSION Gene variant rs2308327(A/G) and promoter hypermethylation regulated MGMT gene can be a good prognostic for treatment response in cervical cancer patients.
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Affiliation(s)
- Maneesh Kumar Gupta
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India
| | - Atar Singh Kushwah
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India
- Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Renu Singh
- Department of Obstetrics and Gynecology, King George's Medical University, Lucknow, 226003, India
| | - Kirti Srivastava
- Department of Radiotherapy, King George's Medical University, Lucknow, 226003, India
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India.
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Zhu J, Chen Q, Zeng L, Gao H, Wu T, He Y, Xu J, Pang J, Peng J, Deng Y, Han Y, Yi W. Multi-omics analysis reveals the involvement of origin recognition complex subunit 6 in tumor immune regulation and malignant progression. Front Immunol 2023; 14:1236806. [PMID: 37901236 PMCID: PMC10602784 DOI: 10.3389/fimmu.2023.1236806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Background Origin recognition complex 6 (ORC6) is one of the six highly conserved subunit proteins required for DNA replication and is essential for maintaining genome stability during cell division. Recent research shows that ORC6 regulates the advancement of multiple cancers; however, it remains unclear what regulatory impact it has on the tumor immune microenvironment. Methods Unpaired Wilcoxon rank sum and signed rank tests were used to analyze the differences in the expression of ORC6 in normal tissues and corresponding tumor tissues. Multiple online databases have evaluated the genetic alterations, protein expression and localization, and clinical relevance of ORC6. To evaluate the potential prognostic impact and diagnostic significance of ORC6 expression, we carried out log-rank, univariate Cox regression, and receiver operating characteristic curve analysis. The ICGC-LIRI-JP cohort, CGGA-301 cohort, CGGA-325 cohort, CGGA-693 cohort, and GSE13041 cohort were used for external validation of the study findings. The associations between ORC6 expression and immune cell infiltration, immune checkpoint expression, and immunotherapy cohorts was further analyzed. To explore the functional and signaling pathways related to ORC6 expression, gene set enrichment analysis was performed. To clarify the expression and function of ORC6 in hepatocellular carcinoma (LIHC) and glioma, we conducted in vitro experiments. Results Expression of ORC6 is upregulated in the majority of cancer types and is associated with poor patient prognosis, notably in cases of LIHC and gliomas. In addition, ORC6 may be involved in multiple signaling pathways related to cancer progression and immune regulation. High expression of ORC6 correlates with an immunosuppressive state in the tumor microenvironment. The results of further immunotherapy cohort analysis suggested that patients in the ORC6 high-expression group benefited from immunotherapy. Inhibiting ORC6 expression suppressed the proliferative and migratory abilities of LIHC and glioma cells. Conclusion High expression of ORC6 may be used as a biomarker to predict the poor prognosis of most tumor patients. The high expression of ORC6 may be involved in the regulation of the tumor immunosuppressive environment, and it is expected to become a molecular target for inhibiting tumor progression.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Hongyu Gao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Tong Wu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yeqing He
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jiachi Xu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jian Pang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jing Peng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yueqiong Deng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yi Han
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
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10
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Norollahi SE, Vahidi S, Shams S, Keymoradzdeh A, Soleymanpour A, Solymanmanesh N, Mirzajani E, Jamkhaneh VB, Samadani AA. Analytical and therapeutic profiles of DNA methylation alterations in cancer; an overview of changes in chromatin arrangement and alterations in histone surfaces. Horm Mol Biol Clin Investig 2023; 44:337-356. [PMID: 36799246 DOI: 10.1515/hmbci-2022-0043] [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: 05/07/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023]
Abstract
DNA methylation is the most important epigenetic element that activates the inhibition of gene transcription and is included in the pathogenesis of all types of malignancies. Remarkably, the effectors of DNA methylation are DNMTs (DNA methyltransferases) that catalyze de novo or keep methylation of hemimethylated DNA after the DNA replication process. DNA methylation structures in cancer are altered, with three procedures by which DNA methylation helps cancer development which are including direct mutagenesis, hypomethylation of the cancer genome, and also focal hypermethylation of the promoters of TSGs (tumor suppressor genes). Conspicuously, DNA methylation, nucleosome remodeling, RNA-mediated targeting, and histone modification balance modulate many biological activities that are essential and indispensable to the genesis of cancer and also can impact many epigenetic changes including DNA methylation and histone modifications as well as adjusting of non-coding miRNAs expression in prevention and treatment of many cancers. Epigenetics points to heritable modifications in gene expression that do not comprise alterations in the DNA sequence. The nucleosome is the basic unit of chromatin, consisting of 147 base pairs (bp) of DNA bound around a histone octamer comprised of one H3/H4 tetramer and two H2A/H2B dimers. DNA methylation is preferentially distributed over nucleosome regions and is less increased over flanking nucleosome-depleted DNA, implying a connection between nucleosome positioning and DNA methylation. In carcinogenesis, aberrations in the epigenome may also include in the progression of drug resistance. In this report, we report the rudimentary notes behind these epigenetic signaling pathways and emphasize the proofs recommending that their misregulation can conclude in cancer. These findings in conjunction with the promising preclinical and clinical consequences observed with epigenetic drugs against chromatin regulators, confirm the important role of epigenetics in cancer therapy.
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Affiliation(s)
- Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shima Shams
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arman Keymoradzdeh
- Department of Neurosurgery, School of Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armin Soleymanpour
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Nazanin Solymanmanesh
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Vida Baloui Jamkhaneh
- Department of Veterinary Medicine, Islamic Azad University of Babol Branch, Babol, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran
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11
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Lee M, Je IG, Kim JE, Yoo Y, Lim JH, Jang E, Lee Y, Song DK, Moon AN, Kim JA, Jeong J, Park JT, Lee JW, Yang JH, Hong CH, Park SY, Park YW, Baek NS, Lee S, Ha KS, Choi S, Lee WS. Venadaparib Is a Novel and Selective PARP Inhibitor with Improved Physicochemical Properties, Efficacy, and Safety. Mol Cancer Ther 2023; 22:333-342. [PMID: 36808277 PMCID: PMC9978881 DOI: 10.1158/1535-7163.mct-22-0068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/27/2022] [Accepted: 01/06/2023] [Indexed: 02/19/2023]
Abstract
PARP inhibitors have been approved by the FDA for use in the treatment of patients with ovarian, breast, pancreatic, and prostate cancers. PARP inhibitors show diverse suppressive effects on PARP family members and PARP-DNA trapping potency. These properties are associated with distinct safety/efficacy profiles. Here, we report the nonclinical characteristics of venadaparib (also known as IDX-1197 or NOV140101), a novel potent PARP inhibitor. The physiochemical properties of venadaparib were analyzed. Furthermore, the efficacy of venadaparib against PARP enzymes, PAR formation, and PARP trapping activities, and growth inhibition of cell lines with BRCA mutations were evaluated. Ex vivo and in vivo models were also established to study pharmacokinetics/pharmacodynamics, efficacy, and toxicity. Venadaparib specifically inhibits PARP-1 and -2 enzymes. Oral administration of venadaparib HCl at doses above 12.5 mg/kg significantly reduced tumor growth in the OV_065 patient-derived xenograft model. Intratumoral PARP inhibition remained at over 90% until 24 hours after dosing. Venadaparib had wider safety margins than olaparib. Notably, venadaparib showed favorable physicochemical properties and superior anticancer effects in homologous recombination-deficient in vitro and in vivo models with improved safety profiles. Our results suggest the possibility of venadaparib as a next-generation PARP inhibitor. On the basis of these findings, phase Ib/IIa studies on the efficacy and safety of venadaparib have been initiated.
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Affiliation(s)
| | - In-Gyu Je
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | | | - Yeongran Yoo
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Jong-Ha Lim
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Eunhye Jang
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Yoonsuk Lee
- iLEAD BMS, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | | | - An-Na Moon
- iLEAD BMS, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Jeong-Ah Kim
- iLEAD BMS, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Jinah Jeong
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Joon-Tae Park
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Jung Woo Lee
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Ji-Hoon Yang
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Chang-Hee Hong
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Sun-Young Park
- Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Young-Whan Park
- National-OncoVenture, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Nam Seok Baek
- National-OncoVenture, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Sungsook Lee
- National-OncoVenture, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | | | - SungKu Choi
- Idience Co., Ltd, Seoul, Republic of Korea.,Research Laboratories, Ildong Pharmaceutical Co., Ltd, Hwaseong-si, Gyeonggi-do, Republic of Korea
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12
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Pan-cancer antagonistic inhibition pattern of ATM-driven G2/M checkpoint pathway vs other DNA repair pathways. DNA Repair (Amst) 2023; 123:103448. [PMID: 36657260 DOI: 10.1016/j.dnarep.2023.103448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/22/2022] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
DNA repair mechanisms keep genome integrity and limit tumor-associated alterations and heterogeneity, but on the other hand they promote tumor survival after radiation and genotoxic chemotherapies. We screened pathway activation levels of 38 DNA repair pathways in nine human cancer types (gliomas, breast, colorectal, lung, thyroid, cervical, kidney, gastric, and pancreatic cancers). We took RNAseq profiles of the experimental 51 normal and 408 tumor samples, and from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium databases - of 500/407 normal and 5752/646 tumor samples, and also 573 normal and 984 tumor proteomic profiles from Proteomic Data Commons portal. For all the samplings we observed a congruent trend that all cancer types showed inhibition of G2/M arrest checkpoint pathway compared to the normal samples, and relatively low activities of p53-mediated pathways. In contrast, other DNA repair pathways were upregulated in most of the cancer types. The G2/M checkpoint pathway was statistically significantly downregulated compared to the other DNA repair pathways, and this inhibition was strongly impacted by antagonistic regulation of (i) promitotic genes CCNB and CDK1, and (ii) GADD45 genes promoting G2/M arrest. At the DNA level, we found that ATM, TP53, and CDKN1A genes accumulated loss of function mutations, and cyclin B complex genes - transforming mutations. These findings suggest importance of activation for most of DNA repair pathways in cancer progression, with remarkable exceptions of G2/M checkpoint and p53-related pathways which are downregulated and neutrally activated, respectively.
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13
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Mehmood S, Aslam S, Dilshad E, Ismail H, Khan AN. Transforming Diagnosis and Therapeutics Using Cancer Genomics. Cancer Treat Res 2023; 185:15-47. [PMID: 37306902 DOI: 10.1007/978-3-031-27156-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In past quarter of the century, much has been understood about the genetic variation and abnormal genes that activate cancer in humans. All the cancers somehow possess alterations in the DNA sequence of cancer cell's genome. In present, we are heading toward the era where it is possible to obtain complete genome of the cancer cells for their better diagnosis, categorization and to explore treatment options.
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Affiliation(s)
- Sabba Mehmood
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan.
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
| | - Hammad Ismail
- Departments of Biochemistry and Biotechnology, University of Gujrat (UOG) Gujrat, Gujrat, Pakistan
| | - Amna Naheed Khan
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
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14
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Tong X, Zhou F. Integrated bioinformatic analysis of mitochondrial metabolism-related genes in acute myeloid leukemia. Front Immunol 2023; 14:1120670. [PMID: 37138869 PMCID: PMC10149950 DOI: 10.3389/fimmu.2023.1120670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a common hematologic malignancy characterized by poor prognoses and high recurrence rates. Mitochondrial metabolism has been increasingly recognized to be crucial in tumor progression and treatment resistance. The purpose of this study was to examined the role of mitochondrial metabolism in the immune regulation and prognosis of AML. Methods In this study, mutation status of 31 mitochondrial metabolism-related genes (MMRGs) in AML were analyzed. Based on the expression of 31 MMRGs, mitochondrial metabolism scores (MMs) were calculated by single sample gene set enrichment analysis. Differential analysis and weighted co-expression network analysis were performed to identify module MMRGs. Next, univariate Cox regression and the least absolute and selection operator regression were used to select prognosis-associated MMRGs. A prognosis model was then constructed using multivariate Cox regression to calculate risk score. We validated the expression of key MMRGs in clinical specimens using immunohistochemistry (IHC). Then differential analysis was performed to identify differentially expressed genes (DEGs) between high- and low-risk groups. Functional enrichment, interaction networks, drug sensitivity, immune microenvironment, and immunotherapy analyses were also performed to explore the characteristic of DEGs. Results Given the association of MMs with prognosis of AML patients, a prognosis model was constructed based on 5 MMRGs, which could accurately distinguish high-risk patients from low-risk patients in both training and validation datasets. IHC results showed that MMRGs were highly expressed in AML samples compared to normal samples. Additionally, the 38 DEGs were mainly related to mitochondrial metabolism, immune signaling, and multiple drug resistance pathways. In addition, high-risk patients with more immune-cell infiltration had higher Tumor Immune Dysfunction and Exclusion scores, indicating poor immunotherapy response. mRNA-drug interactions and drug sensitivity analyses were performed to explore potential druggable hub genes. Furthermore, we combined risk score with age and gender to construct a prognosis model, which could predict the prognosis of AML patients. Conclusion Our study provided a prognostic predictor for AML patients and revealed that mitochondrial metabolism is associated with immune regulation and drug resistant in AML, providing vital clues for immunotherapies.
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15
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DNA Damage Response in Cancer Therapy and Resistance: Challenges and Opportunities. Int J Mol Sci 2022; 23:ijms232314672. [PMID: 36499000 PMCID: PMC9735783 DOI: 10.3390/ijms232314672] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Resistance to chemo- and radiotherapy is a common event among cancer patients and a reason why new cancer therapies and therapeutic strategies need to be in continuous investigation and development. DNA damage response (DDR) comprises several pathways that eliminate DNA damage to maintain genomic stability and integrity, but different types of cancers are associated with DDR machinery defects. Many improvements have been made in recent years, providing several drugs and therapeutic strategies for cancer patients, including those targeting the DDR pathways. Currently, poly (ADP-ribose) polymerase inhibitors (PARP inhibitors) are the DDR inhibitors (DDRi) approved for several cancers, including breast, ovarian, pancreatic, and prostate cancer. However, PARPi resistance is a growing issue in clinical settings that increases disease relapse and aggravate patients' prognosis. Additionally, resistance to other DDRi is also being found and investigated. The resistance mechanisms to DDRi include reversion mutations, epigenetic modification, stabilization of the replication fork, and increased drug efflux. This review highlights the DDR pathways in cancer therapy, its role in the resistance to conventional treatments, and its exploitation for anticancer treatment. Biomarkers of treatment response, combination strategies with other anticancer agents, resistance mechanisms, and liabilities of treatment with DDR inhibitors are also discussed.
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16
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Inference of epigenetic subnetworks by Bayesian regression with the incorporation of prior information. Sci Rep 2022; 12:20224. [PMID: 36418365 PMCID: PMC9684215 DOI: 10.1038/s41598-022-19879-x] [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: 11/17/2020] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Changes in gene expression have been thought to play a crucial role in various types of cancer. With the advance of high-throughput experimental techniques, many genome-wide studies are underway to analyze underlying mechanisms that may drive the changes in gene expression. It has been observed that the change could arise from altered DNA methylation. However, the knowledge about the degree to which epigenetic changes might cause differences in gene expression in cancer is currently lacking. By considering the change of gene expression as the response of altered DNA methylation, we introduce a novel analytical framework to identify epigenetic subnetworks in which the methylation status of a set of highly correlated genes is predictive of a set of gene expression. By detecting highly correlated modules as representatives of the regulatory scenario underling the gene expression and DNA methylation, the dependency between DNA methylation and gene expression is explored by a Bayesian regression model with the incorporation of g-prior followed by a strategy of an optimal predictor subset selection. The subsequent network analysis indicates that the detected epigenetic subnetworks are highly biologically relevant and contain many verified epigenetic causal mechanisms. Moreover, a survival analysis indicates that they might be effective prognostic factors associated with patient survival time.
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17
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Levatić J, Salvadores M, Fuster-Tormo F, Supek F. Mutational signatures are markers of drug sensitivity of cancer cells. Nat Commun 2022; 13:2926. [PMID: 35614096 PMCID: PMC9132939 DOI: 10.1038/s41467-022-30582-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents - including chemotherapy - tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers.
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Affiliation(s)
- Jurica Levatić
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Marina Salvadores
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Francisco Fuster-Tormo
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
- MDS Group, Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain.
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18
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19
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Schnöller LE, Albrecht V, Brix N, Nieto AE, Fleischmann DF, Niyazi M, Hess J, Belka C, Unger K, Lauber K, Orth M. Integrative analysis of therapy resistance and transcriptomic profiling data in glioblastoma cells identifies sensitization vulnerabilities for combined modality radiochemotherapy. Radiat Oncol 2022; 17:79. [PMID: 35440003 PMCID: PMC9020080 DOI: 10.1186/s13014-022-02052-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
Background Inherent resistance to radio/chemotherapy is one of the major reasons for early recurrence, treatment failure, and dismal prognosis of glioblastoma. Thus, the identification of resistance driving regulators as prognostic and/or predictive markers as well as potential vulnerabilities for combined modality treatment approaches is of pivotal importance. Methods We performed an integrative analysis of treatment resistance and DNA damage response regulator expression in a panel of human glioblastoma cell lines. mRNA expression levels of 38 DNA damage response regulators were analyzed by qRT-PCR. Inherent resistance to radiotherapy (single-shot and fractionated mode) and/or temozolomide treatment was assessed by clonogenic survival assays. Resistance scores were extracted by dimensionality reduction and subjected to correlation analyses with the mRNA expression data. Top-hit candidates with positive correlation coefficients were validated by pharmacological inhibition in clonogenic survival assays and DNA repair analyses via residual γH2AX/53BP1-foci staining. Results Inherent resistance to single-shot and similarly also to fractionated radiotherapy showed strong positive correlations with mRNA expression levels of known vulnerabilities of GBM, including PARP1, NBN, and BLM, as well as ATR and LIG4—two so far underestimated targets. Inhibition of ATR by AZD-6738 resulted in robust and dose-dependent radiosensitization of glioblastoma cells, whereas LIG4 inhibition by L189 had no noticeable impact. Resistance against temozolomide showed strong positive correlation with mRNA expression levels of MGMT as to be expected. Interestingly, it also correlated with mRNA expression levels of ATM, suggesting a potential role of ATM in the context of temozolomide resistance in glioblastoma cells. ATM inhibition exhibited slight sensitization effects towards temozolomide treatment in MGMT low expressing glioblastoma cells, thus encouraging further characterization. Conclusions Here, we describe a systematic approach integrating clonogenic survival data with mRNA expression data of DNA damage response regulators in human glioblastoma cell lines to identify markers of inherent therapy resistance and potential vulnerabilities for targeted sensitization. Our results provide proof-of-concept for the feasibility of this approach, including its limitations. We consider this strategy to be adaptable to other cancer entities as well as other molecular data qualities, and its upscaling potential in terms of model systems and observational data levels deserves further investigation.
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Affiliation(s)
- Leon Emanuel Schnöller
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Valerie Albrecht
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Nikko Brix
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Alexander Edward Nieto
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Daniel Felix Fleischmann
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian Niyazi
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Claus Belka
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Kirsten Lauber
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Michael Orth
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.
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20
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Hemmaphan S, Bordeerat NK. Genotoxic Effects of Lead and Their Impact on the Expression of DNA Repair Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074307. [PMID: 35409986 PMCID: PMC8998702 DOI: 10.3390/ijerph19074307] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023]
Abstract
Exposure to lead (Pb) continues to be a significant worldwide problem. Pb is a highly poisonous heavy metal affecting several organ systems in the body. Although Pb has been shown to be genotoxic to experimental animals and humans, the underlying mechanisms are still not understood. An indirect mechanism related to the inhibition of DNA repair systems by Pb has been suggested. Heavy metals can interfere with the activities of several proteins and gene expressions. Recent studies gathered in this review article demonstrated an altered expression of DNA repair genes due to Pb toxicity. However, their findings are conflicting. Furthermore, the interaction of Pb and epigenetic mechanisms regulating gene expression may have a crucial role in the inhibition of DNA repair systems. Therefore, additional studies are needed to evaluate these findings and to obtain a complete picture of the genotoxic properties of Pb and the underlying mechanisms that may have a crucial role in carcinogenesis.
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Affiliation(s)
- Sirirak Hemmaphan
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Rangsit 12121, Thailand;
| | - Narisa K. Bordeerat
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Rangsit 12121, Thailand
- Correspondence: ; Tel.: +66-81-912-2694
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21
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Chen J, Sridharan D, Cross C, Pluth J. Cellular DNA effects of radiation and cancer risk assessment in cells with mitochondrial defects. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2022. [DOI: 10.1016/j.jrras.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Olivares-Hernández A, del Barco Morillo E, Parra Pérez C, Miramontes-González JP, Figuero-Pérez L, Martín-Gómez T, Escala-Cornejo R, Bellido Hernández L, González Sarmiento R, Cruz-Hernández JJ, Ludeña de la Cruz MD. Influence of DNA Mismatch Repair (MMR) System in Survival and Response to Immune Checkpoint Inhibitors (ICIs) in Non-Small Cell Lung Cancer (NSCLC): Retrospective Analysis. Biomedicines 2022; 10:biomedicines10020360. [PMID: 35203569 PMCID: PMC8962390 DOI: 10.3390/biomedicines10020360] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 01/01/2023] Open
Abstract
Mutations in the mismatch repair (MMR) system predict the response to immune checkpoint inhibitors (ICIs) like colon or gastric cancer. However, the MMR system’s involvement in non-small cell lung cancer (NSCLC) remains unknown. Addressing this issue will improve clinical guidelines in the case of mutations in the main genes of the MMR system (MLH1, MSH2, MSH6, and PMS2). This work retrospectively assessed the role that these gene mutations play in the response to and survival of ICIs in NSCLC. Patients with NSCLC treated with nivolumab as the second-line treatment in the University Hospital of Salamanca were enrolled in this study. Survival and response analyses were performed according to groups of MMR system gene expression (MMR expression present or deficiency) and other subgroups, such as toxicity. There was a statistically significant relationship between the best response obtained and the expression of the MMR system (p = 0.045). The presence of toxicity grade ≥ 3 was associated with the deficiency expression of MMR (dMMR/MSI-H) group (p = 0.022; odds ratio = 10.167, 95% confidence interval (CI) 1.669–61.919). A trend towards greater survival and response to ICIs was observed in NSCLC and dMMR. Assessing the genes in the MMR system involved in NSCLC is key to obtaining personalized immunotherapy treatments.
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Affiliation(s)
- Alejandro Olivares-Hernández
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Correspondence: (A.O.-H.); (C.P.P.); Tel.: +34-923-29-11-00 (A.O.-H. & C.P.P.); Fax: +34-923-29-13-25 (A.O.-H. & C.P.P.)
| | - Edel del Barco Morillo
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
| | - Carmen Parra Pérez
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
- Department of Pathology, University Hospital of Salamanca, 37007 Salamanca, Spain
- Correspondence: (A.O.-H.); (C.P.P.); Tel.: +34-923-29-11-00 (A.O.-H. & C.P.P.); Fax: +34-923-29-13-25 (A.O.-H. & C.P.P.)
| | - José Pablo Miramontes-González
- Department of Internal Medicine, University Hospital Rio Hortega, 47012 Valladolid, Spain;
- Department of Medicine, University of Valladolid, 45005 Valladolid, Spain
| | - Luis Figuero-Pérez
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Teresa Martín-Gómez
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
| | | | - Lorena Bellido Hernández
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Rogelio González Sarmiento
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
| | - Juan Jesús Cruz-Hernández
- Department of Medical Oncology, University Hospital of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (L.F.-P.); (T.M.-G.); (L.B.H.); (J.J.C.-H.)
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
| | - María Dolores Ludeña de la Cruz
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain;
- Department of Pathology, University Hospital of Salamanca, 37007 Salamanca, Spain
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23
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Galisa SLG, Jacob PL, de Farias AA, Lemes RB, Alves LU, Nóbrega JCL, Zatz M, Santos S, Weller M. Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil. Genet Mol Biol 2022; 45:e20210172. [PMID: 35112701 PMCID: PMC8811751 DOI: 10.1590/1678-4685-gmb-2021-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local ancestry inference was performed by merging genotyped regions with phase three data from the 1000 Genomes Project Consortium using RFmix. The average ancestry tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All together, 19 risk and eight protective alleles were identified in 23 out of 48 haplotypes. Homozygous individuals were mainly of European ancestry, whereas heterozygotes had at least one Native American and one African ancestry tract. Native-American ancestry for homozygous individuals with risk alleles for HNF1B, CDH1, and BRCA1 was inferred for the first time. Results indicated that analysis of SNP polymorphism in the present admixed population has a high potential to identify new ancestry-associated alleles and haplotypes that modify cancer susceptibility differentially in distinct human populations. Future case-control studies with populations with a complex history of admixture could help elucidate ancestry-associated biological differences in cancer incidence and therapeutic outcomes.
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Affiliation(s)
- Steffany Larissa Galdino Galisa
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Priscila Lima Jacob
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Allysson Allan de Farias
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Renan Barbosa Lemes
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Leandro Ucela Alves
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Júlia Cristina Leite Nóbrega
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Mayana Zatz
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Silvana Santos
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade Estadual da Paraíba (UEPB), Departamento de Biologia,
Campina Grande, PB, Brazil
| | - Mathias Weller
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade Estadual da Paraíba (UEPB), Departamento de Biologia,
Campina Grande, PB, Brazil
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24
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Ahmad M, Hameed Y, Khan M, Usman M, Rehman A, Abid U, Asif R, Ahmed H, Hussain MS, Rehman JU, Asif HM, Arshad R, Atif M, Hadi A, Sarfraz U, Khurshid U. Up-regulation of GINS1 highlighted a good diagnostic and prognostic potential of survival in three different subtypes of human cancer. BRAZ J BIOL 2021; 84:e250575. [PMID: 34852135 DOI: 10.1590/1519-6984.250575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer is a fatal malignancy and its increasing worldwide prevalence demands the discovery of more sensitive and reliable molecular biomarkers. To investigate the GINS1 expression level and its prognostic value in distinct human cancers using a series of multi-layered in silico approach may help to establish it as a potential shared diagnostic and prognostic biomarker of different cancer subtypes. The GINS1 mRNA, protein expression, and promoter methylation were analyzed using UALCAN and Human Protein Atlas (HPA), while mRNA expression was further validated via GENT2. The potential prognostic values of GINS1 were evaluated through KM plotter. Then, cBioPortal was utilized to examine the GINS1-related genetic mutations and copy number variations (CNVs), while pathway enrichment analysis was performed using DAVID. Moreover, a correlational analysis between GINS1 expression and CD8+ T immune cells and a the construction of gene-drug interaction network was performed using TIMER, CDT, and Cytoscape. The GINS1 was found down-regulated in a single subtypes of human cancer while commonly up-regulated in 23 different other subtypes. The up-regulation of GINS1 was significantly correlated with the poor overall survival (OS) of Liver Hepatocellular Carcinoma (LIHC), Lung Adenocarcinoma (LUAD), and Kidney renal clear cell carcinoma (KIRC). The GINS1 was also found up-regulated in LIHC, LUAD, and KIRC patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of GINS1 in two diverse pathways, while few interesting correlations were also documented between GINS1 expression and its promoter methylation level, CD8+ T immune cells level, and CNVs. Moreover, we also predicted few drugs that could be used in the treatment of LIHC, LUAD, and KIRC by regulating the GINS1 expression. The expression profiling of GINS1 in the current study has suggested it a novel shared diagnostic and prognostic biomarker of LIHC, LUAD, and KIRC.
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Affiliation(s)
- M Ahmad
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - Y Hameed
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - M Khan
- The Islamia University of Bahawalpur, Department of Pharmacy, Bahawalpur, Pakistan
| | - M Usman
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - A Rehman
- Qarshi University, Department of Eastern Medicine, Lahore, Pakistan
| | - U Abid
- Bahauddin Zakariya University, Department of Pharmaceutics, Multan, Pakistan
| | - R Asif
- Government College University Faisalabad, Department of Microbiology, Faisalabad, Pakistan
| | - H Ahmed
- Government College University Faisalabad, Department of Eastern Medicine, Faisalabad, Pakistan
| | - M S Hussain
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - J U Rehman
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - H M Asif
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - R Arshad
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - M Atif
- The Islamia University of Bahawalpur, College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, Bahawalpur, Pakistan
| | - A Hadi
- The Islamia University of Bahawalpur, Department of Biochemistry and Biotechnology, Bahawalpur, Pakistan
| | - U Sarfraz
- COMSATS University Islamabad, Department of Biosciences, Islamabad, Pakistan
| | - U Khurshid
- The Islamia University of Bahawalpur, Department of Pharmacy, Bahawalpur, Pakistan
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25
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Panagopoulos DJ, Karabarbounis A, Yakymenko I, Chrousos GP. Human‑made electromagnetic fields: Ion forced‑oscillation and voltage‑gated ion channel dysfunction, oxidative stress and DNA damage (Review). Int J Oncol 2021; 59:92. [PMID: 34617575 PMCID: PMC8562392 DOI: 10.3892/ijo.2021.5272] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022] Open
Abstract
Exposure of animals/biological samples to human‑made electromagnetic fields (EMFs), especially in the extremely low frequency (ELF) band, and the microwave/radio frequency (RF) band which is always combined with ELF, may lead to DNA damage. DNA damage is connected with cell death, infertility and other pathologies, including cancer. ELF exposure from high‑voltage power lines and complex RF exposure from wireless communication antennas/devices are linked to increased cancer risk. Almost all human‑made RF EMFs include ELF components in the form of modulation, pulsing and random variability. Thus, in addition to polarization and coherence, the existence of ELFs is a common feature of almost all human‑made EMFs. The present study reviews the DNA damage and related effects induced by human‑made EMFs. The ion forced‑oscillation mechanism for irregular gating of voltage‑gated ion channels on cell membranes by polarized/coherent EMFs is extensively described. Dysfunction of ion channels disrupts intracellular ionic concentrations, which determine the cell's electrochemical balance and homeostasis. The present study shows how this can result in DNA damage through reactive oxygen species/free radical overproduction. Thus, a complete picture is provided of how human‑made EMF exposure may indeed lead to DNA damage and related pathologies, including cancer. Moreover, it is suggested that the non‑thermal biological effects attributed to RF EMFs are actually due to their ELF components.
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Affiliation(s)
- Dimitris J. Panagopoulos
- Laboratory of Health Physics, Radiobiology and Cytogenetics, Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Center for Scientific Research 'Demokritos', 15310 Athens, Greece
- Choremeion Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Electromagnetic Field-Biophysics Research Laboratory, 10681 Athens, Greece
| | - Andreas Karabarbounis
- Department of Physics, Section of Nuclear and Particle Physics, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Igor Yakymenko
- Institute of Experimental Pathology, Oncology and Radiobiology of National Academy of Science of Ukraine, 03022 Kyiv, Ukraine
- Department of Public Health, Kyiv Medical University, 02000 Kyiv, Ukraine
| | - George P. Chrousos
- Choremeion Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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26
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An Epigenetic Perspective on Intra-Tumour Heterogeneity: Novel Insights and New Challenges from Multiple Fields. Cancers (Basel) 2021; 13:cancers13194969. [PMID: 34638453 PMCID: PMC8508087 DOI: 10.3390/cancers13194969] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Although research on cancer biology in recent decades has unveiled the main genetic perturbations driving the onset of tumorigenesis, we are still far from properly treating this disease without the occurrence of drug resistance and metastatic burden. This achievement is hampered by the onset of intra-tumour heterogeneity (ITH), which increases cancer cell fitness and plasticity, thereby fostering cell adaptation to foreign environments and stimuli. In this review, we discuss the contribution of the epigenetic factors in sustaining ITH and their interplay with the tumour microenvironment. We also highlight the recent technological advancements that are contributing to defining the epigenetic mechanisms governing tumour heterogeneity at the single-cell level. Abstract Cancer is a group of heterogeneous diseases that results from the occurrence of genetic alterations combined with epigenetic changes and environmental stimuli that increase cancer cell plasticity. Indeed, multiple cancer cell populations coexist within the same tumour, favouring cancer progression and metastatic dissemination as well as drug resistance, thereby representing a major obstacle for treatment. Epigenetic changes contribute to the onset of intra-tumour heterogeneity (ITH) as they facilitate cell adaptation to perturbation of the tumour microenvironment. Despite being its central role, the intrinsic multi-layered and reversible epigenetic pattern limits the possibility to uniquely determine its contribution to ITH. In this review, we first describe the major epigenetic mechanisms involved in tumourigenesis and then discuss how single-cell-based approaches contribute to dissecting the key role of epigenetic changes in tumour heterogeneity. Furthermore, we highlight the importance of dissecting the interplay between genetics, epigenetics, and tumour microenvironments to decipher the molecular mechanisms governing tumour progression and drug resistance.
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27
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Making it or breaking it: DNA methylation and genome integrity. Essays Biochem 2021; 64:687-703. [PMID: 32808652 DOI: 10.1042/ebc20200009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
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28
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Kuijpers TJM, Kleinjans JCS, Jennen DGJ. From multi-omics integration towards novel genomic interaction networks to identify key cancer cell line characteristics. Sci Rep 2021; 11:10542. [PMID: 34006939 PMCID: PMC8131752 DOI: 10.1038/s41598-021-90047-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
Cancer is a complex disease where cancer cells express epigenetic and transcriptomic mechanisms to promote tumor initiation, progression, and survival. To extract relevant features from the 2019 Cancer Cell Line Encyclopedia (CCLE), a multi-layer nonnegative matrix factorization approach is used. We used relevant feature genes and DNA promoter regions to construct genomic interaction network to study gene-gene and gene-DNA promoter methylation relationships. Here, we identified a set of gene transcripts and methylated DNA promoter regions for different clusters, including one homogeneous lymphoid neoplasms cluster. In this cluster, we found different methylated transcription factors that affect transcriptional activation of EGFR and downstream interactions. Furthermore, the hippo-signaling pathway might not function properly because of DNA hypermethylation and low gene expression of both LATS2 and YAP1. Finally, we could identify a potential dysregulation of the CD28-CD86-CTLA4 axis. Characterizing the interaction of the epigenome and the transcriptome is vital for our understanding of cancer cell line behavior, not only for deepening insights into cancer-related processes but also for future disease treatment and drug development. Here we have identified potential candidates that characterize cancer cell lines, which give insight into the development and progression of cancers.
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Affiliation(s)
- T J M Kuijpers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.
| | - J C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - D G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
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29
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Guo N, Qu P, Li H, Liu L, Jin H, Liu R, Zhang Z, Zhang X, Li Y, Lu X, Zhao Y. BRCA2 3'-UTR Polymorphism rs15869 Alters Susceptibility to Papillary Thyroid Carcinoma via Binding hsa-mir-1178-3p. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:533-544. [PMID: 33986610 PMCID: PMC8112253 DOI: 10.2147/pgpm.s300783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/13/2021] [Indexed: 12/09/2022]
Abstract
Objective To investigate the associations of polymorphisms in the following DNA double-strand break repair (DSBR) genes with papillary thyroid carcinoma (PTC) risk (including RAD51 rs11852786, RAD51B rs963917, BRCA1 rs12516 and rs8176318, BRCA2 rs15869, XRCC4 rs2035990 and XRCC5 rs2440). Materials and Methods A matched case-control study was implemented to examine associations between PTC risk and the above polymorphisms. Subsequently, we evaluated the effects of the potential PTC susceptibility-related variant rs15869 on BRCA2 mRNA secondary structure and BRCA2 expression through bioinformatics analysis and experiment validation. Additionally, luciferase assay was used to identify whether rs15869 polymorphism can substantially affect the binding of hsa-miR-1178-3p to BRCA2 mRNA. Finally, Pearson correlation analysis was performed to determine the correlation between the expression of hsa-miR-1178-3p and BRCA2 mRNA and protein in thyroid tissues harboring rs15869 different genotypes. Results BRCA2 rs15869 CC genotype was associated with a higher risk of PTC than its AA genotype. Subsequently, stratified analyses came to the same conclusion in the female or age<50 population. Furthermore, we confirmed that the A-to-C substitution of rs15869 changed BRCA2 mRNA secondary structure and contributed to a decreased BRCA2 expression. Mechanistically, a significantly decreased luciferase activity verified a greater binding between hsa-miR-1178-3p and rs15869 C allele, but not the A allele, which was evidenced by the significant negative correlation between hsa-miR-1178-3p with BRCA2 mRNA and protein levels in thyroid tissues with AC and CC genotype but not AA genotype at rs15869. Conclusion BRCA2 rs15869 is characterized as a potential biomarker associated with PTC risk, highlighting the contribution of the hsa-miR-1178-3p via functional exploration.
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Affiliation(s)
- Nan Guo
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, People's Republic of China
| | - Peng Qu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Hao Li
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Liuli Liu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Hao Jin
- Jin Zhou Center for Disease Control and Prevention, Jinzhou, People's Republic of China
| | - Renqi Liu
- Jin Zhou Center for Disease Control and Prevention, Jinzhou, People's Republic of China
| | - Zhen Zhang
- Jin Zhou Center for Disease Control and Prevention, Jinzhou, People's Republic of China
| | - Xuan Zhang
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Yingchun Li
- Department of Central Laboratory, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, People's Republic of China
| | - Xiaobo Lu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Yuejiao Zhao
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, People's Republic of China
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30
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Götting I, Jendrossek V, Matschke J. A New Twist in Protein Kinase B/Akt Signaling: Role of Altered Cancer Cell Metabolism in Akt-Mediated Therapy Resistance. Int J Mol Sci 2020; 21:ijms21228563. [PMID: 33202866 PMCID: PMC7697684 DOI: 10.3390/ijms21228563] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer resistance to chemotherapy, radiotherapy and molecular-targeted agents is a major obstacle to successful cancer therapy. Herein, aberrant activation of the phosphatidyl-inositol-3-kinase (PI3K)/protein kinase B (Akt) pathway is one of the most frequently deregulated pathways in cancer cells and has been associated with multiple aspects of therapy resistance. These include, for example, survival under stress conditions, apoptosis resistance, activation of the cellular response to DNA damage and repair of radiation-induced or chemotherapy-induced DNA damage, particularly DNA double strand breaks (DSB). One further important, yet not much investigated aspect of Akt-dependent signaling is the regulation of cell metabolism. In fact, many Akt target proteins are part of or involved in the regulation of metabolic pathways. Furthermore, recent studies revealed the importance of certain metabolites for protection against therapy-induced cell stress and the repair of therapy-induced DNA damage. Thus far, the likely interaction between deregulated activation of Akt, altered cancer metabolism and therapy resistance is not yet well understood. The present review describes the documented interactions between Akt, its target proteins and cancer cell metabolism, focusing on antioxidant defense and DSB repair. Furthermore, the review highlights potential connections between deregulated Akt, cancer cell metabolism and therapy resistance of cancer cells through altered DSB repair and discusses potential resulting therapeutic implications.
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31
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Xiang K, Jendrossek V, Matschke J. Oncometabolites and the response to radiotherapy. Radiat Oncol 2020; 15:197. [PMID: 32799884 PMCID: PMC7429799 DOI: 10.1186/s13014-020-01638-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/06/2020] [Indexed: 12/18/2022] Open
Abstract
Radiotherapy (RT) is applied in 45-60% of all cancer patients either alone or in multimodal therapy concepts comprising surgery, RT and chemotherapy. However, despite technical innovations approximately only 50% are cured, highlight a high medical need for innovation in RT practice. RT is a multidisciplinary treatment involving medicine and physics, but has always been successful in integrating emerging novel concepts from cancer and radiation biology for improving therapy outcome. Currently, substantial improvements are expected from integration of precision medicine approaches into RT concepts.Altered metabolism is an important feature of cancer cells and a driving force for malignant progression. Proper metabolic processes are essential to maintain and drive all energy-demanding cellular processes, e.g. repair of DNA double-strand breaks (DSBs). Consequently, metabolic bottlenecks might allow therapeutic intervention in cancer patients.Increasing evidence now indicates that oncogenic activation of metabolic enzymes, oncogenic activities of mutated metabolic enzymes, or adverse conditions in the tumor microenvironment can result in abnormal production of metabolites promoting cancer progression, e.g. 2-hyroxyglutarate (2-HG), succinate and fumarate, respectively. Interestingly, these so-called "oncometabolites" not only modulate cell signaling but also impact the response of cancer cells to chemotherapy and RT, presumably by epigenetic modulation of DNA repair.Here we aimed to introduce the biological basis of oncometabolite production and of their actions on epigenetic regulation of DNA repair. Furthermore, the review will highlight innovative therapeutic opportunities arising from the interaction of oncometabolites with DNA repair regulation for specifically enhancing the therapeutic effects of genotoxic treatments including RT in cancer patients.
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Affiliation(s)
- Kexu Xiang
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 173, 45147, Essen, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 173, 45147, Essen, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 173, 45147, Essen, Germany.
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Haider T, Pandey V, Banjare N, Gupta PN, Soni V. Drug resistance in cancer: mechanisms and tackling strategies. Pharmacol Rep 2020; 72:1125-1151. [PMID: 32700248 DOI: 10.1007/s43440-020-00138-7] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/24/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Drug resistance developed towards conventional therapy is one of the important reasons for chemotherapy failure in cancer. The various underlying mechanism for drug resistance development in tumor includes tumor heterogeneity, some cellular levels changes, genetic factors, and others novel mechanisms which have been highlighted in the past few years. In the present scenario, researchers have to focus on these novel mechanisms and their tackling strategies. The small molecules, peptides, and nanotherapeutics have emerged to overcome the drug resistance in cancer. The drug delivery systems with targeting moiety enhance the site-specificity, receptor-mediated endocytosis, and increase the drug concentration inside the cells, thus minimizing drug resistance and improve their therapeutic efficacy. These therapeutic approaches work by modulating the different pathways responsible for drug resistance. This review focuses on the different mechanisms of drug resistance and the recent advancements in therapeutic approaches to improve the sensitivity and effectiveness of chemotherapeutics.
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Affiliation(s)
- Tanweer Haider
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, Madhya Pradesh, India
| | - Vikas Pandey
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, Madhya Pradesh, India
| | - Nagma Banjare
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, Madhya Pradesh, India.,Formulation and Drug Delivery Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, J&K, India
| | - Prem N Gupta
- Formulation and Drug Delivery Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, J&K, India.
| | - Vandana Soni
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, Madhya Pradesh, India.
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Feng JX, Riddle NC. Epigenetics and genome stability. Mamm Genome 2020; 31:181-195. [PMID: 32296924 DOI: 10.1007/s00335-020-09836-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/07/2020] [Indexed: 12/19/2022]
Abstract
Maintaining genome stability is essential to an organism's health and survival. Breakdown of the mechanisms protecting the genome and the resulting genome instability are an important aspect of the aging process and have been linked to diseases such as cancer. Thus, a large network of interconnected pathways is responsible for ensuring genome integrity in the face of the continuous challenges that induce DNA damage. While these pathways are diverse, epigenetic mechanisms play a central role in many of them. DNA modifications, histone variants and modifications, chromatin structure, and non-coding RNAs all carry out a variety of functions to ensure that genome stability is maintained. Epigenetic mechanisms ensure the functions of centromeres and telomeres that are essential for genome stability. Epigenetic mechanisms also protect the genome from the invasion by transposable elements and contribute to various DNA repair pathways. In this review, we highlight the integral role of epigenetic mechanisms in the maintenance of genome stability and draw attention to issues in need of further study.
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Affiliation(s)
- Justina X Feng
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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Song Y, Xie L, Lee Y, Brede DA, Lyne F, Kassaye Y, Thaulow J, Caldwell G, Salbu B, Tollefsen KE. Integrative assessment of low-dose gamma radiation effects on Daphnia magna reproduction: Toxicity pathway assembly and AOP development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135912. [PMID: 31846819 DOI: 10.1016/j.scitotenv.2019.135912] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/25/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
High energy gamma radiation is potentially hazardous to organisms, including aquatic invertebrates. Although extensively studied in a number of invertebrate species, knowledge on effects induced by gamma radiation is to a large extent limited to the induction of oxidative stress and DNA damage at the molecular/cellular level, or survival, growth and reproduction at the organismal level. As the knowledge of causal relationships between effects occurring at different levels of biological organization is scarce, the ability to provide mechanistic explanation for observed adverse effects is limited, and thus development of Adverse Outcome Pathways (AOPs) and larger scale implementation into next generation hazard and risk predictions is restricted. The present study was therefore conducted to assess the effects of high-energy gamma radiation from cobalt-60 across multiple levels of biological organization (i.e., molecular, cellular, tissue, organ and individual) and characterize the major toxicity pathways leading to impaired reproduction in the model freshwater crustacean Daphnia magna (water flea). Following gamma exposure, a number of bioassays were integrated to measure relevant toxicological endpoints such as gene expression, reactive oxygen species (ROS), lipid peroxidation (LPO), neutral lipid storage, adenosine triphosphate (ATP) content, apoptosis, ovary histology and reproduction. A non-monotonic pattern was consistently observed across the levels of biological organization, albeit with some variation at the lower end of the dose-rate scale, indicating a complex response to radiation doses. By integrating results from different bioassays, a novel pathway network describing the key toxicity pathways involved in the reproductive effects of gamma radiation were proposed, such as DNA damage-oocyte apoptosis pathway, LPO-ATP depletion pathway, calcium influx-endocrine disruption pathway and DNA hypermethylation pathway. Three novel AOPs were proposed for oxidative stressor-mediated excessive ROS formation leading to reproductive effect, and thus introducing the world's first AOPs for non-chemical stressors in aquatic invertebrates.
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Affiliation(s)
- You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 OSLO, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway.
| | - Li Xie
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 OSLO, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - YeonKyeong Lee
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Biosciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Dag Anders Brede
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Fern Lyne
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Newcastle University, Newcastle upon Tyne, UK
| | - Yetneberk Kassaye
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Jens Thaulow
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 OSLO, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | | | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 OSLO, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
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Ta TV, Nguyen QN, Chu HH, Truong VL, Vuong LD. RAS/RAF mutations and their associations with epigenetic alterations for distinct pathways in Vietnamese colorectal cancer. Pathol Res Pract 2020; 216:152898. [PMID: 32089414 DOI: 10.1016/j.prp.2020.152898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
KRAS, NRAS, and BRAF are potential tumor-driven genes that are involved in the RAS/RAF/MAPK signaling pathway. RAS/RAF mutations importantly contribute to colorectal tumorigenesis since they remain the activated status of downstream pathways without regulation of the upstream EGFR signal. However, it has not been unclear how epigenetic alterations involved in colorectal tumorigenesis mediated by KRAS, NRAS, or BRAF mutations. Therefore, in this study, we investigated the frequency and distribution of KRAS/NRAS/BRAF mutations in Vietnamese colorectal cancer (CRC) and explored the relationship between genetic and epigenetic abnormalities in 156 tumors of CRC. Somatic mutations of KRAS (exon 2, codon 12/13; exon 3, codon 61), NRAS (exon 2, codon 12/13; exon 3, codon 61), and BRAF (exon 15, codon 600) was determined by Cobas® KRAS Mutation Test, Therascreen NRAS Pyro Kit and Cobas® 4800 BRAF V600 Mutation Test, respectively. Methylation status of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC was detected by methylation-specific PCR. Distribution of each abnormality in clinicopathological features was also analyzed. Results showed the mutation rates of KRAS, NRAS, and BRAF were 41.0 %, 9.6 %, 8.3 % respectively, while the methylation rates of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC were 16.7 %, 16.7 %, 32.7 %, 30.1 %, 30.1 %, and 37.2 % respectively. The distribution of KRAS mutation was mutually exclusive against that of NRAS (p < 0.001) and BRAF (p < 0.001) mutations in CRC. RAS/RAF mutations were more common in adenocarcinoma subtype (p = 0.020), whereas RASSF1A methylation was more frequent in mucinous adenocarcinoma subtype (p = 0.007). In addition, the frequency of having KRAS mutations was significantly higher in MGMT (p = 0.035) or RASSF1A (p = 0.043) methylated cases than in those without methylation. BRAF mutations were positively associated with MLH1 hypermethylation (p = 0.028) but were inversely associated with APC hypermethylation (p = 0.032). Overall, our results show specific interactions of genetic and epigenetic alterations and suggest the presence of independent oncogenic pathways in tumorigenesis of CRC.
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Affiliation(s)
- To Van Ta
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Quang Ngoc Nguyen
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Ha Hoang Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Viet Nam
| | - Van-Long Truong
- Department of Smart Food and Drug, College of BNIT, Inje University, Gimhae 50834, South Korea.
| | - Linh Dieu Vuong
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam.
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Vernolactone Promotes Apoptosis and Autophagy in Human Teratocarcinomal (NTERA-2) Cancer Stem-Like Cells. Stem Cells Int 2020; 2019:6907893. [PMID: 31949439 PMCID: PMC6942914 DOI: 10.1155/2019/6907893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Vernonia zeylanica, is a shrub endemic to Sri Lanka. V. zeylanica has been used in Sri Lankan traditional medicine for the treatment of various diseases and conditions. The present study was designed to determine antiproliferative, apoptotic, autophagic, and antioxidant effects of vernolactone, isolated from V. zeylanica, in human embryonal carcinoma cells (NTERA-2, a cancer stem cell model). Antiproliferative effects of vernolactone in NTERA-2 cells and human peripheral blood mononuclear cells (control cells) were evaluated using the Sulforhodamine B (SRB) assay and WST-1 antiproliferative assays, respectively. The antiproliferative effect of vernolactone was further investigated using the colony formation assay. Effects of vernolactone on apoptosis were investigated by phase contrast light microscopic and fluorescence microscopic analysis, caspase 3/7 expression, and real-time PCR of apoptosis-associated genes p53 and Survivin. The effect of vernolactone on NTERA-2 cell migration was monitored using the wound healing assay. Effects of vernolactone on the expression of autophagy-related genes (LC3, Beclin 1, PI3K, Akt, and mTOR) were evaluated using real-time PCR. 2,2-Diphenyl-1-2,2-diphenyl-picrylhydrazyl (DPPH) radical scavenging assay, 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging, and ferric reducing antioxidant power (FRAP) assays were also carried out to evaluate the antioxidant activity of vernolactone. Overall results confirm that vernolactone can exert antiproliferative effects, induce apoptosis and autophagy, and decrease NTERA-2 cell migration in a dose- and time-dependent manner with a very small antioxidant property.
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Babaei K, Khaksar R, Zeinali T, Hemmati H, Bandegi A, Samidoust P, Ashoobi MT, Hashemian H, Delpasand K, Talebinasab F, Naebi H, Mirpour SH, Keymoradzadeh A, Norollahi SE. Epigenetic profiling of MUTYH, KLF6, WNT1 and KLF4 genes in carcinogenesis and tumorigenesis of colorectal cancer. Biomedicine (Taipei) 2019; 9:22. [PMID: 31724937 PMCID: PMC6855188 DOI: 10.1051/bmdcn/2019090422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is distinguished by epigenetic elements like DNA methylation, histone modification, histone acetylation and RNA remodeling which is related with genomic instability and tumor initiation. Correspondingly, as a main epigenetic regulation, DNA methylation has an impressive ability in order to be used in CRC targeted therapy. Meaningly, DNA methylation is identified as one of most important epigenetic regulators in gene expression and is considered as a notable potential driver in tumorigenesis and carcinogenesis through gene-silencing of tumor suppressors genes. Abnormal methylation situation, even in the level of promoter regions, does not essentially change the gene expression levels, particularly if the gene was become silenced, leaving the mechanisms of methylation without any response. According to the methylation situation which has a strong eagerness to be highly altered on CpG islands in carcinogenesis and tumorigenesis, considering its epigenetic fluctuations in finding new biomarkers is of great importance. Modifications in DNA methylation pattern and also enrichment of methylated histone signs in the promoter regions of some certain genes like MUTYH, KLF4/6 and WNT1 in different signaling pathways could be a notable key contributors to the upregulation of tumor initiation in CRC. These epigenetic alterations could be employed as a practical diagnostic biomarkers for colorectal cancer. In this review, we will be discuss these fluctuations of MUTYH, KLF4/6 and WNT1 genes in CRC.
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Affiliation(s)
- Kosar Babaei
- Department of Biology, Islamic Azad University of Tonekabon Branch, Tonekabon, Iran
| | - Roya Khaksar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Hossein Hemmati
- Razi Clinical Research Development Unit, Guilan University of Medical Sciences, Rasht, Iran
| | - Ahmadreza Bandegi
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Pirouz Samidoust
- Razi Clinical Research Development Unit, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Taghi Ashoobi
- Department of Surgery, Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Hooman Hashemian
- Pediatric Diseases Research Center,Guilan University of Medical ciences, Rasht, Iran
| | - Kourosh Delpasand
- School of Medicine, Kurdistan University of Mdical Ciences, Sanandaj, Iran
| | - Fereshteh Talebinasab
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hoora Naebi
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Seyed Hossein Mirpour
- Department of Hematology and Oncology, Razi hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arman Keymoradzadeh
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyedeh Elham Norollahi
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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Pan-Cancer Landscape of Aberrant DNA Methylation across Human Tumors. Cell Rep 2019; 25:1066-1080.e8. [PMID: 30355485 DOI: 10.1016/j.celrep.2018.09.082] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/29/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
The discovery of cancer-associated alterations has primarily focused on genetic variants. Nonetheless, altered epigenomes contribute to deregulate transcription and promote oncogenic pathways. Here, we designed an algorithmic approach (RESET) to identify aberrant DNA methylation and associated cis-transcriptional changes across >6,000 human tumors. Tumors exhibiting mutations of chromatin remodeling factors and Wnt signaling displayed DNA methylation instability, characterized by numerous hyper- and hypo-methylated loci. Most silenced and enhanced genes coalesced in specific pathways including apoptosis, DNA repair, and cell metabolism. Cancer-germline antigens (CG) were frequently epigenomically enhanced and their expression correlated with response to anti-PD-1, but not anti-CTLA4, in skin melanoma. Finally, we demonstrated the potential of our approach to explore DNA methylation changes in pediatric tumors, which frequently lack genetic drivers and exhibit epigenomic modifications. Our results provide a pan-cancer map of aberrant DNA methylation to inform functional and therapeutic studies.
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Expression deregulation of DNA repair pathway genes in gastric cancer. Cancer Genet 2019; 237:39-50. [DOI: 10.1016/j.cancergen.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 05/08/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
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Ermolaeva M, Neri F, Ori A, Rudolph KL. Cellular and epigenetic drivers of stem cell ageing. Nat Rev Mol Cell Biol 2019; 19:594-610. [PMID: 29858605 DOI: 10.1038/s41580-018-0020-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tissue stem cells have a pivotal role in tissue maintenance and regeneration throughout the lifespan of multicellular organisms. Loss of tissue homeostasis during post-reproductive lifespan is caused, at least in part, by a decline in stem cell function and is associated with an increased incidence of diseases. Hallmarks of ageing include the accumulation of molecular damage, failure of quality control systems, metabolic changes and alterations in epigenome stability. In this Review, we discuss recent evidence in support of a novel concept whereby cell-intrinsic damage that accumulates during ageing and cell-extrinsic changes in ageing stem cell niches and the blood result in modifications of the stem cell epigenome. These cumulative epigenetic alterations in stem cells might be the cause of the deregulation of developmental pathways seen during ageing. In turn, they could confer a selective advantage to mutant and epigenetically drifted stem cells with altered self-renewal and functions, which contribute to the development of ageing-associated organ dysfunction and disease.
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Affiliation(s)
- Maria Ermolaeva
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - K Lenhard Rudolph
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany. .,Medical Faculty Jena, University Hospital Jena (UKJ), Jena, Germany.
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Ponnusamy L, Mahalingaiah PKS, Singh KP. Epigenetic reprogramming and potential application of epigenetic-modifying drugs in acquired chemotherapeutic resistance. Adv Clin Chem 2019; 94:219-259. [PMID: 31952572 DOI: 10.1016/bs.acc.2019.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemotherapy is the most common clinical choice of treatment for cancer, however, acquired chemoresistance is a major challenge that limits the successful outcome of this option. Systematic review of in vitro, in vivo, preclinical and clinical studies suggests that acquired chemoresistance is polygenic, progressive, and involve both genetic and epigenetic heterogeneities and perturbations. Various mechanisms that confer resistance to chemotherapy are tightly controlled by epigenetic regulations. Poised epigenetic plasticity and temporal increase in epigenetic alterations upon chemotherapy make chemoresistance likely an epigenetic-driven process. The transient and reversible nature of epigenetic modulations enable ways to intervene the epigenetic re-programing associated with acquired chemoresistance via application of epigenetic modifying drugs. This review discusses recent understandings behind the various mechanisms of acquired chemoresistance that are under the control of epigenetic drivers, potential application of epigenetic-based drugs in resensitizing refractory cancers to chemotherapy, the limitations and future scope for clinical application of epigenetic therapeutics in successfully addressing chemoresistance.
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Affiliation(s)
- Logeswari Ponnusamy
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States
| | - Prathap Kumar S Mahalingaiah
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States
| | - Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States.
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AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation. Biochim Biophys Acta Gen Subj 2019; 1863:129415. [PMID: 31404619 DOI: 10.1016/j.bbagen.2019.129415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. METHODS Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. RESULTS All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. CONCLUSIONS AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. GENERAL SIGNIFICANCE Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
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Luo F, Wang YZ, Lin D, Li J, Yang K. Exonuclease 1 expression is associated with clinical progression, metastasis, and survival prognosis of prostate cancer. J Cell Biochem 2019; 120:11383-11389. [PMID: 30775798 DOI: 10.1002/jcb.28415] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/16/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Prostate cancer (PCa) is the most prevalent malignancy and the second leading cause of cancer-related deaths in the male population in western countries, and we explored the association between exonuclease 1 (EXO1) expression and clinical progression, metastasis (Met), and survival prognosis of PCa. EXO1 expression of high/low-metastatic patient-derived xenografts model was investigated and clinical correlation and prognosis outcomes were validated. EXO1 in high-metastatic models was significantly increased compared with low-metastatic lines. In memorial sloan-kettering cancer center (MSKCC) cohort, EXO1 expression positively correlated with PCa Met, and patients with high EXO1 had poor biochemical recurrence-free survival in primary PCa cohort. Validation in The Cancer Genome Atlas primary cohort indicated EXO1 expression was significantly associated with lymph node Met and disease-free survival. The overexpression of EXO1 is significantly associated with PCa poor survival outcome, and is a promising biomarker for PCa, especially for primary PCa. A prospective study is clearly needed to validate these findings.
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Affiliation(s)
- Fei Luo
- Department of Urology, Tianjin Union Medical Center, Tianjin, China.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yu-Zhuo Wang
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Dong Lin
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jian Li
- Department of Urology, Tianjin Union Medical Center, Tianjin, China
| | - Kuo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China
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Liu J, François JM, Capp JP. Gene Expression Noise Produces Cell-to-Cell Heterogeneity in Eukaryotic Homologous Recombination Rate. Front Genet 2019; 10:475. [PMID: 31164905 PMCID: PMC6536703 DOI: 10.3389/fgene.2019.00475] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 05/03/2019] [Indexed: 11/13/2022] Open
Abstract
Variation in gene expression among genetically identical individual cells (called gene expression noise) directly contributes to phenotypic diversity. Whether such variation can impact genome stability and lead to variation in genotype remains poorly explored. We addressed this question by investigating whether noise in the expression of genes affecting homologous recombination (HR) activity either directly (RAD52) or indirectly (RAD27) confers cell-to-cell heterogeneity in HR rate in Saccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we show that spontaneous HR rate is highly heterogeneous from cell-to-cell in clonal populations depending on the cellular amount of proteins affecting HR activity. Phleomycin-induced HR is even more heterogeneous, showing that RAD27 expression variation strongly affects the rate of recombination from cell-to-cell. Strong variations in HR rate between subpopulations are not correlated to strong changes in cell cycle stage. Moreover, this heterogeneity occurs even when simultaneously sorting cells at equal expression level of another gene involved in DNA damage response (BMH1) that is upregulated by DNA damage, showing that the initiating DNA damage is not responsible for the observed heterogeneity in HR rate. Thus gene expression noise seems mainly responsible for this phenomenon. Finally, HR rate non-linearly scales with Rad27 levels showing that total amount of HR cannot be explained solely by the time- or population-averaged Rad27 expression. Altogether, our data reveal interplay between heterogeneity at the gene expression and genetic levels in the production of phenotypic diversity with evolutionary consequences from microbial to cancer cell populations.
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Affiliation(s)
- Jian Liu
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
| | - Jean-Marie François
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
| | - Jean-Pascal Capp
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
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Csiszar A, Balasubramanian P, Tarantini S, Yabluchanskiy A, Zhang XA, Springo Z, Benbrook D, Sonntag WE, Ungvari Z. Chemically induced carcinogenesis in rodent models of aging: assessing organismal resilience to genotoxic stressors in geroscience research. GeroScience 2019; 41:209-227. [PMID: 31037472 DOI: 10.1007/s11357-019-00064-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023] Open
Abstract
There is significant overlap between the cellular and molecular mechanisms of aging and pathways contributing to carcinogenesis, including the role of genome maintenance pathways. In the field of geroscience analysis of novel genetic mouse models with either a shortened, or an extended, lifespan provides a unique opportunity to evaluate the synergistic roles of longevity assurance pathways in cancer resistance and regulation of lifespan and to develop novel targets for interventions that both delay aging and prevent carcinogenesis. There is a growing need for robust assays to assess the susceptibility of cancer in these models. The present review focuses on a well-characterized method frequently used in cancer research, which can be adapted to study resilience to genotoxic stress and susceptibility to genotoxic stress-induced carcinogenesis in geroscience research namely, chemical carcinogenesis induced by treatment with 7,12-dimethylbenz(a)anthracene (DMBA). Recent progress in understanding how longer-living mice may achieve resistance to chemical carcinogenesis and how these pathways are modulated by anti-aging interventions is reviewed. Strain-specific differences in sensitivity to DMBA-induced carcinogenesis are also explored and contrasted with mouse lifespan. The clinical relevance of inhibition of DMBA-induced carcinogenesis for the pathogenesis of mammary adenocarcinomas in older human subjects is discussed. Finally, the potential role of insulin-like growth factor-1 (IGF-1) in the regulation of pathways responsible for cellular resilience to DMBA-induced mutagenesis is discussed.
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Affiliation(s)
- Anna Csiszar
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Priya Balasubramanian
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA
| | - Stefano Tarantini
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA
| | - Andriy Yabluchanskiy
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Xin A Zhang
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zsolt Springo
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Doris Benbrook
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William E Sonntag
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zoltan Ungvari
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA. .,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary. .,Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary. .,Department of Public Health, Semmelweis University, Budapest, Hungary.
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46
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Review of the evidence for thresholds for DNA-Reactive and epigenetic experimental chemical carcinogens. Chem Biol Interact 2019; 301:88-111. [DOI: 10.1016/j.cbi.2018.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
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47
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Meng X, Duan C, Pang H, Chen Q, Han B, Zha C, Dinislam M, Wu P, Li Z, Zhao S, Wang R, Lin L, Jiang C, Cai J. DNA damage repair alterations modulate M2 polarization of microglia to remodel the tumor microenvironment via the p53-mediated MDK expression in glioma. EBioMedicine 2019; 41:185-199. [PMID: 30773478 PMCID: PMC6442002 DOI: 10.1016/j.ebiom.2019.01.067] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/25/2022] Open
Abstract
Background DNA damage repair (DDR) alterations are important events in cancer initiation, progression, and therapeutic resistance. However, the involvement of DDR alterations in glioma malignancy needs further investigation. This study aims to characterize the clinical and molecular features of gliomas with DDR alterations and elucidate the biological process of DDR alterations that regulate the cross talk between gliomas and the tumor microenvironment. Methods Integrated transcriptomic and genomic analyses were undertaken to conduct a comprehensive investigation of the role of DDR alterations in glioma. The prognostic DDR-related cytokines were identified from multiple datasets. In vivo and in vitro experiments validated the role of p53, the key molecule of DDR, regulating M2 polarization of microglia in glioma. Findings DDR alterations are associated with clinical and molecular characteristics of glioma. Gliomas with DDR alterations exhibit distinct immune phenotypes, and immune cell types and cytokine processes. DDR-related cytokines have an unfavorable prognostic implication for GBM patients and are synergistic with DDR alterations. Overexpression of MDK mediated by p53, the key transcriptional factor in DDR pathways, remodels the GBM immunosuppressive microenvironment by promoting M2 polarization of microglia, suggesting a potential role of DDR in regulating the glioma microenvironment. Interpretation Our work suggests that DDR alterations significantly contribute to remodeling the glioma microenvironment via regulating the immune response and cytokine pathways. Fund This study was supported by: 1. The National Key Research and Development Plan (No. 2016YFC0902500); 2. National Natural Science Foundation of China (No. 81702972, No. 81874204, No. 81572701, No. 81772666); 3. China Postdoctoral Science Foundation (2018M640305); 4. Special Fund Project of Translational Medicine in the Chinese-Russian Medical Research Center (No. CR201812); 5. The Research Project of the Chinese Society of Neuro-oncology, CACA (CSNO-2016-MSD12); 6. The Research Project of the Health and Family Planning Commission of Heilongjiang Province (2017–201); and 7. Harbin Medical University Innovation Fund (2017LCZX37, 2017RWZX03). Gliomas with DNA damage repair alterations had distinct genomic variation spectrum. DDR alterations exhibit distinct immune phenotypes, cytokine processes and immune cell types in glioma. DDR-related cytokines in GME have an unfavorable prognostic implication for GBM patients. P53-mediated midkine expression derived from glioma cells promotes M2 polarization of microglia.
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Affiliation(s)
- Xiangqi Meng
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Chunbin Duan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Hengyuan Pang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qun Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Bo Han
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Caijun Zha
- Department of Laboratory Diagnosis, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Magafurov Dinislam
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neurosurgical department, Bashkir State Medical University, Ufa 450008, Russia
| | - Pengfei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Ziwei Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Shihong Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ruijia Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Lin Lin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Chuanlu Jiang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China.
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China; Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China.
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Interplay between early-life malnutrition, epigenetic modulation of the immune function and liver diseases. Nutr Res Rev 2019; 32:128-145. [PMID: 30707092 DOI: 10.1017/s0954422418000239] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Early-life nutrition plays a critical role in fetal growth and development. Food intake absence and excess are the two main types of energy malnutrition that predispose to the appearance of diseases in adulthood, according to the hypothesis of 'developmental origins of health and disease'. Epidemiological data have shown an association between early-life malnutrition and the metabolic syndrome in later life. Evidence has also demonstrated that nutrition during this period of life can affect the development of the immune system through epigenetic mechanisms. Thus, epigenetics has an essential role in the complex interplay between environmental factors and genetics. Altogether, this leads to the inflammatory response that is commonly seen in non-alcoholic fatty liver disease (NAFLD), the hepatic manifestation of the metabolic syndrome. In conjunction, DNA methylation, covalent modification of histones and the expression of non-coding RNA are the epigenetic phenomena that affect inflammatory processes in the context of NAFLD. Here, we highlight current understanding of the mechanisms underlying developmental programming of NAFLD linked to epigenetic modulation of the immune system and environmental factors, such as malnutrition.
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49
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Kogan AA, Lapidus RG, Baer MR, Rassool FV. Exploiting epigenetically mediated changes: Acute myeloid leukemia, leukemia stem cells and the bone marrow microenvironment. Adv Cancer Res 2019; 141:213-253. [PMID: 30691684 DOI: 10.1016/bs.acr.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukemia (AML) derives from the clonal expansion of immature myeloid cells in the bone marrow, and results in the disruption of normal hematopoiesis and subsequent bone marrow failure. The bone marrow microenvironment (BME) and its immune and other supporting cells are regarded to facilitate the survival, differentiation and proliferation of leukemia stem cells (LSCs), which enables AML cells to persist and expand despite treatment. Recent studies have identified epigenetic modifications among AML cells and BME constituents in AML, and have shown that epigenetic therapy can potentially reprogram these alterations. In this review, we summarize the interactions between the BME and LSCs, and discuss changes in how the BME and immune cells interact with AML cells. After describing the epigenetic modifications seen across chromatin, DNA, the BME, and the immune microenvironment, we explore how demethylating agents may reprogram these pathological interactions, and potentially re-sensitize AML cells to treatment.
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Affiliation(s)
- Aksinija A Kogan
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, United States; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
| | - Rena G Lapidus
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Maria R Baer
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Feyruz V Rassool
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, United States; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States.
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50
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Rampias T, Karagiannis D, Avgeris M, Polyzos A, Kokkalis A, Kanaki Z, Kousidou E, Tzetis M, Kanavakis E, Stravodimos K, Manola KN, Pantelias GE, Scorilas A, Klinakis A. The lysine-specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer. EMBO Rep 2019; 20:embr.201846821. [PMID: 30665945 PMCID: PMC6399616 DOI: 10.15252/embr.201846821] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Genome‐wide studies in tumor cells have indicated that chromatin‐modifying proteins are commonly mutated in human cancers. The lysine‐specific methyltransferase 2C (KMT2C/MLL3) is a putative tumor suppressor in several epithelia and in myeloid cells. Here, we show that downregulation of KMT2C in bladder cancer cells leads to extensive changes in the epigenetic status and the expression of DNA damage response and DNA repair genes. More specifically, cells with low KMT2C activity are deficient in homologous recombination‐mediated double‐strand break DNA repair. Consequently, these cells suffer from substantially higher endogenous DNA damage and genomic instability. Finally, these cells seem to rely heavily on PARP1/2 for DNA repair, and treatment with the PARP1/2 inhibitor olaparib leads to synthetic lethality, suggesting that cancer cells with low KMT2C expression are attractive targets for therapies with PARP1/2 inhibitors.
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Affiliation(s)
| | | | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Antonis Kokkalis
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Zoi Kanaki
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Evgenia Kousidou
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Emmanouil Kanavakis
- Department of Medical Genetics, Medical School, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,University Research Institute for the Study and Treatment of Childhood Genetic and Malignant Diseases, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kalliopi N Manola
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
| | - Gabriel E Pantelias
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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