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Xue M, Xu Z, Wang X, Chen J, Kong X, Zhou S, Wu J, Zhang Y, Li Y, Christiani DC, Chen F, Zhao Y, Zhang R. ARTEMIS: An independently validated prognostic prediction model of breast cancer incorporating epigenetic biomarkers with main effects and gene-gene interactions. J Adv Res 2024:S2090-1232(24)00358-8. [PMID: 39137864 DOI: 10.1016/j.jare.2024.08.015] [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: 01/07/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 08/15/2024] Open
Abstract
INTRODUCTION Breast cancer, a heterogeneous disease, is influenced by multiple genetic and epigenetic factors. The majority of prognostic models for breast cancer focus merely on the main effects of predictors, disregarding the crucial impacts of gene-gene interactions on prognosis. OBJECTIVES Using DNA methylation data derived from nine independent breast cancer cohorts, we developed an independently validated prognostic prediction model of breast cancer incorporating epigenetic biomarkers with main effects and gene-gene interactions (ARTEMIS) with an innovative 3-D modeling strategy. ARTEMIS was evaluated for discrimination ability using area under the receiver operating characteristics curve (AUC), and calibration using expected and observed (E/O) ratio. Additionally, we conducted decision curve analysis to evaluate its clinical efficacy by net benefit (NB) and net reduction (NR). Furthermore, we conducted a systematic review to compare its performance with existing models. RESULTS ARTEMIS exhibited excellent risk stratification ability in identifying patients at high risk of mortality. Compared to those below the 25th percentile of ARTEMIS scores, patients with above the 90th percentile had significantly lower overall survival time (HR = 15.43, 95% CI: 9.57-24.88, P = 3.06 × 10-29). ARTEMIS demonstrated satisfactory discrimination ability across four independent populations, with pooled AUC3-year = 0.844 (95% CI: 0.805-0.883), AUC5-year = 0.816 (95% CI: 0.775-0.857), and C-index = 0.803 (95% CI: 0.776-0.830). Meanwhile, ARTEMIS had well calibration performance with pooled E/O ratio 1.060 (95% CI: 1.038-1.083) and 1.090 (95% CI: 1.057-1.122) for 3- and 5-year survival prediction, respectively. Additionally, ARTEMIS is a clinical instrument with acceptable cost-effectiveness for detecting breast cancer patients at high risk of mortality (Pt = 0.4: NB3-year = 19‰, NB5-year = 62‰; NR3-year = 69.21%, NR5-year = 56.01%). ARTEMIS has superior performance compared to existing models in terms of accuracy, extrapolation, and sample size, as indicated by the systematic review. ARTEMIS is implemented as an interactive online tool available at http://bigdata.njmu.edu.cn/ARTEMIS/. CONCLUSION ARTEMIS is an efficient and practical tool for breast cancer prognostic prediction.
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Affiliation(s)
- Maojie Xue
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ziang Xu
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, China; Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiang Wang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jiajin Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital of Xiamen University, Xiamen, Fujian 361006, China
| | - Xinxin Kong
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shenxuan Zhou
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jiamin Wu
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yuhao Zhang
- Department of General Biology, Eberly College of Science, Pennsylvania State University, Pennsylvania 16802, USA
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David C Christiani
- Pulmonary and Critical Care Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Jiangsu 211166, China.
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Jiangsu 211166, China.
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Jiangsu 211166, China; Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu 213164, China.
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He Y, Hu Y, Cheng Y, Li X, Chen C, Zhang S, He H, Cao F. Multi-Omics Insights into Disulfidptosis-Related Genes Reveal RPN1 as a Therapeutic Target for Liver Cancer. Biomolecules 2024; 14:677. [PMID: 38927080 PMCID: PMC11201601 DOI: 10.3390/biom14060677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Disulfidptosis, a newly identified mode of programmed cell death, is yet to be comprehensively elucidated with respect to its multi-omics characteristics in tumors, specific pathogenic mechanisms, and antitumor functions in liver cancer. This study included 10,327 tumor and normal tissue samples from 33 cancer types. In-depth analyses using various bioinformatics tools revealed widespread dysregulation of disulfidptosis-related genes (DRGs) in pan-cancer and significant associations with prognosis, genetic variations, tumor stemness, methylation levels, and drug sensitivity. Univariate and multivariate Cox regression and LASSO regression were used to screen and construct prognosis-related hub DRGs and predictive models in the context of liver cancer. Subsequently, single cell analysis was conducted to investigate the subcellular localization of RPN1, a hub DRG, in various solid tumors. Western blotting was performed to validate the expression of RPN1 at both cellular and tissue levels. Additionally, functional experiments, including CCK8, EdU, clone, and transwell assays, indicated that RPN1 knockdown promoted the proliferative and invasive capacities of liver cancer cells. Therefore, this study elucidated the multi-omics characteristics of DRGs in pan-cancer and established a prognostic model for liver cancer. Additionally, this study revealed the molecular functions of RPN1 in liver cancer, suggesting its potential as a therapeutic target for this disease.
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Affiliation(s)
- Yan He
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Yue Hu
- Pathology Department, Hefei Cancer Hospital, Chinese Academy of Sciences (CAS), Hefei 230000, China;
| | - Yunsheng Cheng
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230000, China
| | - Xutong Li
- Department of Infectious Diseases, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Chuanhong Chen
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Shijie Zhang
- Department of General Surgery, The Fuyang Hospital of Anhui Medical University, Fuyang 236000, China;
| | - Huihu He
- Department of General Surgery, The Fuyang Hospital of Anhui Medical University, Fuyang 236000, China;
| | - Feng Cao
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
- Medical Faculty, University Hospital RWTH Aachen, 52074 Aachen, Germany
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Zhang Y, Gao C, Luo J, Khan A, Salem‐Bekhit MM, Salem MM, Qi Z, Jiang B. Deciphering the role of wound healing genes in skin cutaneous melanoma: Insights into expression, methylation, mutations, and therapeutic implications. Int Wound J 2024; 21:e14807. [PMID: 38591163 PMCID: PMC11002634 DOI: 10.1111/iwj.14807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 04/10/2024] Open
Abstract
Skin Cutaneous Melanoma (SKCM) is a form of cancer that originates in the pigment-producing cells, known as melanocytes, of the skin. Delay wound healing is often correlated with the occurrence of and progression of SKCM. In this comprehensive study, we investigated the intricate roles of two important wound healing genes in SKCM, including Matrix Metalloproteinase-2 (MMP2) and Matrix Metalloproteinase-9 (MMP9). Through a multi-faceted approach, we collected clinical samples, conducted molecular experiments, including RT-qPCR, bisulphite sequencing, cell culture, cell Counting Kit-8, colony formation, and wound healing assays. Beside this, we also used various other databases/tools/approaches for additional analysis including, UALCAN, GEPIA, HPA, MEXPRESS, cBioPortal, KM plotter, DrugBank, and molecular docking. Our results revealed a significant up-regulation of MMP2 and MMP9 in SKCM tissues compared to normal counterparts. Moreover, promoter methylation analysis suggested an epigenetic regulatory mechanism. Validations using TCGA datasets and immunohistochemistry emphasized the clinical relevance of MMP2 and MMP9 dysregulation. Functional assays demonstrated their synergistic impact on proliferation and migration in SKCM cells. Furthermore, we identified potential therapeutic candidates, Estradiol and Calcitriol, through drug prediction and molecular docking analyses. These compounds exhibited binding affinities, suggesting their potential as MMP2/MMP9 inhibitors. Overall, our study elucidates the diagnostic, prognostic, and therapeutic implications of MMP2 and MMP9 in SKCM, shedding light on their complex interplay in SKCM occurrence and progression.
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Affiliation(s)
- Yulong Zhang
- Department of Traditional Chinese Medicine Oncology, Cancer CenterThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
| | - Chenxi Gao
- Department of Traditional Chinese Medicine Oncology, Cancer CenterThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
| | - Juncong Luo
- Department of OncologyThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
| | - Arsalan Khan
- Health DepartmentGovernment of Khyber PakhtunkhwaDera Ismail KhanPakistan
| | | | - Mohamed M. Salem
- College of MedicineHuazhong University of Science and TechnologyWuhanChina
| | - Zeng Qi
- Department of Traditional Chinese Medicine Oncology, Cancer CenterThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
| | - Bo Jiang
- Emergency DepartmentThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
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Xu D, Lai Y, Liu H, Li H, Feng N, Liu Y, Gong C, Zhang Y, Zhou J, Shen Y. A diagnostic model based on DNA methylation haplotype block characteristics for identifying papillary thyroid carcinoma from thyroid adenoma. Transl Res 2024; 264:76-84. [PMID: 37863284 DOI: 10.1016/j.trsl.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer. Methylation of some genes plays a crucial role in the tendency to malignancy as well as poor prognosis of thyroid cancer, suggesting that methylation features can serve as complementary markers for molecular diagnosis. In this study, we aimed to develop and validate a diagnostic model for PTC based on DNA methylation markers. A total of 142 thyroid nodule tissue samples containing 84 cases of PTC and 58 cases of thyroid adenoma (TA) were collected for reduced representation bisulfite sequencing (RRBS) and subsequent analysis. The diagnostic model was constructed by the logistic regression (LR) method followed by 5-cross validation and based on 94 tissue methylation haplotype block (MHB) markers. The model achieved an area under the receiver operating characteristic curve (AUROC) of 0.974 (95% CI, 0.964-0.981) on 108 training samples and 0.917 (95% CI, 0.864-0.973) on 27 independent testing samples. The diagnostic model scores showed significantly high in males (P = 0.0016), age ≤ 45 years (P = 0.026), high body mass index (BMI) (P = 0.040), lymph node metastasis (P = 0.00052) and larger nodules (P = 0.0017) in the PTC group, and the risk score of this diagnostic model showed significantly high in recurrent PTC group (P = 0.0005). These results suggest that the diagnostic model can be expected to be a powerful tool for PTC diagnosis and there are more potential clinical applications of methylation markers to be excavated.
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Affiliation(s)
- Dong Xu
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Yi Lai
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China; Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Hongmei Liu
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - He Li
- Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Ningning Feng
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Yiying Liu
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Chengxiang Gong
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Yunzhi Zhang
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Jiaqing Zhou
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China.
| | - Yuling Shen
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China.
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Alotaibi N, Alotaibi MO, Alshammari N, Adnan M, Patel M. Network Pharmacology Combined with Molecular Docking, Molecular Dynamics, and In Vitro Experimental Validation Reveals the Therapeutic Potential of Thymus vulgaris L. Essential Oil (Thyme Oil) against Human Breast Cancer. ACS OMEGA 2023; 8:48344-48359. [PMID: 38144096 PMCID: PMC10734022 DOI: 10.1021/acsomega.3c07782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023]
Abstract
Breast cancer is a major global health issue for women. Thyme oil, extracted from Thymus vulgaris L., has shown promising anticancer effects. In the present study, we investigated how Thyme oil can influence breast cancer treatment using a multimethod approach. We used network pharmacology to identify the active compounds of Thyme oil, their molecular targets, and the pathways involved in breast cancer. We found that Thyme oil can modulate several key proteins (EGFR, AKT1, ESR1, HSP90AA1, STAT-3, SRC, IL-6, HIF1A, JUN, and BCL2) and pathways (EGFR tyrosine kinase inhibitor resistance, prolactin signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, ERBB signaling pathway, AGE-RAGE signaling pathway, JAK-STAT signaling pathway, FoxO signaling pathway, and PI3K-AKT signaling pathway) related to breast cancer progression. We then used molecular docking and dynamics to study the interactions and stability of the Thyme oil-compound complexes. We discovered three potent compounds (aromadendrene, α-humulene, and viridiflorene) that can bind strongly to important breast cancer proteins. We also performed in vitro experiments on MCF-7 cells to confirm the cytotoxicity and antiproliferative effects of Thyme oil. We observed that Thyme oil can inhibit cancer cell growth and proliferation at a concentration of 365.37 μg/mL. Overall, our results provide a comprehensive understanding of the pharmacological mechanism of Thyme oil in breast cancer treatment and suggest its potential as a new or adjuvant therapy. Further studies are needed to validate and optimize the therapeutic efficacy of Thyme oil and its active compounds.
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Affiliation(s)
- Nahaa
M. Alotaibi
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Modhi O. Alotaibi
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nawaf Alshammari
- Department
of Biology, College of Science, University
of Ha’il, P.O. Box 2440, Ha’il 55473, Saudi Arabia
| | - Mohd Adnan
- Department
of Biology, College of Science, University
of Ha’il, P.O. Box 2440, Ha’il 55473, Saudi Arabia
| | - Mitesh Patel
- Research
and Development Cell, Department of Biotechnology, Parul Institute
of Applied Sciences, Parul University, Vadodara 391760, India
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Zhang YL, Wang YW, He MJ, Chang JL. An updated meta-analysis investigating the association between DNMTs gene polymorphism andgastric cancer risk. PLoS One 2023; 18:e0293466. [PMID: 37878642 PMCID: PMC10599511 DOI: 10.1371/journal.pone.0293466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Gastric cancer (GC) is a prominent global health issue, as it ranks as the fifth most prevalent type of cancer and the fourth most significant cause of cancer-related mortality worldwide. Although H. pylori is known to play a role in the development of GC, genetic factors also play a role in its onset and progression. Recent studies have shown that genetic polymorphisms are strongly associated with the development of GC and that certain single nucleotide polymorphisms (SNPs) can be used as biomarkers for early diagnosis and prevention. Epigenetic disturbances, such as DNA methylation, are involved in the development of GC, and mutations in the DNA methyltransferase (DNMT) gene have been found to increase the risk of GC. However, previous findings on the association between DNMTs SNPs and GC risk have been inconsistent. In this study, an updated meta-analysis of three well-studied and controversial DNMTs polymorphic loci, DNMT1 rs16999593, DNMT3A rs1550117 and DNMT3B rs1569686, was performed to provide more reliable results. It was found that DNMT1 rs16999593 was not associated with GC, DNMT3A rs1550117 may have a positive association with GC risk, and DNMT3B rs1569686 may be a protective factor for GC. These findings may provide valuable information for early diagnosis and prevention of GC, but further studies are needed to confirm these results.
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Affiliation(s)
- Yu-Long Zhang
- Department of Oncology, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
| | - Yu-Wei Wang
- Changzhi Medical College, Shanxi Province, Changzhi, China
| | - Ming-Jie He
- Changzhi Medical College, Shanxi Province, Changzhi, China
| | - Jian-Lan Chang
- Department of Oncology, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
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An N, Yang X. Prediction of disease-free survival of N1/2 non-small cell lung cancer after adjuvant chemotherapy by the biomarker RPMB. Heliyon 2023; 9:e18266. [PMID: 37501955 PMCID: PMC10368914 DOI: 10.1016/j.heliyon.2023.e18266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
No molecular biomarkers have been proven applicable in clinical practice to identify patients who can benefit from adjuvant chemotherapy in non-small cell lung cancer (NSCLC). In this study, we established a biomarker, RPMB, short for promotor methylation burden of DNA repair genes (DRGs), to identify the subgroup of patients who might benefit from adjuvant chemotherapy in NSCLC. Methylation profiles of 828 NSCLC primary tumors and their clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. The RPMB for each patient after radical resection was calculated and its correlation with the prognosis of NSCLC was extensively investigated. DRGs of NSCLC were much more hypomethylated than the other genes (all p<0.001). RPMB was defined as the ratio of methylated DRGs to the total number of all the DRGs. Patients with higher RPMB values tended to be nonsmokers, had adenocarcinoma, were female and had peripheral tumors. Subgroup analysis of forest plot among different clinical factors showed that high RPMB was significantly correlated to better disease-free survival (DFS) in pathologic N-positive patients after adjuvant chemotherapy (HR = 0.404, n = 62, p = 0.034). Notably, more superior DFS was exhibited in high RPMB NSCLCs with N1 nodal stage compared with those with low RPMB values (HR = 0.348, n = 47, p = 0.043). High RPMB might be used as a potential predictor to identify suitable N-positive NSCLC patients who can benefit from adjuvant chemotherapy after radical surgery.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
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Sanya DRA, Onésime D. Roles of non-coding RNAs in the metabolism and pathogenesis of bladder cancer. Hum Cell 2023:10.1007/s13577-023-00915-5. [PMID: 37209205 DOI: 10.1007/s13577-023-00915-5] [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: 01/29/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Bladder cancer (BC) is featured as the second most common malignancy of the urinary tract worldwide with few treatments leading to high incidence and mortality. It stayed a virtually intractable disease, and efforts to identify innovative and effective therapies are urgently needed. At present, more and more evidence shows the importance of non-coding RNA (ncRNA) for disease-related study, diagnosis, and treatment of diverse types of malignancies. Recent evidence suggests that dysregulated functions of ncRNAs are closely associated with the pathogenesis of numerous cancers including BC. The detailed mechanisms underlying the dysregulated role of ncRNAs in cancer progression are still not fully understood. This review mainly summarizes recent findings on regulatory mechanisms of the ncRNAs, long non-coding RNAs, microRNAs, and circular RNAs, in cancer progression or suppression and focuses on the predictive values of ncRNAs-related signatures in BC clinical outcomes. A deeper understanding of the ncRNA interactive network could be compelling framework for developing biomarker-guided clinical trials.
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Affiliation(s)
- Daniel Ruben Akiola Sanya
- Micalis Institute, Diversité génomique et fonctionnelle des levures, domaine de Vilvert, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France.
| | - Djamila Onésime
- Micalis Institute, Diversité génomique et fonctionnelle des levures, domaine de Vilvert, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
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Hu S, Tao J, Peng M, Ye Z, Chen Z, Chen H, Yu H, Wang B, Fan JB, Ni B. Accurate detection of early-stage lung cancer using a panel of circulating cell-free DNA methylation biomarkers. Biomark Res 2023; 11:45. [PMID: 37101220 PMCID: PMC10134678 DOI: 10.1186/s40364-023-00486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer mortality worldwide. Early detection of lung cancer helps improve treatment and survival. Numerous aberrant DNA methylations have been reported in early-stage lung cancer. Here, we sought to identify novel DNA methylation biomarkers that could potentially be used for noninvasive early diagnosis of lung cancers. METHODS This prospective-specimen collection and retrospective-blinded-evaluation trial enrolled a total of 317 participants (198 tissues and 119 plasmas) comprising healthy controls, patients with lung cancer and benign disease between January 2020 and December 2021. Tissue and plasma samples were subjected to targeted bisulfite sequencing with a lung cancer specific panel targeting 9,307 differential methylation regions (DMRs). DMRs associated with lung cancer were identified by comparing the methylation profiles of tissue samples from patients with lung cancer and benign disease. Markers were selected with minimum redundancy and maximum relevance algorithm. A prediction model for lung cancer diagnosis was built through logistic regression algorithm and validated independently in tissue samples. Furthermore, the performance of this developed model was evaluated in a set of plasma cell-free DNA (cfDNA) samples. RESULTS We identified 7 DMRs corresponding to 7 differentially methylated genes (DMGs) including HOXB4, HOXA7, HOXD8, ITGA4, ZNF808, PTGER4, and B3GNTL1 that were highly associated with lung cancer by comparing the methylation profiles of lung cancer and benign nodule tissue. Based on the 7-DMR biomarker panel, we developed a new diagnostic model in tissue samples, termed "7-DMR model", to distinguish lung cancers from benign diseases, achieving AUCs of 0.97 (95%CI: 0.93-1.00)/0.96 (0.92-1.00), sensitivities of 0.89 (0.82-0.95)/0.92 (0.86-0.98), specificities of 0.94 (0.89-0.99)/1.00 (1.00-1.00), and accuracies of 0.90 (0.84-0.96)/0.94 (0.89-0.99) in the discovery cohort (n = 96) and the independent validation cohort (n = 81), respectively. Furthermore, the 7-DMR model was applied to noninvasive discrimination of lung cancers and non-lung cancers including benign lung diseases and healthy controls in an independent validation cohort of plasma samples (n = 106), yielding an AUC of 0.94 (0.86-1.00), sensitivity of 0.81 (0.73-0.88), specificity of 0.98 (0.95-1.00), and accuracy of 0.93 (0.89-0.98). CONCLUSION The 7 novel DMRs could be promising methylation biomarkers that merits further development as a noninvasive test for early detection of lung cancer.
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Affiliation(s)
- Shuo Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | | | - Zhujia Ye
- Anchordx Medical Co., Ltd, Guangzhou, China
| | - Zhiwei Chen
- Anchordx Medical Co., Ltd, Guangzhou, China
- AnchorDx Inc, Fremont, CA, USA
| | | | - Haifeng Yu
- The Fifth People's Hospital of Wuxi, Wuxi, China
| | - Bo Wang
- Anchordx Medical Co., Ltd, Guangzhou, China.
| | - Jian-Bing Fan
- Anchordx Medical Co., Ltd, Guangzhou, China.
- Department of Pathology, Southern Medical University, Guangzhou, China.
| | - Bin Ni
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Luzna P, Weiser Drozdkova D, Flodrova P, Ondruskova K, Uberall I, Minarik J, Kolar Z, Smesny Trtkova K. Global DNA methylation and increased DNMT3A expression in multiple myeloma patients. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2023; 167:43-49. [PMID: 35173353 DOI: 10.5507/bp.2022.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
AIMS The aim of this study was to compare the expression profile of selected DNA methyltransferases and global DNA methylation status in patients with different phases of multiple myeloma (MM) . For the analysis, different cellular populations including unsorted myeloma cells and a set of plasma cells purified by relevant antibodies were used. Consequently, laboratory data were compared to patients' clinical data. PATIENTS AND METHODS For the analysis, unsorted bone marrow cell population of 44 MM patients (30 newly diagnosed, 9 relapsed and 5 patients in remission) and a set of 8 patients' samples of sorted plasma cells were used. We used commercially available RNA isolated from BM of 3 healthy individuals as control samples. Expression analysis of three DNA methyltransferases - DNMT1, DNMT3A, and DNMT3B was performed by quantitative RT-PCR and the patient global DNA methylation profiles were detected by colorimetric assay. RESULTS Unchanged DNMT1 expression was detected in the selected cohort of patients. Normalized DNMT3A gene expression was globally higher in comparison with controls in unsorted and sorted cell populations. Low (0.08-1.81%) global DNA methylation status in unsorted samples of multiple myeloma patients did not correlate either with expression profiles of monitored DNA methyltransferases or with the stages of MM based on Durie-Salmon and International Staging System. CONCLUSION This is the first comparative study between DNA methyltransferases expression profiles and global DNA methylation status in different phases of multiple myeloma patients. No significant correlation between the level of global methylation and the clinical stage of the unsorted cell population of patients with multiple myeloma was registered. Overexpression of the DNMT3A gene occurred in both sorted and unsorted cell populations of patients with multiple myeloma. This fact highlights the DNMT3A as a potential marker of multiple myeloma tumor progression. Moreover, we demonstrated comparable results in the expression of DNA methyltransferases in both sorted and unsorted cell populations. This is a promising result from the methodical point of view because when compared to samples of unsorted multiple myeloma cells, samples of sorted cells bring reduction of the number of possible analyses performed.
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Affiliation(s)
- Petra Luzna
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Denisa Weiser Drozdkova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Pavla Flodrova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Katarina Ondruskova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Ivo Uberall
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Jiri Minarik
- Department of Hemato-Oncology, University Hospital Olomouc, Czech Republic.,Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Zdenek Kolar
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Katerina Smesny Trtkova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
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11
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Zhang Z, Wang G, Li Y, Lei D, Xiang J, Ouyang L, Wang Y, Yang J. Recent progress in DNA methyltransferase inhibitors as anticancer agents. Front Pharmacol 2022; 13:1072651. [PMID: 37077808 PMCID: PMC10107375 DOI: 10.3389/fphar.2022.1072651] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
DNA methylation mediated by DNA methyltransferase is an important epigenetic process that regulates gene expression in mammals, which plays a key role in silencing certain genes, such as tumor suppressor genes, in cancer, and it has become a promising therapeutic target for cancer treatment. Similar to other epigenetic targets, DNA methyltransferase can also be modulated by chemical agents. Four agents have already been approved to treat hematological cancers. In order to promote the development of a DNA methyltransferase inhibitor as an anti-tumor agent, in the current review, we discuss the relationship between DNA methylation and tumor, the anti-tumor mechanism, the research progress and pharmacological properties of DNA methyltransferase inhibitors, and the future research trend of DNA methyltransferase inhibitors.
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Affiliation(s)
- Zhixiong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Yuyan Li
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Dongsheng Lei
- School of Physical Science and Technology, Electron Microscopy Center of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Jin Xiang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Science and Technology Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yanyan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Science and Technology Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yanyan Wang, ; Jinliang Yang,
| | - Jinliang Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- *Correspondence: Yanyan Wang, ; Jinliang Yang,
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12
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High RPMB predicts poor disease-free survival of male N1 papillary thyroid cancer after adjuvant radioiodine therapy. Heliyon 2022; 8:e11783. [DOI: 10.1016/j.heliyon.2022.e11783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/17/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022] Open
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13
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White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet 2022; 13:1037134. [PMID: 36386798 PMCID: PMC9650216 DOI: 10.3389/fgene.2022.1037134] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/26/2024] Open
Abstract
Next generation sequencing (NGS) has provided biologists with an unprecedented view into biological processes and their regulation over the past 2 decades, fueling a wave of development of high throughput methods based on short read DNA and RNA sequencing. For nucleic acid modifications, NGS has been coupled with immunoprecipitation, chemical treatment, enzymatic treatment, and/or the use of reverse transcriptase enzymes with fortuitous activities to enrich for and to identify covalent modifications of RNA and DNA. However, the majority of nucleic acid modifications lack commercial monoclonal antibodies, and mapping techniques that rely on chemical or enzymatic treatments to manipulate modification signatures add additional technical complexities to library preparation. Moreover, such approaches tend to be specific to a single class of RNA or DNA modification, and generate only indirect readouts of modification status. Third generation sequencing technologies such as the commercially available "long read" platforms from Pacific Biosciences and Oxford Nanopore Technologies are an attractive alternative for high throughput detection of nucleic acid modifications. While the former can indirectly sense modified nucleotides through changes in the kinetics of reverse transcription reactions, nanopore sequencing can in principle directly detect any nucleic acid modification that produces a signal distortion as the nucleic acid passes through a nanopore sensor embedded within a charged membrane. To date, more than a dozen endogenous DNA and RNA modifications have been interrogated by nanopore sequencing, as well as a number of synthetic nucleic acid modifications used in metabolic labeling, structure probing, and other emerging applications. This review is intended to introduce the reader to nanopore sequencing and key principles underlying its use in direct detection of nucleic acid modifications in unamplified DNA or RNA samples, and outline current approaches for detecting and quantifying nucleic acid modifications by nanopore sequencing. As this technology matures, we anticipate advances in both sequencing chemistry and analysis methods will lead to rapid improvements in the identification and quantification of these epigenetic marks.
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Affiliation(s)
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
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14
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Xue MQ, Wang YL, Wang JC, Wang XD, Wang XJ, Zhang YQ. Comprehensive analysis of the PD-L1 and immune infiltrates of N6-methyladenosine related long non-coding RNAs in bladder cancer. Sci Rep 2022; 12:10082. [PMID: 35710698 PMCID: PMC9203575 DOI: 10.1038/s41598-022-14097-x] [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: 02/09/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
Bladder cancer (BLCA) is one of the most frequent genitourinary cancers, with a high rate of morbidity and mortality. The connection of m6A-related lncRNAs with PD-L1 and tumor immune microenvironment (TIME) in BLCA prognosis was extensively investigated in this study, which could suggest novel therapeutic targets for further investigation. 30 m6A-associated lncRNAs with predictive values from the TCGA data set were identified with co-expression analysis. Cluster2 was correlated with a poor prognosis, upregulated PD-L1 expression, and higher immune ratings. Cluster2 had larger amounts of resting CD4 memory-activated T cells, M2 macrophages, neutrophils, and NK cells infiltration. "CHEMOKINE SIGNALING PATHWAY" was the most significantly enriched signaling pathway according to GSEA, which may play an important role in the different immune cell infiltrates between cluster1/2. The risk model for m6A-related lncRNAs could be employed in a prognostic model to predict BLCA prognosis, regardless of other clinical features. Collectively, m6A-related lncRNAs were linked to PD-L1 and TIME, which would dynamically affect the number of tumor-infiltrating immune cells. m6A-related lncRNAs may be key mediators of PD-L1 expression and immune cells infiltration and may strongly affect the TIME of BLCA.
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Affiliation(s)
- M Q Xue
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Y L Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Bioengineering Technology Reseach Center, Zhengzhou, 450010, People's Republic of China.
| | - J C Wang
- Henan Bioengineering Technology Reseach Center, Zhengzhou, 450010, People's Republic of China
| | - X D Wang
- Henan General Hospital, Zhengzhou, 450002, People's Republic of China
| | - X J Wang
- Henan General Hospital, Zhengzhou, 450002, People's Republic of China
| | - Y Q Zhang
- Zhengzhou Technical College, Zhengzhou, 450010, People's Republic of China
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15
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Wang J, Shi M, Zhang H, Zhou H, Huang Z, Zhou Y, Shi J. PRKCB is relevant to prognosis of lung adenocarcinoma through methylation and immune infiltration. Thorac Cancer 2022; 13:1837-1849. [PMID: 35567329 PMCID: PMC9200888 DOI: 10.1111/1759-7714.14466] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/30/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is one of the tumor‐related diseases with high morbidity worldwide. Epigenetic modifications such as DNA methylation changes may involve in tumorigenesis. This study aimed to explore new biomarkers that have prognostic significance of LUAD. Methods First, we downloaded the gene expression and methylation data set from Gene Expression Omnibus. R software was then used to identify abnormally methylated differentially expressed genes (MDEGs). Next, R package Cluster Profiler was used to analyze the enrichment and pathway of the MDEGs. Analysis using STRING revealed the protein–protein interaction network. The result was then visualized by Cytoscape and obtained 10 hub genes. Afterward, they were further verified by The Cancer Genome Atlas to select candidate genes. Moreover, quantitative real‐time polymerase chain reaction (qRT‐PCR) and immunohistochemistry were used to verify the expression and prognostic value of candidate genes in LUAD patients. Results The results showed that the expressions of ADCY5 and PRKCB are indeed related to LUAD. The clinical relevance to PRKCB was confirmed by its clinical correlation analysis. Gene set enrichment analysis (GSEA) and tumor immune estimation resource (TIMER) tumor immune correlations showed that PRKCB is involved in the cancer‐related Kyoto Encyclopedia of Genes and Genomes pathway and is involved in immune infiltration. It was also verified by qRT‐PCR and immunohistochemistry that PRKCB was lowly expressed in LUAD patients and correlated with prognosis. Conclusions PRKCB is relevant to prognosis of LUAD through methylation and immune infiltration.
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Affiliation(s)
- Jinjie Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Muqi Shi
- Medical College of Nantong University, Nantong, China
| | - Haijian Zhang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Hao Zhou
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhanghao Huang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China.,School of Public Health, Nantong University, Nantong, China
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16
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Wang D, Wang X, Huang B, Zhao Y, Tu W, Jin X, Shao Y, Zhu Y, Lu G. METTL3 promotes prostate cancer progression by regulating miR-182 maturation in m6A-dependent manner. Andrologia 2022; 54:1581-1591. [PMID: 35413135 DOI: 10.1111/and.14422] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/21/2022] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
METTL3 was known to run through the whole cycle of RNA. It relied on m6A modification in the mRNAs of cancer-related genes to regulate tumour progression. The development of prostate cancer cells could be promoted by METTL3 via hedgehog pathway. Recent studies had shown that the effect of METTL3 on non-coding RNA was mainly dependent on the modification of m6A. However, it is still unknown whether METTL3 promotes tumour development through this mechanism in prostate cancer. The expression of METTL3 in prostate cancer tissues and cells was analysed by qRT-PCR and Western blot assays. CCK-8 assay, colony formation assay, wound-healing assay and transwell assays were conducted to detect the impact of METTL3 on cell proliferation, migration and invasion. Nude mice tumour models were built to evaluate the role of METTL3 in tumorigenesis. N6-methyladenosine (m6A) RNA immunoprecipitation assay (MeRIP) and co-immunoprecipitations assays were performed to verified that METTL3 upregulated the m6A level, interacted with microprocessor protein DGCR8, recognized the m6A modification of pre-miR-182 to regulate its maturation.METTL3 was highly expressed in prostate cancer, and knockdown of METTL3 significantly inhibited cell proliferation, migration, invasion and tumorigenesis, while overexpression of METTL3 promoted cell proliferation, migration, invasion and tumorigenesis in PCa. In addition, we found that METTL3 upregulating the level of m6A, and interacted with DGCR8 to recognize the m6A modification of pre-miR-182 to regulate its splicing and maturation and promote the high expression of miRNA. Our study suggests that METTL3 could be used in targeted therapies for PCa.
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Affiliation(s)
- Dawei Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaojing Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Baoxing Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Zhao
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weichao Tu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xingwei Jin
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuan Shao
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu Zhu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guoliang Lu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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17
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Joshi S, Garlapati C, Aneja R. Epigenetic Determinants of Racial Disparity in Breast Cancer: Looking beyond Genetic Alterations. Cancers (Basel) 2022; 14:cancers14081903. [PMID: 35454810 PMCID: PMC9025441 DOI: 10.3390/cancers14081903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary A substantial disparity in breast cancer incidence and mortality exists between African American (AA) and European American (EA) women. However, the basis for these disparities is poorly understood. In this article, we describe that gene–environment interactions mediated through epigenetic modifications may play a significant role in racial disparities in BC incidence and outcomes. Our in silico analyses and an in-depth literature survey suggest that there exists a significant difference in epigenetic patterns between AA and EA women with breast cancer. Herein, we describe the environmental factors that contribute to these epigenetic changes, which may underlie the disparate racial burden in patients with breast cancer. We suggest that AA women with higher basal epigenetic changes, may have higher pre-disposition to cancer onset, and an aggressive disease course. Pre-existing racial differences in epigenetic profiles of breast tissues raises the possibility of examining these profiles for early diagnosis. Abstract Breast cancer (BC) is the most commonly diagnosed cancer in women. Despite advancements in BC screening, prevention, and treatment, BC incidence and mortality remain high among African American (AA) women. Compared with European American (EA) women, AA women tend to be diagnosed with more advanced and aggressive tumors and exhibit worse survival outcomes. Most studies investigating the determinants of racial disparities in BC have focused on genetic factors associated with African ancestry. However, various environmental and social stressors over an individual’s life course can also shape racial stratification in BC. These social and environmental exposures result in long-term changes in gene expression mediated by epigenetic mechanisms. Epigenetics is often portrayed as an intersection of socially patterned stress and genetic expression. The enduring nature of epigenetic changes makes them suitable for studying the effects of different environmental exposures over an individual’s life course on gene expression. The role of differential social and environmental exposures in racial disparities in BC suggests varied epigenetic profiles or signatures associated with specific BC subtypes in AA and EA women. These epigenetic profiles in EA and AA women could be used as biomarkers for early BC diagnosis and disease prognosis and may prove valuable for the development of targeted therapies for BC. This review article discusses the current state of knowledge regarding epigenetic differences between AA and EA women with BC. We also discuss the role of socio-environmental factors, including psychosocial stress, environmental toxicants, and dietary factors, in delineating the different epigenetic profiles in AA and EA patients with BC.
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Affiliation(s)
- Shriya Joshi
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
| | | | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
- Department of Clinical and Diagnostics Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: or
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18
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Huang M, Xu S, Liu L, Zhang M, Guo J, Yuan Y, Xu J, Chen X, Zou J. m6A Methylation Regulates Osteoblastic Differentiation and Bone Remodeling. Front Cell Dev Biol 2022; 9:783322. [PMID: 34993198 PMCID: PMC8724434 DOI: 10.3389/fcell.2021.783322] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 01/15/2023] Open
Abstract
Osteoporosis is a prevalent bone disease of the aging population, which is characterized by a decrease in bone mass because of the imbalance of bone metabolism. Although the prevention and treatment of osteoporosis have been explored by different researchers, the mechanisms underlying osteoporosis are not clear exactly. N6 methyladenosine (m6A) is a methylated adenosine nucleotide, which functions through its interaction with the proteins called “writers,” “readers” and “erasers.” The epigenetic regulation of m6A has been demonstrated to affect mRNA processing, nuclear export, translation, and splicing. At the cellular level, m6A modification has been known to affect cell proliferation, differentiation, and apoptosis of bone-related cells, such as bone marrow mesenchymal stem cells (BMSC), osteoblasts, and osteoclasts by regulating the expression of ALP, Runx2, Osterix, VEGF, and other related genes. Furthermore, PTH/Pth1r, PI3K‐Akt, Wnt/β‐Catenin, and other signaling pathways, which play important roles in the regulation of bone homeostasis, are also regulated by m6A. Thus, m6A modification may provide a new approach for osteoporosis treatment. The key roles of m6A modification in the regulation of bone health and osteoporosis are reviewed here in this article.
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Affiliation(s)
- Mei Huang
- School of Kinesiology, Shanghai University of Sport, Shanghai, China.,School of Sports Science, Wenzhou Medical University, Wenzhou, China
| | - Shaozhe Xu
- School of Sports Science, Wenzhou Medical University, Wenzhou, China
| | - Lifei Liu
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Miao Zhang
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Jianmin Guo
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Yu Yuan
- School of Kinesiology, Shanghai University of Sport, Shanghai, China.,School of Physical Education and Sports Science, South China Normal University, Guangzhou, China
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Xi Chen
- School of Sports Science, Wenzhou Medical University, Wenzhou, China
| | - Jun Zou
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
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19
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Norollahi SE, Foumani MG, Pishkhan MK, Shafaghi A, Alipour M, Jamkhaneh VB, Marghoob MN, Vahidi S. DNA Methylation Profiling of MYC, SMAD2/3 and DNMT3A in Colorectal Cancer. Oman Med J 2021; 36:e315. [PMID: 34804598 PMCID: PMC8581152 DOI: 10.5001/omj.2020.93] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022] Open
Abstract
Epigenetic modifications, particularly DNA methylation, is commonplace and a remarkable factor in carcinogenesis transformation. Conspicuously, previous findings have presented a cluster of irregular promoter methylation alterations related with silencing of tumor suppressor genes, little is accepted regarding their sequential DNA methylation (hypo and hyper) modifications during the cancer progression. In this way, fluctuations of DNA methylation of many genes, especially MYC, SMAD2/3, and DNMT3A, have an impressive central key role in many different cancers, including colorectal cancer (CRC). CRC is distinguished by DNA methylation, which is related to tumorigenesis and also genomic instability. Importantly, molecular heterogeneity between multiple adenomas in different patients with CRC may show diverse developmental phenotypes for these kinds of tumors. Conclusively, studying factors that are involved in CRC carcinogenesis, especially the alterations in epigenetic elements, such as DNA methylation besides RNA remodeling, and histone modification, acetylation and phosphorylation, can be influential to find new therapeutic and diagnostic biomarkers in this type of malignancy. In this account, we discuss and address the potential significant methylated modifications of these genes and their importance during the development of CRC carcinogenesis.
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Affiliation(s)
- Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | | | | | - Afshin Shafaghi
- Faculty of Medicine, Department of Gastroenterology, Guilan University of Medical Sciences, Rasht, Iran
| | - Majid Alipour
- Department of Biology, Islamic Azad University of Babol Branch, Babol, Iran
| | - Vida Baloui Jamkhaneh
- Department of Veterinary Medicine, Islamic Azad University of Babol Branch, Babol, Iran
| | - Mohammad Namayan Marghoob
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran.,Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sogand Vahidi
- Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
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20
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Sankarasubramanian S, Pfohl U, Regenbrecht CRA, Reinhard C, Wedeken L. Context Matters-Why We Need to Change From a One Size Fits all Approach to Made-to-Measure Therapies for Individual Patients With Pancreatic Cancer. Front Cell Dev Biol 2021; 9:760705. [PMID: 34805167 PMCID: PMC8599957 DOI: 10.3389/fcell.2021.760705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer is one of the deadliest cancers and remains a major unsolved health problem. While pancreatic ductal adenocarcinoma (PDAC) is associated with driver mutations in only four major genes (KRAS, TP53, SMAD4, and CDKN2A), every tumor differs in its molecular landscape, histology, and prognosis. It is crucial to understand and consider these differences to be able to tailor treatment regimens specific to the vulnerabilities of the individual tumor to enhance patient outcome. This review focuses on the heterogeneity of pancreatic tumor cells and how in addition to genetic alterations, the subsequent dysregulation of multiple signaling cascades at various levels, epigenetic and metabolic factors contribute to the oncogenesis of PDAC and compensate for each other in driving cancer progression if one is tackled by a therapeutic approach. This implicates that besides the need for new combinatorial therapies for PDAC, a personalized approach for treating this highly complex cancer is required. A strategy that combines both a target-based and phenotypic approach to identify an effective treatment, like Reverse Clinical Engineering® using patient-derived organoids, is discussed as a promising way forward in the field of personalized medicine to tackle this deadly disease.
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Affiliation(s)
| | - Ulrike Pfohl
- CELLphenomics GmbH, Berlin, Germany
- ASC Oncology GmbH, Berlin, Germany
- Institute for Molecular Bio Science, Goethe University Frankfurt Am Main, Frankfurt, Germany
| | - Christian R. A. Regenbrecht
- CELLphenomics GmbH, Berlin, Germany
- ASC Oncology GmbH, Berlin, Germany
- Institute for Pathology, Universitätsklinikum Göttingen, Göttingen, Germany
| | | | - Lena Wedeken
- CELLphenomics GmbH, Berlin, Germany
- ASC Oncology GmbH, Berlin, Germany
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21
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Yang X, Jin X, Xu R, Yu Z, An N. ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection. BMC Cancer 2021; 21:1043. [PMID: 34548052 PMCID: PMC8456567 DOI: 10.1186/s12885-021-08777-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Background Clinical options for lung squamous carcinoma (LUSC) are still quite limited. Carcinogenesis is an exceedingly complicated process involving multi-level dysregulations. Therefore, only looking into one layer of genomic dysregulation is far from sufficient. Methods We identified differentially expressed genes with consistent upstream genetic or epigenetic dysregulations in LUSC. Random walk was adopted to identify genes significantly affected by upstream abnormalities. Expression differentiation and survival analysis were conducted for these significant genes, respectively. Prognostic power of selected gene was also tested in 102 male LUSC samples through immunohistochemistry assay. Results Twelve genes were successfully retrieved from biological network, including ERα (ESRS1), EGFR, AR, ATXN1, MAPK3, PRKACA, PRKCA, SMAD4, TP53, TRAF2, UBQLN4 and YWHAG, which were closely related to sex hormone signaling pathway. Survival analysis in public datasets indicated ERα was significantly associated with a poor overall survival (OS) in male LUSC. The result of our immunohistochemistry assay also demonstrated this correlation using R0 resected tumors (n = 102, HR: 2.152, 95% CI: 1.089–4.255, p = 0.024). Although disease-free survival (DFS) difference was non-significant (n = 102, p = 0.12), the tendency of distinction was straight-forward. Cox analysis indicated ERα was the only independent prognostic factor for male patients’ OS after R0 resection (HR = 2.152, p = 0.037). Conclusion ERα was significantly related to a poor prognosis in LUSC, especially for male patients after radical surgery, confirmed by our immunohistochemistry data. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08777-6.
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Affiliation(s)
- Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Xiangfeng Jin
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Rongjian Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhuang Yu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China.
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22
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Wang P, Wang Z, Zhang M, Wu Q, Shi F, Yuan S. KIAA1429 and ALKBH5 Oppositely Influence Aortic Dissection Progression via Regulating the Maturation of Pri-miR-143-3p in an m6A-Dependent Manner. Front Cell Dev Biol 2021; 9:668377. [PMID: 34490238 PMCID: PMC8416753 DOI: 10.3389/fcell.2021.668377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/15/2021] [Indexed: 02/03/2023] Open
Abstract
Despite decades of study into aortic dissection (AD), a lethal cardiovascular emergency due to a tear in the aorta intima or bleeding within the aortic wall, leading to the separation of the different layers of it, the factors that influence its progression and the deeper regulatory mechanisms remain poorly understood. Nowadays, with the maturity of N6-methyladenosine (m6A) sequence technology, m6A modification, one type of RNA epigenesis, has gradually become a new research hotspot for epigenetic molecular regulation. Especially recently, increasing evidence has revealed that m6A modification functions as a pivotal post-transcriptional modification to influence the progression of multiple diseases. Based on these findings, it is reasonable to speculate that m6A modification may affect the onset and progression of AD. To explore the validity of our conjecture and to elucidate its underlying molecular mechanism of action, we conducted the present study. In this study, we found that KIAA1429 is downregulated while ALKBH5 is upregulated in aortic tissues from AD patients. Furthermore, gain- and loss-of-function studies showed that KIAA1429 and ALKBH5 can oppositely regulate HASMC proliferation, HAEC apoptosis, and AD progression in AngII-infused mice. Mechanistically, we demonstrated that KIAA1429/ALKBH5-mediated m6A modifications can regulate the processing of pri-miR-143-3p through interacting with the microprocessor protein DGCR8, thus indirectly regulating the downstream target gene of mature miR-143-3p, DDX6, to perform their biological functions in vitro and in vivo. Our findings have revealed a novel connection between m6A modification and AD progression and may provide a novel molecular basis for subsequent researchers to search for novel therapeutic approaches to improve the health of patients struggling with AD.
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Affiliation(s)
- Peng Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiwei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Zhang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qi Wu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Shi
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shun Yuan
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Surgery Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
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23
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A deep embedded refined clustering approach for breast cancer distinction based on DNA methylation. Neural Comput Appl 2021. [DOI: 10.1007/s00521-021-06357-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractEpigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In this work, we propose a deep embedded refined clustering method for breast cancer differentiation based on DNA methylation. In concrete, the deep learning system presented here uses the levels of CpG island methylation between 0 and 1. The proposed approach is composed of two main stages. The first stage consists in the dimensionality reduction of the methylation data based on an autoencoder. The second stage is a clustering algorithm based on the soft assignment of the latent space provided by the autoencoder. The whole method is optimized through a weighted loss function composed of two terms: reconstruction and classification terms. To the best of the authors’ knowledge, no previous studies have focused on the dimensionality reduction algorithms linked to classification trained end-to-end for DNA methylation analysis. The proposed method achieves an unsupervised clustering accuracy of 0.9927 and an error rate (%) of 0.73 on 137 breast tissue samples. After a second test of the deep-learning-based method using a different methylation database, an accuracy of 0.9343 and an error rate (%) of 6.57 on 45 breast tissue samples are obtained. Based on these results, the proposed algorithm outperforms other state-of-the-art methods evaluated under the same conditions for breast cancer classification based on DNA methylation data.
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24
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Identification of Prognostic Risk Model Based on DNA Methylation-Driven Genes in Esophageal Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6628391. [PMID: 34222478 PMCID: PMC8213479 DOI: 10.1155/2021/6628391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/15/2021] [Accepted: 05/08/2021] [Indexed: 01/10/2023]
Abstract
Background DNA methylation is an important part of epigenetic modification, and its abnormality is closely related to esophageal adenocarcinoma (EAC). This study was aimed at using bioinformatics analysis to identify methylation-driven genes (MDGs) in EAC patients and establish a risk model as a biological indicator of EAC prognosis. Method Downloaded EAC DNA methylation, transcriptome, and related clinical data from TCGA database. MethylMix was used to identify MDGs. R package clusterProfiler and the ConsensusPathDB online database were used to analyze the rich functions and pathways of these MDGs. The prognostic risk model was established by univariate Cox regression, Lasso regression, and multivariate Cox regression analysis. Finally each MDG in the model were carried out through the survival R package. Results A total of 273 MDGs were identified, which were enriched in transcriptional regulation and embryonic organ morphogenesis. Cox regression analysis established a risk model consisting of GPBAR1, OLFM4, FOXI2, and CASP10. In addition, further survival analysis revealed that OLFM4 and its two related sites were significantly related to the EAC patients' survival. Conclusion In summary, this study used bioinformatics methods to identify EAC MDGs and established a reliable risk prognosis model. It provided potential biomarkers for the early treatment and prognosis evaluation of EAC.
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25
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Gao Y, Wang X, Li S, Zhang Z, Li X, Lin F. Identification of a DNA Methylation-Based Prognostic Signature for Patients with Triple-Negative Breast Cancer. Med Sci Monit 2021; 27:e930025. [PMID: 34003815 PMCID: PMC8140526 DOI: 10.12659/msm.930025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is an important biological regulatory mechanism in malignant tumors. However, it remains underutilized for establishing prognostic models for triple-negative breast cancer (TNBC). MATERIAL AND METHODS Methylation data and expression data downloaded from The Cancer Genome Atlas (TCGA) were used to identify differentially methylated sites (DMSs). The prognosis-related DMSs were selected by univariate Cox regression analysis. Functional enrichment was analyzed using DAVID. A protein-protein interaction (PPI) network was constructed using STRING. Finally, a methylation-based prognostic signature was constructed using LASSO method and further validated in 2 validation cohorts. RESULTS Firstly, we identified 743 DMSs corresponding to 332 genes, including 357 hypermethylated sites and 386 hypomethylated sites. Furthermore, we selected 103 prognosis-related DMSs by univariate Cox regression. Using a LASSO algorithm, we established a 5-DMSs prognostic signature in TCGA-TNBC cohort, which could classify TNBC patients with significant survival difference (log-rank p=4.97E-03). Patients in the high-risk group had shorter overall survival than patients in the low-risk group. The excellent performance was validated in GSE78754 (HR=2.42, 95%CI: 1.27-4.59, log-rank P=0.0055). Moreover, for disease-free survival, the prognostic performance was verified in GSE141441 (HR=2.09, 95%CI: 1.28-3.44, log-rank P=0.0027). Multivariate Cox regression analysis indicated that the 5-DMSs signature could serve as an independent risk factor. CONCLUSIONS We constructed a 5-DMSs signature with excellent performance for the prediction of disease-free survival and overall survival, providing a guide for clinicians in directing personalized therapeutic regimen selection of TNBC patients.
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Affiliation(s)
- Yinqi Gao
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Xuelong Wang
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Shihui Li
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Zhiqiang Zhang
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Xuefei Li
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Fangcai Lin
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
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26
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Moderate DNA hypomethylation suppresses intestinal tumorigenesis by promoting caspase-3 expression and apoptosis. Oncogenesis 2021; 10:38. [PMID: 33947834 PMCID: PMC8096944 DOI: 10.1038/s41389-021-00328-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/18/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Global DNA hypomethylation is a most common epigenetic alteration in human neoplasia. However, accumulative evidence shows that global DNA hypomethylation impacts tumorigenesis in a tissue-specific manner, promoting tumorigenesis in some but suppressing tumorigenesis in others including colorectal cancer. The underlying mechanisms, especially how DNA hypomethylation suppresses tumorigenesis, remain largely unknown. Here, we investigate how DNA hypomethylation affects intestinal tumorigenesis by using an Uhrf1 tandem tudor domain knockin mutant mouse model (Uhrf1ki/ki) that exhibits a moderate ~10% reduction of global DNA methylation. We found that both chemical-induced colorectal carcinogenesis and Apc loss of heterozygosity (LOH)-induced intestinal tumorigenesis are substantially suppressed in the Uhrf1 mutant mice. Furthermore, unlike Dnmt1 hypomorphic mice in which DNA hypomethylation suppresses the incidence of macroscopic intestinal tumors but promotes the formation of microadenoma in ApcMin/+ background, Uhrf1ki/ki/ApcMin/+ mice have markedly reduced incidence of both microadenoma and macroadenoma. DNA hypomethylation does not appear to affect Apc LOH, activation of the Wnt or Hippo pathway, or tumor cell proliferation, but acts cooperatively with activated Wnt pathway to enhance the caspase-3 gene expression, activation, and apoptosis. Furthermore, increased caspase-3 expression correlates with DNA hypomethylation within the caspase-3 enhancer regions. Taken together, we present a new mouse model for investigating the role of and the molecular mechanisms by which DNA hypomethylation suppresses intestinal tumorigenesis. Our finding that a moderate DNA hypomethylation is sufficient to suppress intestinal tumorigenesis by promoting caspase-3 expression and apoptosis sheds new light on DNA-methylation inhibitor-based colorectal cancer therapeutics.
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27
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Corona A, Blobe GC. The role of the extracellular matrix protein TGFBI in cancer. Cell Signal 2021; 84:110028. [PMID: 33940163 DOI: 10.1016/j.cellsig.2021.110028] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 02/07/2023]
Abstract
The secreted extracellular protein, transforming growth factor beta induced (TGFBI or βIGH3), has roles in regulating numerous biological functions, including cell adhesion and bone formation, both during embryonic development and during the pathogenesis of human disease. TGFBI has been most studied in the context of hereditary corneal dystrophies, where mutations in TGFBI result in accumulation of TGFBI in the cornea. In cancer, early studies focused on TGFBI as a tumor suppressor, in part by promoting chemotherapy sensitivity. However, in established tumors, TGFBI largely has a role in promoting tumor progression, with elevated levels correlating to poorer clinical outcomes. As an important regulator of cancer progression, TGFBI expression and function is tightly regulated by numerous mechanisms including epigenetic silencing through promoter methylation and microRNAs. Mechanisms to target TGFBI have potential clinical utility in treating advanced cancers, while assessing TGFBI levels could be a biomarker for chemotherapy resistance and tumor progression.
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Affiliation(s)
- Armando Corona
- Department of Pharmacology and Cancer Biology, Duke University Medical center, USA
| | - Gerard C Blobe
- Department of Pharmacology and Cancer Biology, Duke University Medical center, USA; Department of Medicine, Duke University Medical Center, USA.
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28
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Sarno F, Benincasa G, List M, Barabasi AL, Baumbach J, Ciardiello F, Filetti S, Glass K, Loscalzo J, Marchese C, Maron BA, Paci P, Parini P, Petrillo E, Silverman EK, Verrienti A, Altucci L, Napoli C. Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside. Clin Epigenetics 2021; 13:66. [PMID: 33785068 PMCID: PMC8010949 DOI: 10.1186/s13148-021-01047-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Despite impressive efforts invested in epigenetic research in the last 50 years, clinical applications are still lacking. Only a few university hospital centers currently use epigenetic biomarkers at the bedside. Moreover, the overall concept of precision medicine is not widely recognized in routine medical practice and the reductionist approach remains predominant in treating patients affected by major diseases such as cancer and cardiovascular diseases. By its' very nature, epigenetics is integrative of genetic networks. The study of epigenetic biomarkers has led to the identification of numerous drugs with an increasingly significant role in clinical therapy especially of cancer patients. Here, we provide an overview of clinical epigenetics within the context of network analysis. We illustrate achievements to date and discuss how we can move from traditional medicine into the era of network medicine (NM), where pathway-informed molecular diagnostics will allow treatment selection following the paradigm of precision medicine.
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Affiliation(s)
- Federica Sarno
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Albert-Lazlo Barabasi
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg, Germany
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | | | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Bradley A Maron
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paola Paci
- Department of Computer, Control, and Management Engineering, Sapienza University, Rome, Italy
| | - Paolo Parini
- Department of Laboratory Medicine and Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Enrico Petrillo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy.
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Department of Internal Medicine and Specialistic Units, AOU, University of Campania "Luigi Vanvitelli", Naples, Italy
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Quan Y, Liang F, Deng SM, Zhu Y, Chen Y, Xiong J. Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype. Front Mol Biosci 2021; 8:597513. [PMID: 33842534 PMCID: PMC8034267 DOI: 10.3389/fmolb.2021.597513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various studies are often quite small, and it might be due to the fact that methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial to interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mine the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5 to 17%) between different datasets. In addition, the biological significance of phenotype-related genes identified by SIMPO algorithm is comparable to that of the traditional probe-based methods. Then, we selected two disease contents (e.g., insulin resistance and Parkinson's disease) to show that the biological efficiency of disease-related gene identification increased from 15.43 to 44.44% (p-value = 1.20e-28). In summary, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene's promoter region can reflect the essence of disease.
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Affiliation(s)
- Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Fengji Liang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Si-Min Deng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yuexing Zhu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
| | - Ying Chen
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Jianghui Xiong
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, Jiangsu, China
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30
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ALKBH5 Exacerbates Aortic Dissection by Promoting Inflammatory Response and Apoptosis of Aortic Smooth Muscle Cells via Regulating lnc-TMPO-AS1/EZH2/IRAK4 Signals in an m6A Modification Manner. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021. [DOI: 10.1155/2021/5513966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, mounting evidence indicates that N6-methyladenosine (m6A) modification functions as a pivotal posttranscriptional modification that regulates noncoding RNA biogenesis to influence the progression of multiple diseases. However, whether m6A modification is involved in aortic dissection (AD) development has never been reported. Meanwhile, numerous studies have shown that AngII-induced inflammatory damage and excessive apoptosis of human aortic smooth muscle cells (HASMCs) are the crucial pathological features of AD development. Therefore, in this study, we intended to explore whether m6A modification can regulate AD progression by influencing the damage effects of AngII on HASMCs and elucidate the underlying mechanisms. Firstly, we screened and confirmed the high expression of alkylation repair homolog protein 5 (ALKBH5), a key m6A demethylase, in aortic tissues from AD patients, indicating that m6A modification may indeed be involved in AD progression. Subsequently, we demonstrated that ALKBH5 can exacerbate the AngII-induced HASMC inflammatory injury as well as apoptosis and shorten the survival time of AngII-infused mice. Mechanistically, we revealed that lncRNA TMPO-AS1 is a downstream target for ALKBH5 to affect AD progression in vitro and vivo. Meanwhile, we confirmed that ALKBH5-mediated m6A demethylation downregulates lnc-TMPO-AS1 by decreasing the stability of its nascent. Further, we demonstrated that lnc-TMPO-AS1 exhibits its functions in HASMCs, at least partly, through downregulating IRAK4 at the epigenetic level by combining with EZH2. Finally, the direct positive correlation between ALKBH5 and IRAK4 in terms of the expression level and biological function was confirmed, which further enforced the preciseness and correctness of our findings. In conclusion, our study demonstrated that ALKBH5 aggravates AD by promoting inflammatory response and apoptosis of HASMCs via regulating lnc-TMPO-AS1/EZH2/IRAK4 signals in an m6A modification manner and may provide a novel molecular basis for subsequent researchers to searching for novel therapeutic approaches to improve the health of patients fighting AD and other cardiovascular diseases.
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31
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Sumei S, Xiangyun K, Fenrong C, Xueguang S, Sijun H, Bin B, Xiaolei S, Yongjiu T, Kaichun W, Qingchuan Z, Yongzhan N, Bin X. Hypermethylation of DHRS3 as a Novel Tumor Suppressor Involved in Tumor Growth and Prognosis in Gastric Cancer. Front Cell Dev Biol 2021; 9:624871. [PMID: 33553182 PMCID: PMC7859350 DOI: 10.3389/fcell.2021.624871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background/Aims The role of DHRS3 in human cancer remains unclear. Our study explored the role of DHRS3 in gastric cancer (GC) and its clinicopathological significance and associated mechanisms. Materials Bisulfite-assisted genomic sequencing PCR and a Mass-Array system were used to evaluate and quantify the methylation levels of the promoter. The expression levels and biological function of DHRS3 was examined by both in vitro and in vivo assays. A two-way hierarchical cluster analysis was used to classify the methylation profiles, and the correlation between the methylation status of the DHRS3 promoter and the clinicopathological characteristics of GC were then assessed. Results The DHRS3 promoter was hypermethylated in GC samples, while the mRNA and protein levels of DHRS3 were significantly downregulated. Ectopic expression of DHRS3 in GC cells inhibited cell proliferation and migration in vitro, decreased tumor growth in vivo. DHRS3 methylation was correlated with histological type and poor differentiation of tumors. GC patients with high degrees of CpG 9.10 methylation had shorter survival times than those with lower methylation. Conclusion DHRS3 was hypermethylated and downregulated in GC patients. Reduced expression of DHRS3 is implicated in gastric carcinogenesis, which suggests DHRS3 is a tumor suppressor.
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Affiliation(s)
- Sha Sumei
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Kong Xiangyun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Xi'an No.1 Hospital, Xi'an, China
| | - Chen Fenrong
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Sun Xueguang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Hu Sijun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Bai Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Shi Xiaolei
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Dongfang Hospital of Xiamen University, Fuzhou, China
| | - Tu Yongjiu
- The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
| | - Wu Kaichun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Zhao Qingchuan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Nie Yongzhan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Xu Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
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Wei B, Wang C, Teng T, Guo P, Chen M, Xia F, Liu H, Xie J, Feng J, Huang H. Chemotherapeutic efficacy of cucurmosin for pancreatic cancer as an alternative of gemcitabine: a comparative metabolomic study. Gland Surg 2020; 9:1428-1442. [PMID: 33224818 DOI: 10.21037/gs-20-202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background As the preferred drug for single chemotherapeutic application in pancreatic cancer, gemcitabine often demonstrated low sensitivity and strong chemotherapy resistance in patients. Therefore, the search for other drugs with high efficiency and low side effects has become of high importance. The aim of this study was to assess the therapeutic effects of cucurmosin on pancreatic cancer as an alternative of gemcitabine and explore its underlying biochemical mechanism. Methods The subcutaneous xenograft mice with pancreatic cancer were treated by high- and low-dose cucurmosin and gemcitabine, respectively. A comparative metabolomic analysis was performed on the serum samples from the different groups by 1H nuclear magnetic resonance (NMR) techniques and then subjected to univariate and multivariate statistical analysis. Results Cucurmosin demonstrated a dose-dependent inhibition to the pancreatic tumors. High-dose cucurmosin provided similar chemotherapeutic efficacy with gemcitabine by positively regulating pyruvate metabolism, glycolysis or gluconeogenesis, and cysteine and methionine metabolism. Inactivating GFR signaling pathway and further inducing apoptosis of tumor cells are the important mechanism of anti-tumor function of cucurmosin. Conclusions Cucurmosin is a promising chemotherapeutic drug for pancreatic cancer. However, the dose selection and surface modification should be optimized according to the stage of pancreatic cancer, and an expanded study in both laboratory and clinical regimes needs to be performed.
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Affiliation(s)
- Binbin Wei
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Congfei Wang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Tianhong Teng
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Pengfei Guo
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Minghuang Chen
- State Structural Chemistry Key Laboratory of Fujian Institute of Research on Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Feng Xia
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Huili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Jieming Xie
- Department of Pharmacology, Fujian Medical University, Fuzhou, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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Esteve M. Mechanisms Underlying Biological Effects of Cruciferous Glucosinolate-Derived Isothiocyanates/Indoles: A Focus on Metabolic Syndrome. Front Nutr 2020; 7:111. [PMID: 32984393 PMCID: PMC7492599 DOI: 10.3389/fnut.2020.00111] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
An inverse correlation between vegetable consumption and the incidence of cancer has long been described. This protective effect is stronger when cruciferous vegetables are specifically consumed. The beneficial properties of vegetables are attributed to their bioactive components like fiber, antioxidants vitamins, antioxidants, minerals, and phenolic compounds. Cruciferous vegetables contain all these molecules; however, what makes them different are their sulfurous components, called glucosinolates, responsible for their special smell and taste. Glucosinolates are inactive biologically in the organism but are hydrolyzed by the enzyme myrosinase released as a result of chewing, leading to the formation of active derivatives such as isothiocyanates and indoles. A considerable number of in vitro and in vivo studies have reported that isothiocyanates and indoles elicit chemopreventive potency through multiple mechanisms that include modulation of phases I and II detoxification pathway enzymes, regulation of cell cycle arrest, and control of cell growth, induction of apoptosis, antioxidant activity, anti-angiogenic effects, and epigenetic regulation. Nuclear erythroid 2-related factor 2 (Nrf2) and Nuclear factor-κB (NF-κB) are key and central regulators in all these processes with a main role in oxidative stress and inflammation control. It has been described that isothiocyanates and indoles regulate their activity directly and indirectly. Today, the metabolic syndrome (central obesity, insulin resistance, hyperlipidemia, and hypertension) is responsible for a majority of deaths worldwide. All components of metabolic syndrome are characterized by chronic inflammation with deregulation of the PI3K/AKT/mTOR, MAPK/EKR/JNK, Nrf2, and NF-κB signaling pathways. The effects of GLSs derivatives controlling these pathways have been widely described in relation to cancer. Changes in food consumption patterns observed in the last decades to higher consumption of ultra-processed foods, with elevation in simple sugar and saturated fat contents and lower consumption of vegetables and fruits have been directly correlated with metabolic syndrome prevalence. In this review, it is summarized the knowledge regarding the mechanisms by which cruciferous glucosinolate derivatives (isothiocyanates and indoles) directly and indirectly regulate these pathways. However, the review places a special focus on the knowledge of the effects of glucosinolates derivatives in metabolic syndrome, since this has not been reviewed before.
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Affiliation(s)
- Montserrat Esteve
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
- Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
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An N, Yu Z, He XJ, Zhao YY, Yu L, Zhang YC, Lu HJ, Yang X. Promoter Methylation of DNA Repair Genes Predicts Disease-free Survival of Gastric Adenocarcinoma after Adjuvant Radiotherapy. Mol Ther Oncolytics 2020; 18:109-117. [PMID: 32671186 PMCID: PMC7334297 DOI: 10.1016/j.omto.2020.06.006] [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: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
The relentless debate on postoperative adjuvant radiotherapy in gastric adenocarcinoma (GA) has been lasting for decades. In this study, a new biomarker, named promoter methylation burden of DNA repair genes (RPMB), was established to identify the subgroup of patients who might benefit from adjuvant radiotherapy. Methylation profiles of 397 GA tumor samples were downloaded from The Cancer Genome Atlas (TCGA). RPMB for a patient was defined as the ratio of methylated DNA repair genes to the number of all DNA repair genes. Subgroup analyses in term of overall survival (OS) and disease-free survival (DFS) indicated that most of the subgroups favored the high-RMPB group. Kaplan-Meier analysis showed that overall the patients with high RPMB after R0 resection had a significantly better clinical outcome regarding DFS (hazard ratio [HR] = 0.013, p = 0.042). Additionally, high-RPMB patients, who underwent adjuvant radiotherapy with both ≥T2 tumor and positive lymph nodes, showed superior DFS in comparison with the low-RPMB group (HR = 5.35 × 10−10, n = 26, p = 0.010). RPMB might be considered as a promising biomarker for decision-making with regard to postoperative adjuvant radiotherapy for GA patients.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Zhuang Yu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Xin-Jia He
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Yuan-Yuan Zhao
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Li Yu
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Yong-Chun Zhang
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Yongchun Zhang, Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
| | - Hai-Jun Lu
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Haijun Lu, Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Xue Yang, Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
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Peng Y, Shui L, Xie J, Liu S. Development and validation of a novel 15-CpG-based signature for predicting prognosis in triple-negative breast cancer. J Cell Mol Med 2020; 24:9378-9387. [PMID: 32649035 PMCID: PMC7417707 DOI: 10.1111/jcmm.15588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 02/05/2023] Open
Abstract
DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple‐negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15‐CpG‐based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15‐CpG‐based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG‐based signature and TNM stage was generated to predict the 1‐, 3‐ and 5‐year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.
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Affiliation(s)
- Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Shui
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Xie
- Department of General Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Shengchun Liu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Yan YL, Huang ZN, Zhu Z, Cui YY, Li MQ, Huang RM, Yan J, Shen B. Downregulation of TET1 Promotes Bladder Cancer Cell Proliferation and Invasion by Reducing DNA Hydroxymethylation of AJAP1. Front Oncol 2020; 10:667. [PMID: 32528872 PMCID: PMC7253684 DOI: 10.3389/fonc.2020.00667] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Ten-eleven translocation 1 (TET1) is a member of methylcytosine dioxygenase, which catalyzes 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5 hmC) to promote the demethylation process. The dysregulated TET1 protein and 5 hmC level were reported to either suppress or promote carcinogenesis in a cancer type-dependent manner. Currently, the role of TET1 in the development of urinary bladder cancer (UBC) and its underlying molecular mechanisms remain unclear. Herein, we found that TET1 expression was downregulated in UBC specimens compared with normal urothelium and was inversely related to tumor stage and grade and overall survival, suggesting its negative association with UBC progression. TET1 silencing in UBC cells increased cell proliferation and invasiveness while the ectopic expression of wild-type TET1-CD, but not its enzymatic inactive mutant, reversed these effects and suppressed tumorigenicity in vivo. In addition, as a direct regulator of TET1 activity, vitamin C treatment increased 5 hmC level and inhibited the anchorage-independent growth and tumorigenicity of UBC cells. Furthermore, we found that TET1 maintained the hypomethylation in the promoter of the AJAP1 gene, which codes for adherens junction-associated protein 1. The downregulation of AJAP1 reversed TET1-CD-induced nuclear translocation of β-catenin, thus inhibiting the expression of its downstream genes. In human UBC specimens, AJAP1 is frequently downregulated and positively associated with TET1. Notably, low expression levels of both TET1 and AJAP1 predict poor prognosis in UBC patients. In conclusion, we found that the frequently downregulated TET1 level reduces the hydroxymethylation of AJAP1 promoter and subsequently activates β-catenin signaling to promote UBC development. The downregulation of both TET1 and AJAP1 might be a promising prognostic biomarker for UBC patients.
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Affiliation(s)
- Yi-Lin Yan
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zheng-Nan Huang
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhen Zhu
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Yang-Yan Cui
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Mei-Qian Li
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Rui-Min Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Yan
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Bing Shen
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Yang F, Liu D, Deng Y, Wang J, Mei S, Ge S, Li H, Zhang C, Zhang T. Frequent promoter methylation of HOXD10 in endometrial carcinoma and its pathological significance. Oncol Lett 2020; 19:3602-3608. [PMID: 32269635 DOI: 10.3892/ol.2020.11467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/02/2020] [Indexed: 02/07/2023] Open
Abstract
Homeobox D 10 (HOXD10) is important in cell differentiation and morphogenesis and serves as a tumor suppressor gene (TSG) in a number of malignancies. The present study investigated its promoter methylation status and association with the clinicopathological features of endometrial cancer (EC), and measured HOXD10 protein expression levels. EC samples (n=62), including 50 endometroid adenocarcinoma (EA) and 12 mucinous endometrial carcinoma samples (EC) and 70 non-cancerous samples were collected. All samples were evaluated for the methylation status of several TSGs, including HOXD10, using methylation-specific PCR. HOXD10 expression level was evaluated using immunohistochemistry. 5-Aza-2-deoxycytidine treatment was performed in the EC cell line Ishikawa to observe the change in HOXD10 expression levels. HOXD10 promoter methylation was more frequent in cancer samples (P<0.001). Downregulation of HOXD10 in EC samples was confirmed at the protein level using immunohistochemistry (P<0.001) and immunohistochemical staining was negatively associated with methylation status (P<0.05). Less HOXD10 protein was expressed in MEC compared with EA samples (P<0.001). The HOXD10 promoter was hypermethylated in both EA and MEC, causing decreased HOXD10 protein expression levels in EC cells. HOXD10 expression levels were partially reversed by 5-Aza-2-deoxycytidine treatment. The results of the present study demonstrated that epigenetic silencing of HOXD10 putatively contributed to the tumorigenesis of EA. Although there was no significant difference in HOXD10 methylation between EA and MEC, HOXD10 protein expression levels differed between these two diseases, indicating that it may be a useful protein biomarker for distinguishing between these two lesions.
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Affiliation(s)
- Fan Yang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China.,Department of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Dongchen Liu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Yupeng Deng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Jun Wang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Shuyu Mei
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Shuang Ge
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Hailing Li
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Tingguo Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
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38
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Bow YD, Wang YY, Chen YK, Su CW, Hsu CW, Xiao LY, Yuan SS, Li RN. Silencing of FOXA2 decreases E-cadherin expression and is associated with lymph node metastasis in oral cancer. Oral Dis 2020; 26:756-765. [PMID: 31957176 DOI: 10.1111/odi.13282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/02/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVES FOXA2 gene methylation links to the progression of cancers, but has not been documented in oral cancer. Herein, we explore the role of FOXA2 in the migration of oral cancer cells. MATERIAL AND METHODS Methylation-specific PCR was applied for gene methylation. Wound healing and transwell experiments were tested for cell migration. FOXA2 expression in oral cancer tissues was addressed by immunohistochemistry, followed by statistical analysis of its association with clinical manifestations and patient survival. RESULTS FOXA2 bound to the promoter of CDH1 and enhanced the expression of its gene product E-cadherin, and decreased the cancer cell migration activity. High FOXA2 expression in oral cancer tissues was associated with high E-cadherin expression, decreased lymph node metastasis, and increased patient survival. CONCLUSION FOXA2-E-cadherin link is involved in regulation of oral cancer cell metastasis and provides a new insight for the tumor suppressor activity of FOXA2 in oral cancer.
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Affiliation(s)
- Yung-Ding Bow
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Yun Wang
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuk-Kwan Chen
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Oral Pathology & Maxillofacial Radiology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Oral & Maxillofacial Imaging Center, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chang-Wei Su
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Oral and Maxillofacial Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Wei Hsu
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Oral and Maxillofacial Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ling-Yi Xiao
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shyng-Shiou Yuan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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39
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Maumy L, Harrissart G, Dewaele P, Aljaber A, Bonneau C, Rouzier R, Eliès A. Impact des régimes alimentaires sur la mortalité et le risque de récidive de cancer du sein : revue de la littérature. Bull Cancer 2020; 107:61-71. [DOI: 10.1016/j.bulcan.2019.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 01/14/2023]
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40
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Dan H, Zhang S, Zhou Y, Guan Q. DNA Methyltransferase Inhibitors: Catalysts For Antitumour Immune Responses. Onco Targets Ther 2019; 12:10903-10916. [PMID: 31849494 PMCID: PMC6913319 DOI: 10.2147/ott.s217767] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is a kind of heritable change that involves the unaltered DNA sequence and can have effects on gene expression. The regulatory mechanism mainly includes DNA methylation, histone modification and non-coding RNA regulation. DNA methylation is currently the most studied aspect of epigenetics. It is widely present in eukaryotic cells and is the most important epigenetic mark in the regulation of gene expression in the cell. DNA methyltransferase inhibitors (DNMTi) have been increasingly recognized in the field of cancer immunotherapy, have been approved for the treatment of acute myeloid leukaemia (AML) and are widely being used in clinical trials of cancer immunotherapies. DNMTi promote the reactivation of tumour suppressor genes, enhance tumour immunogenicity, and stimulate a variety of immune cells to secrete cytokines that exert cytotoxic effects, promote tumour cell death, including macrophages, natural killer (NK) cells and CD8+ T cells, and upregulate major histocompatibility complex (MHC) class I expression levels. Here, we mainly summarize the epigenetics related to DNMTi and their regulation of the antitumour immune response and DNMTi combined with immuno-therapeutics or histone deacetylase inhibitors to demonstrate the great development potential and clinical application value of DNMTi.
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Affiliation(s)
- Huimin Dan
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Shanshan Zhang
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Yongning Zhou
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Quanlin Guan
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
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41
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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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Arora I, Sharma M, Tollefsbol TO. Combinatorial Epigenetics Impact of Polyphenols and Phytochemicals in Cancer Prevention and Therapy. Int J Mol Sci 2019; 20:ijms20184567. [PMID: 31540128 PMCID: PMC6769666 DOI: 10.3390/ijms20184567] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
Polyphenols are potent micronutrients that can be found in large quantities in various food sources and spices. These compounds, also known as phenolics due to their phenolic structure, play a vital nutrient-based role in the prevention of various diseases such as diabetes, cardiovascular diseases, neurodegenerative diseases, liver disease, and cancers. However, the function of polyphenols in disease prevention and therapy depends on their dietary consumption and biological properties. According to American Cancer Society statistics, there will be an expected rise of 23.6 million new cancer cases by 2030. Due to the severity of the increased risk, it is important to evaluate various preventive measures associated with cancer. Relatively recently, numerous studies have indicated that various dietary polyphenols and phytochemicals possess properties of modifying epigenetic mechanisms that modulate gene expression resulting in regulation of cancer. These polyphenols and phytochemicals, when administrated in a dose-dependent and combinatorial-based manner, can have an enhanced effect on epigenetic changes, which play a crucial role in cancer prevention and therapy. Hence, this review will focus on the mechanisms of combined polyphenols and phytochemicals that can impact various epigenetic modifications such as DNA methylation and histone modifications as well as regulation of non-coding miRNAs expression for treatment and prevention of various types of cancer.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Manvi Sharma
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA.
- Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA.
- Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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Liu L, Liu X, Dong Z, Li J, Yu Y, Chen X, Ren F, Cui G, Sun R. N6-methyladenosine-related Genomic Targets are Altered in Breast Cancer Tissue and Associated with Poor Survival. J Cancer 2019; 10:5447-5459. [PMID: 31632489 PMCID: PMC6775703 DOI: 10.7150/jca.35053] [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: 03/19/2019] [Accepted: 08/12/2019] [Indexed: 12/28/2022] Open
Abstract
Purpose: The ectopic expression of N6-methyladenosine (m6A) associated genes is a common feature of multiple tumors. However, little is known about the expression status and the prognostic value of these genes in human breast cancer (BRC). Herein, we conducted a comprehensive analysis to identify the expression profiling and clinical significance of m6A-related genomic targets in BRC. Materials and Methods: The expression data including 1109 BRC tissues and 113 normal breast tissues were obtained from The Cancer Genome Atlas (TCGA) database to evaluate the mRNA expression levels of m6A-related genomic targets. In addition, 6 independent BRCA cohorts retrieved from the Gene Expression Omnibus (GEO) database were enrolled to further ascertain the expression profiling of m6A-related genomic targets. Meanwhile, the immunohistochemical (IHC) staining data from BRC tissue microarray (TMA) cohort and the Human Protein Atlas (HPA) database were used to evaluate the proteomic expression of m6A-related genomic targets. Immunofluorescence (IF) analysis was performed to validate the subcellular location of m6A-related genomic targets. Moreover, the prognostic value of m6A-related genomic targets in BRC was analyzed by Kaplan-Meier analysis and Cox regression models. Results: m6A-related genomic targets were differentially expressed in BRC tissues. TMA IHC staining showed that most of the m6A-related genomic targets were significantly altered at the protein level (either upregulated or downregulated), consistent with their changes in the genomic profile. IF analysis showed the subcellular location of m6A-related genomic targets in BRC cell lines. Furthermore, we demonstrated that overexpression of YTHDF1 (P=0.049), YTHDF3 (P<0.001) and KIAA1429 (P=0.032) predicted poor prognosis in terms of overall survival (OS). Upregulation of YTHDF3 was an independent prognostic factor for OS in patients with BRC (P=0.036). Conclusion: m6A-related genomic targets are significantly altered in BRC and predict poor prognosis. These m6A-related genomic targets could serve as novel prognostic biomarkers for BRC.
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Affiliation(s)
- Liwen Liu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Liu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zihui Dong
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jianhao Li
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yan Yu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaolong Chen
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Fang Ren
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Guangying Cui
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ranran Sun
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,National Engineering Laboratory for Internet Medical System and Application, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
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Norollahi SE, Alipour M, Rashidy-Pour A, Samadani AA, Larijani LV. Regulatory Fluctuation of WNT16 Gene Expression Is Associated with Human Gastric Adenocarcinoma. J Gastrointest Cancer 2019; 50:42-47. [PMID: 29110228 DOI: 10.1007/s12029-017-0022-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Gastric cancer is one of the most serious and lethal kinds of cancer in the world. It is a multi-step, multi-factor, and elaborated process that is associated to gene abnormal expression. This study intended to investigate the WNT16 gene's expression in human gastric tumor and the margin tissues of the stomach (normal tissues). METHODS Correspondingly, 40 samples (20 tumoral tissues and 20 non tumoral or margins tissues) were investigated in Imam Khomeini Hospital in Sari City, Mazandaran Province, Iran. In this way, real-time PCR, Taqman assay was employed to evaluate the upregulation and downregulation of this gene in both tissues in triplicate form. The GAPDH gene was selected as housekeeping gene. RESULTS Conspicuously, the results have shown a remarkable modification in tumoral tissues, and the gene expression increased significantly in tumoral tissue. CONCLUSIONS Conclusively, the upregulation of WNTt16 gene expression in tumoral tissues was impressive and the P value was 0.005 and the SE range was 0.064-142.154.
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Affiliation(s)
- Seyedeh Elham Norollahi
- Faculty of Medicine, Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Majid Alipour
- Department of Biology, Islamic Azad University of Babol, Babol, Iran
| | - Ali Rashidy-Pour
- Faculty of Medicine, Research Center of Physiology, Semnan University of Medical Sciences, Semnan, Iran.,Faculty of Medicine, Department of Physiology, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Samadani
- Faculty of Medicine, Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran. .,Faculty of Medicine, Research Center of Physiology, Semnan University of Medical Sciences, Semnan, Iran.
| | - Laleh Vahedi Larijani
- Faculty of Medicine, Department of Pathology, Mazandaran University of Medical Sciences, Sari, Iran
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Han J, Wang JZ, Yang X, Yu H, Zhou R, Lu HC, Yuan WB, Lu JC, Zhou ZJ, Lu Q, Wei JF, Yang H. METTL3 promote tumor proliferation of bladder cancer by accelerating pri-miR221/222 maturation in m6A-dependent manner. Mol Cancer 2019; 18:110. [PMID: 31228940 PMCID: PMC6588935 DOI: 10.1186/s12943-019-1036-9] [Citation(s) in RCA: 456] [Impact Index Per Article: 91.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/06/2019] [Indexed: 01/17/2023] Open
Abstract
Background METTL3 is known to be involved in all stages in the life cycle of RNA. It affects the tumor formation by the regulation the m6A modification in the mRNAs of critical oncogenes or tumor suppressors. In bladder cancer, METTL3 could promote the bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner. Recently, METTL3 was also found to affect the m6A modification in non-coding RNAs including miRNAs, lincRNAs and circRNAs. However, whether this mechanism is related to the proliferation of tumors induced by METTL3 is not reported yet. Methods Quantitative real-time PCR, western blot and immunohistochemistry were used to detect the expression of METTL3 in bladder cancer. The survival analysis was adopted to explore the association between METTL3 expression and the prognosis of bladder cancer. Bladder cancer cells were stably transfected with lentivirus and cell proliferation and cell cycle, as well as tumorigenesis in nude mice were performed to assess the effect of METTL3 in bladder cancer. RNA immunoprecipitation (RIP), co-immunoprecipitations and RNA m6A dot blot assays were conducted to confirm that METTL3 interacted with the microprocessor protein DGCR8 and modulated the pri-miR221/222 process in an m6A-dependent manner. Luciferase reporter assay was employed to identify the direct binding sites of miR221/222 with PTEN. Colony formation assay and CCK8 assays were conducted to confirm the function of miR-221/222 in METTL3-induced cell growth in bladder cancer. Results We confirmed the oncogenic role of METTL3 in bladder cancer by accelerating the maturation of pri-miR221/222, resulting in the reduction of PTEN, which ultimately leads to the proliferation of bladder cancer. Moreover, we found that METTL3 was significantly increased in bladder cancer and correlated with poor prognosis of bladder cancer patients. Conclusions Our findings suggested that METTL3 may have an oncogenic role in bladder cancer through interacting with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner. To our knowledge, this is the first comprehensive study that METTL3 affected the tumor formation by the regulation the m6A modification in non-coding RNAs, which might provide fresh insights into bladder cancer therapy. Electronic supplementary material The online version of this article (10.1186/s12943-019-1036-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Jing-Zi Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Rui Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Hong-Cheng Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Wen-Bo Yuan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Jian-Chen Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Zi-Jian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
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Hao Y, Li D, Xu Y, Ouyang J, Wang Y, Zhang Y, Li B, Xie L, Qin G. Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data. BMC Bioinformatics 2019; 20:195. [PMID: 31074374 PMCID: PMC6509864 DOI: 10.1186/s12859-019-2734-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Increasing evidences suggest that the alterations in tumor metabolism, including metabolite abundance and accumulation of metabolic products, lead to local immunosuppression in the tumor microenvironment. An integrated analysis of lipid metabolism in cancers from different tissues using multiple omics data may provide novel insight into the understanding of tumorigenesis and progression. Results Through systematic analysis of the multiple omics data from TCGA, we found that the most-widely altered lipid metabolism pathways in pan-cancer are fatty acid metabolism, arachidonic acid metabolism, cholesterol metabolism and PPAR signaling. Gene expression profiles of fatty acid metabolism show commonalities across pan-cancer, while the alteration in cholesterol metabolism and arachidonic acid metabolism differ with tissue origin, suggesting tissue specific lipid metabolism features in different tumor types. An integrated analysis of gene expression, DNA methylation and mutations revealed factors that regulate gene expression, including the differentially methylated sites and mutations of the lipid genes, as well as mutation and differential expression of the up-stream transcription factors for the lipid metabolism pathways. Correlation analysis of the proportion of immune cells in the tumor microenvironment and the expression of lipid metabolism genes revealed immune-related differentially expressed lipid metabolic genes, indicating the potential crosstalk between lipid metabolism and immune response. Genes related to lipid metabolism and immune response that are associated with poor prognosis were discovered including HMGCS2, GPX2 and CD36, which may provide clues for tumor biomarkers or therapeutic targets. Conclusions Our study provides an integrated analysis of lipid metabolism in pan-cancer, highlights the perturbation of key metabolism processes in tumorigenesis and clarificates the regulation mechanism of abnormal lipid metabolism and effects of lipid metabolism on tumor immune microenvironment. This study also provides new clues for biomarkers or therapeutic targets of lipid metabolism in tumors. Electronic supplementary material The online version of this article (10.1186/s12859-019-2734-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Hao
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Daixi Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Yong Xu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Yongkun Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Yuqi Zhang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Baoguo Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China.
| | - Guangrong Qin
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China. .,Institute for Systems Biology, Seattle, WA, 98109, USA.
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Mitsiogianni M, Koutsidis G, Mavroudis N, Trafalis DT, Botaitis S, Franco R, Zoumpourlis V, Amery T, Galanis A, Pappa A, Panayiotidis MI. The Role of Isothiocyanates as Cancer Chemo-Preventive, Chemo-Therapeutic and Anti-Melanoma Agents. Antioxidants (Basel) 2019; 8:E106. [PMID: 31003534 PMCID: PMC6523696 DOI: 10.3390/antiox8040106] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/03/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022] Open
Abstract
Many studies have shown evidence in support of the beneficial effects of phytochemicals in preventing chronic diseases, including cancer. Among such phytochemicals, sulphur-containing compounds (e.g., isothiocyanates (ITCs)) have raised scientific interest by exerting unique chemo-preventive properties against cancer pathogenesis. ITCs are the major biologically active compounds capable of mediating the anticancer effect of cruciferous vegetables. Recently, many studies have shown that a higher intake of cruciferous vegetables is associated with reduced risk of developing various forms of cancers primarily due to a plurality of effects, including (i) metabolic activation and detoxification, (ii) inflammation, (iii) angiogenesis, (iv) metastasis and (v) regulation of the epigenetic machinery. In the context of human malignant melanoma, a number of studies suggest that ITCs can cause cell cycle growth arrest and also induce apoptosis in human malignant melanoma cells. On such basis, ITCs could serve as promising chemo-therapeutic agents that could be used in the clinical setting to potentiate the efficacy of existing therapies.
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Affiliation(s)
- Melina Mitsiogianni
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
| | - Georgios Koutsidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
| | - Nikos Mavroudis
- Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK.
| | - Dimitrios T Trafalis
- Laboratory of Pharmacology, Unit of Clinical Pharmacology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Sotiris Botaitis
- Second Department of Surgery, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Rodrigo Franco
- Redox Biology Centre, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Vasilis Zoumpourlis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Tom Amery
- The Watrercress Company / The Wasabi Company, Waddock, Dorchester, Dorset DT2 8QY, UK.
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Aglaia Pappa
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Mihalis I Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
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Anticancer Activities of Thymus vulgaris L. in Experimental Breast Carcinoma in Vivo and in Vitro. Int J Mol Sci 2019; 20:ijms20071749. [PMID: 30970626 PMCID: PMC6479806 DOI: 10.3390/ijms20071749] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/02/2019] [Accepted: 04/06/2019] [Indexed: 12/21/2022] Open
Abstract
Naturally-occurring mixtures of phytochemicals present in plant foods are proposed to possess tumor-suppressive activities. In this work, we aimed to evaluate the antitumor effects of Thymus vulgaris L. in in vivo and in vitro mammary carcinoma models. Dried T. vulgaris (as haulm) was continuously administered at two concentrations of 0.1% and 1% in the diet in a chemically-induced rat mammary carcinomas model and a syngeneic 4T1 mouse model. After autopsy, histopathological and molecular analyses of rodent mammary carcinomas were performed. In addition, in vitro evaluations using MCF-7 and MDA-MB-231 cells were carried out. In mice, T. vulgaris at both doses reduced the volume of 4T1 tumors by 85% (0.1%) and 84% (1%) compared to the control, respectively. Moreover, treated tumors showed a substantial decrease in necrosis/tumor area ratio and mitotic activity index. In the rat model, T. vulgaris (1%) decreased the tumor frequency by 53% compared to the control. Analysis of the mechanisms of anticancer action included well-described and validated diagnostic and prognostic markers that are used in both clinical approach and preclinical research. In this regard, the analyses of treated rat carcinoma cells showed a CD44 and ALDH1A1 expression decrease and Bax expression increase. Malondialdehyde (MDA) levels and VEGFR-2 expression were decreased in rat carcinomas in both the T. vulgaris treated groups. Regarding the evaluations of epigenetic changes in rat tumors, we found a decrease in the lysine methylation status of H3K4me3 in both treated groups (H3K9m3, H4K20m3, and H4K16ac were not changed); up-regulations of miR22, miR34a, and miR210 expressions (only at higher doses); and significant reductions in the methylation status of four gene promoters—ATM serin/threonine kinase, also known as the NPAT gene (ATM); Ras-association domain family 1, isoform A (RASSF1); phosphatase and tensin homolog (PTEN); and tissue inhibitor of metalloproteinase-3 (TIMP3) (the paired-like homeodomain transcription factor (PITX2) promoter was not changed). In vitro study revealed the antiproliferative and proapoptotic effects of essential oils of T. vulgaris in MCF-7 and MDA-MB-231 cells (analyses of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) (MTS); 5-bromo-20-deoxyuridine (BrdU); cell cycle; annexin V/PI; caspase-3/7; Bcl-2; PARP; and mitochondrial membrane potential). T. vulgaris L. demonstrated significant chemopreventive and therapeutic activities against experimental breast carcinoma.
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Namba S, Sato K, Kojima S, Ueno T, Yamamoto Y, Tanaka Y, Inoue S, Nagae G, Iinuma H, Hazama S, Ishihara S, Aburatani H, Mano H, Kawazu M. Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer. Cancer Sci 2019; 110:1096-1104. [PMID: 30637877 PMCID: PMC6398885 DOI: 10.1111/cas.13937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 12/11/2022] Open
Abstract
The silencing of tumor suppressor genes by promoter CpG island (CGI) methylation is an important cause of oncogenesis. Silencing of MLH1 and BRCA1, two examples of oncogenic events, results from promoter CGI methylation. Interestingly, both MLH1 and BRCA1 have a divergent promoter, from which another gene on the opposite strand is also transcribed. Although studies have shown that divergent transcription is an important factor in transcriptional regulation, little is known about its implication in aberrant promoter methylation in cancer. In this study, we analyzed the methylation status of CGI in divergent promoters using a recently enriched transcriptome database. We measured the extent of CGI methylation in 119 colorectal cancer (CRC) clinical samples (65 microsatellite instability high [MSI‐H] CRC with CGI methylator phenotype, 28 MSI‐H CRC without CGI methylator phenotype and 26 microsatellite stable CRC) and 21 normal colorectal tissues using Infinium MethylationEPIC BeadChip. We found that CGI within divergent promoters are less frequently methylated than CGI within unidirectional promoters in normal cells. In the genome of CRC cells, CGI within unidirectional promoters are more vulnerable to aberrant methylation than CGI within divergent promoters. In addition, we identified three DNA sequence motifs that correlate with methylated CGI. We also showed that methylated CGI are associated with genes whose expression is low in normal cells. Thus, we here provide fundamental observations regarding the methylation of divergent promoters that are essential for the understanding of carcinogenesis and development of cancer prevention strategies.
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Affiliation(s)
- Shinichi Namba
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hisae Iinuma
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Shoichi Hazama
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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50
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Curcumin suppresses wilms' tumor metastasis by inhibiting RECK methylation. Biomed Pharmacother 2019; 111:1204-1212. [DOI: 10.1016/j.biopha.2018.12.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
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