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Bu C, Wang Z, Lv X, Zhao Y. A dual-gene panel of two fragments of methylated IRF4 and one of ZEB2 in plasma cell-free DNA for gastric cancer detection. Epigenetics 2024; 19:2374988. [PMID: 39003776 PMCID: PMC11249030 DOI: 10.1080/15592294.2024.2374988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Early detection is crucial for increasing the survival rate of gastric cancer (GC). We aimed to identify a methylated cell-free DNA (cfDNA) marker panel for detecting GC. The differentially methylated CpGs (DMCs) were selected from datasets of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The selected DMCs were validated and further selected in tissue samples (40 gastric cancer and 36 healthy white blood cell samples) and in a quarter sample volume of plasma samples (37 gastric cancer, 12 benign gastric disease, and 43 healthy individuals). The marker combination selected was then evaluated in a normal sample volume of plasma samples (35 gastric cancer, 39 control diseases, and 40 healthy individuals) using real-time methylation-specific PCR (MSP). The analysis of the results compared methods based on 2-ΔΔCt values and Ct values. In the results, 30 DMCs were selected through bioinformatics methods, and then 5 were selected for biological validation. The marker combination of two fragments of IRF4 (IRF4-1 and IRF4-2) and one of ZEB2 was selected due to its good performance. The Ct-based method was selected for its good results and practical advantages. The assay, IRF4-1 and IRF4-2 in one fluorescence channel and ZEB2 in another, obtained 74.3% sensitivity for the GC group at any stage, at 92.4% specificity. In conclusion, the panel of IRF4 and ZEB2 in plasma cfDNA demonstrates good diagnostic performance and application potential in clinical settings.
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Affiliation(s)
- Chunxiao Bu
- Department of Magnetic Resonance Imaging,The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhilong Wang
- Henan Academy of Medical Sciences, Zhengzhou, Henan, China
| | - Xianping Lv
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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2
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Sha R, Zhang J, Meng F, Zhaori G. Gastric cancer metastasis-related NT5DC2 indicates unfavorable prognosis of patients. Medicine (Baltimore) 2023; 102:e35030. [PMID: 37800836 PMCID: PMC10553061 DOI: 10.1097/md.0000000000035030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE Approximately 80 to 90% of patients with gastric cancer (GC) eventually develop into metastatic GC nowadays,because GC is difficult to be diagnosed at an early stage. GC patients with metastases typically have a poor prognosis. It is necessary to explore a potential prognostic marker in metastatic GC. METHODS All GC data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The metastasis-related candidate gene and its role in GC were analyzed by comprehensive analysis. RESULTS Totally 1049 metastasis-related genes were identified in GC. Univariate Cox regression analysis screened the top 10 genes (PDHX, SLC43A1, CSAG2, NT5DC2, CSAG1, FMN1, MED1, HIVEP2, FNDC3A, and PPP1R2) that were closely correlated with prognosis of GC patients. Among which, NT5DC2 was screened as the target gene for subsequent study. The NT5DC2 expression were increased in primary GC and metastatic GC samples. Moreover, GC patients with high NT5DC2 expression exhibited shorter overall survival and post progression survival, and the NT5DC2 was metastatic GC patients' independent prognostic factor. Totally 29 pathways were activated in metastatic GC samples with high NT5DC2 expression. Four immune cells' infiltration were significantly different between NT5DC2 high and low expressed metastatic GC patients. NT5DC2 showed significantly negative correlations with 6 types of immune cells' critical marker genes and 5 types of immune cell infiltration. The 10 immune checkpoint expressions were decreased in high NTDC2 expression metastatic GC patients. CONCLUSIONS NT5DC2 plays a prognostic role in metastatic GC. GC patients with high NT5DC2 expression indicates unfavorable prognosis.
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Affiliation(s)
- Rula Sha
- Department of Internal Medicine-Oncology, Inner Mongolia Autonomous Region People’s Hospital, Hohhot, Inner Mongolia, P.R. China
| | - Jiaming Zhang
- Department of Internal Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, P.R. China
| | - Fanjie Meng
- Department of Internal Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, P.R. China
| | - Getu Zhaori
- Department of Abdominal Surgery, The Affiliated People’s Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, P.R. China
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3
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Kim JL, Kim SG, Natsagdorj E, Chung H, Cho SJ. Helicobacter pylori Eradication Can Reverse Rho GTPase Expression in Gastric Carcinogenesis. Gut Liver 2023; 17:741-752. [PMID: 36718103 PMCID: PMC10502497 DOI: 10.5009/gnl220301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/13/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023] Open
Abstract
Background/Aims Altered DNA methylation is a key mechanism of epigenetic modification in gastric cancer (GC). This study aimed to evaluate the changes in epigenetic and genetic expression of multiple Rho GTPases in Helicobacter pylori-related gastric carcinogenesis by comparing H. pylori-positive GCs and negative controls. Methods The messenger RNA expression and methylation of Rho GTPases (RhoA, Rac1, DOCK180, ELMO1, and CDC42) were evaluated in H. pylori-negative (control) human gastric tissues and H. pylori-positive GCs by using real-time reverse transcription-polymerase chain reaction and the quantitative MethyLight assay, respectively. Changes in expression and methylation levels of the genes were also compared between H. pylori-eradicated and -persistent GCs at 1-year follow-up. Results In GCs, the methylation and expression levels of DOCK180 and ELMO1 were higher than in controls, while RhoA and Rac1 had lower levels than controls. CDC42 had the same expression pattern as DOCK180 and ELMO1 without DNA methylation. Although methylation levels of DOCK180 and ELMO1 had no difference between H. pylori-eradicated and -persistent GCs at the index endoscopic resection, those of H. pylori-persistent GCs increased and H. pylori-eradicated GCs decreased for 1 year. The expression levels of DOCK180, ELMO1, and CDC42 in H. pylori-persistent GCs were higher than those in H. pylori-eradicated GCs over 1 year, unlike those of RhoA and Rac1. The methylation levels at index and the degrees of change over time of RhoA and Rac1 had no difference between H. pylori-persistent and -eradicated GCs. Conclusions Epigenetic alterations of DOCK180 and ELMO1 are involved in H. pylori-related gastric carcinogenesis. This epigenetic field could be improved by H. pylori eradication.
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Affiliation(s)
- Jue Lie Kim
- Department of Internal Medicine, Health Promotion Center, Seoul National University Hospital, Seoul, Korea
| | - Sang Gyun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Enerelt Natsagdorj
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunsoo Chung
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Soo-Jeong Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Shen X, Liu H, Zhou H, Cheng Z, Liu G, Huang C, Dou R, Liu F, You X. Galectin-1 promotes gastric cancer peritoneal metastasis through peritoneal fibrosis. BMC Cancer 2023; 23:559. [PMID: 37328752 DOI: 10.1186/s12885-023-11047-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Peritoneal metastasis is one of the main causes of death in patients with gastric cancer (GC). Galectin-1 regulates various undesirable biological behaviors in GC and may be key in GC peritoneal metastasis. METHODS In this study, we elucidated the regulatory role of galectin-1 in GC cell peritoneal metastasis. GC and peritoneal tissues underwent hematoxylin-eosin (HE), immunohistochemical (IHC), and Masson trichrome staining to analyze the difference in galectin-1 expression and peritoneal collagen deposition in different GC clinical stages. The regulatory role of galectin-1 in GC cell adhesion to mesenchymal cells and in collagen expression was determined using HMrSV5 human peritoneal mesothelial cells (HPMCs). Collagen and corresponding mRNA expression were detected with western blotting and reverse transcription PCR, respectively. The promoting effect of galectin-1 on GC peritoneal metastasis was verified in vivo. Collagen deposition and collagen I, collagen III, and fibronectin 1 (FN1) expression in the peritoneum of the animal models were detected by Masson trichrome and IHC staining. RESULTS Galectin-1 and collagen deposition in the peritoneal tissues was correlated with GC clinical staging and were positively correlated. Galectin-1 enhanced the ability of GC cells to adhere to the HMrSV5 cells by promoting collagen I, collagen III, and FN1 expression. The in vivo experiments confirmed that galectin-1 promoted GC peritoneal metastasis by promoting peritoneal collagen deposition. CONCLUSION Galectin-1-induced peritoneal fibrosis may create a favorable environment for GC cell peritoneal metastasis.
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Affiliation(s)
- Xianhe Shen
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Huilan Liu
- Oncology department, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Haihua Zhou
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Zhiyi Cheng
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Guiyuan Liu
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Chuanjiang Huang
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Rongrong Dou
- Department of the Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Fuxing Liu
- Department of the Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Xiaolan You
- Department of Gastrointestinal Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
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Li H, Zhao G, Guo Y, Fang Y, Wang K, Ma Y, Feng C, Zhou X, Chen Q, Liu X, Wang W, Xiong S, Chen G, Zheng M, Fei S. Feasibility and reproducibility of a plasma-based multiplex DNA methylation assay for early detection of gastric cancer. Pathol Res Pract 2022; 238:154086. [PMID: 36031696 DOI: 10.1016/j.prp.2022.154086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Gastric cancer (GC) is a leading cause of cancer death and an important barrier to increasing life expectancy in China. Early detection of GC can significantly reduce its mortality rate. METHODS A new plasma-based multiplex DNA methylation assay combining simultaneous detection of three biomarkers (KCNQ5, C9orf50 and CLIP4) and one control gene (ACTB) was developed. It was used to examine 12 paired tissue samples and a training cohort of 151 plasma samples. Its performance was subsequently confirmed in validation cohort 1 (n = 105) and validation cohort 2 (n = 139). RESULTS Three methylation markers showed significantly higher methylation levels in GC tissues than in paired adjacent tissues. The assay showed a sensitivity of 67.9 % with a specificity of 86.6 % for GC detection in the training cohort, and the AUC was 0.786 (95 % CI: 0.701-0.855). The methylation levels in GC patients were significantly higher than those in benign gastric tumors and in control group. Meanwhile, the assay achieved a sensitivity of 65.5 % with a specificity of 90.0 % in the validation cohort 1, and the AUC was 0.805 (95 % CI: 0.716-0.876). In the validation cohort 2, its sensitivity and specificity were 73.7 % and 84.1 %, respectively, and the AUC was 0.851 (95 % CI: 0.776-0.909). CONCLUSION The plasma-based multiplex DNA methylation assay was highly specific for GC early detection. It has the potential to become an alternative approach to improve diagnosis of GC in the clinics.
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Affiliation(s)
- Hui Li
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China; Department of Gastroenterology, The First People's Hospital of Xuzhou, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Guodong Zhao
- Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210009, China
| | - Yahui Guo
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Yu Fang
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Kai Wang
- Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Yong Ma
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Chenxi Feng
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Xilang Zhou
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Qi Chen
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Xin Liu
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
| | - Weifeng Wang
- Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Shangmin Xiong
- Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China
| | - Guangxia Chen
- Department of Gastroenterology, The First People's Hospital of Xuzhou, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu 221002, China.
| | - Minxue Zheng
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| | - Sujuan Fei
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China.
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Tocci S, Ibeawuchi SR, Das S, Sayed IM. Role of ELMO1 in inflammation and cancer-clinical implications. Cell Oncol (Dordr) 2022; 45:505-525. [PMID: 35668246 DOI: 10.1007/s13402-022-00680-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Engulfment and cell motility protein 1 (ELMO1) is a key protein for innate immunity since it is required for the clearance of apoptotic cells and pathogenic bacteria as well as for the control of inflammatory responses. ELMO1, through binding with Dock180 and activation of the Rac1 signaling pathway, plays a significant role in cellular shaping and motility. Rac-mediated actin cytoskeletal rearrangement is essential for bacterial phagocytosis, but also plays a crucial role in processes such as cancer cell invasion and metastasis. While the role of ELMO1 in bacterial infection and inflammatory responses is well established, its implication in cancer is not widely explored yet. Molecular changes or epigenetic alterations such as DNA methylation, which ultimately leads to alterations in gene expression and deregulation of cellular signaling, has been reported for ELMO1 in different cancer types. CONCLUSIONS In this review, we provide an updated and comprehensive summary of the roles of ELMO1 in infection, inflammatory diseases and cancer. We highlight the possible mechanisms regulated by ELMO1 that are relevant for cancer development and progression and provide insight into the possible use of ELMO1 as a diagnostic biomarker and therapeutic target.
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Affiliation(s)
- Stefania Tocci
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego, La Jolla, CA, USA. .,Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt.
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7
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Novel Biomarkers of Gastric Adenocarcinoma: Current Research and Future Perspectives. Cancers (Basel) 2021; 13:cancers13225660. [PMID: 34830815 PMCID: PMC8616337 DOI: 10.3390/cancers13225660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Gastric cancer is characterized by poor survival rates despite surgery and chemotherapy. Current research focuses on biomarkers to improve diagnosis and prognosis, and to enable targeted treatment strategies. The aim of our review was to give an overview over the wide range of novel biomarkers in gastric cancer. These biomarkers are targets of a specific treatment, such as antibodies against human epidermal growth factor receptor 2. Other promising biomarkers for targeted therapies that have shown relevance in clinical trials are vascular endothelial growth factor, programmed cell death protein 1, and Claudin 18.2. There is a vast number of biomarkers based on DNA, RNA, and protein expression, as well as detection of circulating tumor cells and the immune tumor microenvironment. Abstract Overall survival of gastric cancer remains low, as patients are often diagnosed with advanced stage disease. In this review, we give an overview of current research on biomarkers in gastric cancer and their implementation in treatment strategies. The HER2-targeting trastuzumab is the first molecular targeted agent approved for gastric cancer treatment. Other promising biomarkers for targeted therapies that have shown relevance in clinical trials are VEGF and Claudin 18.2. Expression of MET has been shown to be a negative prognostic factor in gastric cancer. Targeting the PD-1/PD-L1 pathway with immune checkpoint inhibitors has proven efficacy in advanced gastric cancer. Recent technology advances allow the detection of circulating tumor cells that may be used as diagnostic and prognostic indicators and for therapy monitoring in gastric cancer patients. Prognostic molecular subtypes of gastric cancer have been identified using genomic data. In addition, transcriptome profiling has allowed a comprehensive characterization of the immune and stromal microenvironment in gastric cancer and development of novel risk scores. These prognostic and predictive markers highlight the rapidly evolving field of research in gastric cancer, promising improved treatment stratification and identification of molecular targets for individualized treatment in gastric cancer.
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Garcia‐Pelaez J, Barbosa‐Matos R, Gullo I, Carneiro F, Oliveira C. Histological and mutational profile of diffuse gastric cancer: current knowledge and future challenges. Mol Oncol 2021; 15:2841-2867. [PMID: 33724653 PMCID: PMC8564639 DOI: 10.1002/1878-0261.12948] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 03/12/2021] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC) pathogenesis is complex and heterogeneous, reflecting morphological, molecular and genetic diversity. Diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC) are the major histological types. GC may be sporadic or hereditary; sporadic GC is related to environmental and genetic low-risk factors and hereditary GC is caused by inherited high-risk mutations, so far identified only for the diffuse histotype. DGC phenotypic heterogeneity challenges the current understanding of molecular mechanisms underlying carcinogenesis. The definition of a DGC-specific mutational profile remains controversial, possibly reflecting the heterogeneity of DGC-related histological subtypes [signet-ring cell carcinoma (SRCC) and poorly cohesive carcinoma not otherwise specified (PCC-NOS)]. Indeed, DGC and DGC-related subtypes may present specific mutational profiles underlying the particularly aggressive behaviour and dismal prognosis of DGC vs IGC and PCC-NOS vs SRCC. In this systematic review, we revised the histological presentations, molecular classifications and approved therapies for gastric cancer, with a focus on DGC. We then analysed results from the most relevant studies, reporting mutational analysis data specifying mutational frequencies, and their relationship with DGC and IGC histological types, and with specific DGC subtypes (SRCC and PCC-NOS). We aimed at identifying histology-associated mutational profiles with an emphasis in DGC and its subtypes (DGC vs IGC; sporadic vs hereditary DGC; and SRCC vs PCC-NOS). We further used these mutational profiles to identify the most commonly affected molecular pathways and biological functions, and explored the clinical trials directed specifically to patients with DGC. This systematic analysis is expected to expose a DGC-specific molecular profile and shed light into potential targets for therapeutic intervention, which are currently missing.
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Affiliation(s)
- José Garcia‐Pelaez
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do PortoPortugal
- IPATIMUP – Institute of Molecular Pathology and ImmunologyUniversity of PortoPortugal
- Doctoral Programme on BiomedicineFaculty of MedicineUniversity of PortoPortugal
| | - Rita Barbosa‐Matos
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do PortoPortugal
- IPATIMUP – Institute of Molecular Pathology and ImmunologyUniversity of PortoPortugal
- Doctoral Programme on Cellular and Molecular Biotechnology Applied to Health Sciences (BiotechHealth)ICBAS – Institute of Biomedical Sciences Abel SalazarUniversity of PortoPortugal
| | - Irene Gullo
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do PortoPortugal
- IPATIMUP – Institute of Molecular Pathology and ImmunologyUniversity of PortoPortugal
- Department of PathologyFMUP ‐ Faculty of Medicine of the University of PortoPortugal
- Department of PathologyCHUSJ – Centro Hospitalar Universitário São JoãoPortoPortugal
| | - Fátima Carneiro
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do PortoPortugal
- IPATIMUP – Institute of Molecular Pathology and ImmunologyUniversity of PortoPortugal
- Department of PathologyFMUP ‐ Faculty of Medicine of the University of PortoPortugal
- Department of PathologyCHUSJ – Centro Hospitalar Universitário São JoãoPortoPortugal
| | - Carla Oliveira
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do PortoPortugal
- IPATIMUP – Institute of Molecular Pathology and ImmunologyUniversity of PortoPortugal
- Department of PathologyFMUP ‐ Faculty of Medicine of the University of PortoPortugal
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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10
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Shetty NP, Prabhakaran M, Srivastava AK. Pleiotropic nature of curcumin in targeting multiple apoptotic-mediated factors and related strategies to treat gastric cancer: A review. Phytother Res 2021; 35:5397-5416. [PMID: 34028111 DOI: 10.1002/ptr.7158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/24/2022]
Abstract
Gastric cancer (GC) is one of the major reasons for cancer-associated death and exhibits the second-highest mortality rate worldwide. Several advanced approaches have been designed to treat GC; however, these strategies possess many innate complications. In view of this, the upcoming research relying on natural products could result in designing potential anticancer agents with fewer side effects. Curcumin, isolated from the rhizomes of Curcuma longa L. has several medicinal properties like antiinflammatory, antioxidant, antiapoptotic, antitumor, and antimetastatic. Such pleiotropic nature of curcumin impedes the invasion and proliferation of GC by targeting several oncogenic factors like p23, human epidermal factor receptor2 including Helicobacter pylori. The side effect of chemotherapy, that is, chemotherapeutic resistance and radiotherapy could be reduced combination therapy of curcumin. Moreover, the photodynamic therapy of curcumin destroys the cancer cells without affecting normal cells. However, further more potential studies are required to establish the potent efficacy of curcumin in the treatment of GC. The current review details the anticancer activities of curcumin and related strategies which could be employed to treat GC with additional focus on its inhibitory properties against viability, proliferation, and migration of GC cells through cell cycle arrest and stimulation by apoptosis-mediated factors.
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Affiliation(s)
- Nandini P Shetty
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Manoj Prabhakaran
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
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11
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Kang X, Li W, Liu W, Liang H, Deng J, Wong CC, Zhao S, Kang W, To KF, Chiu PWY, Wang G, Yu J, Ng EKW. LIMK1 promotes peritoneal metastasis of gastric cancer and is a therapeutic target. Oncogene 2021; 40:3422-3433. [PMID: 33883692 PMCID: PMC8116207 DOI: 10.1038/s41388-021-01656-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/06/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Peritoneal metastasis is a common form of metastasis among advanced gastric cancer patients. In this study, we reported the identification of LIM domain kinase 1 (LIMK1) as a promoter of gastric cancer peritoneal metastasis, and its potential to be a therapeutic target of dabrafenib (DAB). Using transcriptomic sequencing of paired gastric cancer peritoneal metastasis, primary tumors, and normal gastric tissues, we first unveiled that LIMK1 is selectively up-regulated in metastatic tumors. Increased LIMK1 in gastric cancer peritoneal metastasis was validated by immunohistochemistry analysis of an independent patient cohort. In vitro functional studies demonstrated that LIMK1 knockout or knockdown significantly inhibited cell migration and invasion of gastric cancer cells. LIMK1 knockout also abrogated peritoneal and liver metastases of gastric cancer cells in nude mice in vivo. Dabrafenib, a small molecule targeting LIMK1, was found to decrease cell migration and invasion of gastric cancer cells in vitro and abolish peritoneal and liver metastasis formation in vivo. Mechanistically, either LIMK1 knockout or Dabrafenib inhibited LIMK1 expression and phosphorylation of its downstream target cofilin. Taken together, our results demonstrated that LIMK1 functions as a metastasis promoter in gastric cancer by inhibiting LIMK1-p-cofilin and that Dabrafenib has the potential to serve as a novel treatment for gastric cancer peritoneal metastasis.
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Affiliation(s)
- Xi Kang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Surgery, Hebei Medical University 4th Hospital, Shijiazhuang, China
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Weixin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Han Liang
- Department of Gastroenterology, Tianjin Medical University Cancer Hospital, City Key Laboratory of Tianjin Cancer Center and National Clinical Research Center for Cancer, Tianjin, China
| | - Jingyu Deng
- Department of Gastroenterology, Tianjin Medical University Cancer Hospital, City Key Laboratory of Tianjin Cancer Center and National Clinical Research Center for Cancer, Tianjin, China
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sinan Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Endocrinology, Hebei Medical University 2nd Hospital, Shijiazhuang, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Philip Wai Yan Chiu
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Guiying Wang
- Department of Surgery, Hebei Medical University 4th Hospital, Shijiazhuang, China.
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Enders Kwok Wai Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
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12
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Smyth LJ, Kilner J, Nair V, Liu H, Brennan E, Kerr K, Sandholm N, Cole J, Dahlström E, Syreeni A, Salem RM, Nelson RG, Looker HC, Wooster C, Anderson K, McKay GJ, Kee F, Young I, Andrews D, Forsblom C, Hirschhorn JN, Godson C, Groop PH, Maxwell AP, Susztak K, Kretzler M, Florez JC, McKnight AJ. Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. Clin Epigenetics 2021; 13:99. [PMID: 33933144 PMCID: PMC8088646 DOI: 10.1186/s13148-021-01081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation. CONCLUSIONS Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - V Nair
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - H Liu
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Brennan
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - K Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R M Salem
- Department of Family Medicine and Public Health, UC San Diego, San Diego, CA, USA
| | - R G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - H C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - C Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - F Kee
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - I Young
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - D Andrews
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - C Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C Godson
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.,Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - K Susztak
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - M Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - J C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
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13
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Cao Y, Zhao G, Cao Y, Chen Z, Liu X, Yuan M, Yang J, Wang X, Ma Y, Liu Z, Xiong S, Zheng M, Fei S. Feasibility of Methylated CLIP4 in Stool for Early Detection of Colorectal Cancer: A Training Study in Chinese Population. Front Oncol 2021; 11:647066. [PMID: 33968748 PMCID: PMC8100593 DOI: 10.3389/fonc.2021.647066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Background Early detection of colorectal cancer (CRC) and precancerous lesion is vitally important for mitigating CRC morbidity and mortality. Aberrant DNA methylations in certain promoter regions have been identified to be closely associated with CRC development and progression, suggesting their potential as diagnostic biomarkers for early detection. In this study, we evaluated the performance of methylated CLIP4 in stool specimens as a potential biomarker for CRC detection. Methods A total of 321 subjects out of 365 enrolled participants were included in the final analysis, including 154 CRC patients, 23 advanced adenoma (AA) patients, 49 small polyp (SP) patients, and 95 healthy controls. CLIP4 methylation level was examined by qPCR with bisulfite converted DNA purified from approximately 5 g stool specimen. Results Methylated CLIP4 test showed high sensitivities of 78.3% (95% CI: 55.8%-91.7%) and 90.3% (95% CI: 84.2%-94.3%) for detecting AA and CRC, respectively, with a specificity of 88.4% (95% CI: 79.8%-93.8%). CLIP4 methylation level discriminated AA and CRC patients from control subjects with area under the curve values of 0.892 (95% CI: 0.795-0.988) and 0.961 (95% CI: 0.938-0.983). Further analysis indicated no significant difference in sensitivities among different ages, genders, stages, locations, sides, tumor sizes and differentiation statuses. Conclusions Methylated CLIP4 showed a strong potential as a noninvasive biomarker for early CRC detection.
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Affiliation(s)
- Yang Cao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, China
| | - Yaping Cao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Zhiliang Chen
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Xiaoyu Liu
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Mufa Yuan
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Jun Yang
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Xiaomei Wang
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Yong Ma
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhaocheng Liu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, China
| | - Minxue Zheng
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Sujuan Fei
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
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14
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Fan Y, He L, Wang Y, Fu S, Han Y, Fan J, Wen Q. CLIP4 Shows Putative Tumor Suppressor Characteristics in Breast Cancer: An Integrated Analysis. Front Mol Biosci 2021; 7:616190. [PMID: 33575272 PMCID: PMC7870488 DOI: 10.3389/fmolb.2020.616190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background: CAP-Gly domain containing linker protein family member 4 (CLIP4) plays an important role in cancers. However, its expression, prognostic value, and biological effect in breast cancer remain unclear. Methods: Data on patients diagnosed with breast cancer were retrieved from the TCGA-BRCA and other public omics databases. The expression profile of CLIP4 was analyzed using Oncomine, bc-GenExMiner, and TCGA. The prognostic value of CLIP4 was determined by Kaplan-Meier Plotter and Human Protein Atlas. Identification of genes co-expressed with CLIP4 and potential mechanism analyses were performed using UALCAN, STRING, Metascape, and GSEA. The epigenetic characteristics of CLIP4 were determined by DiseaseMeth and MEXPRESS. Results: CLIP4 was downregulated and its expression was negatively correlated with estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor type 2 (HER2) status, Nottingham prognostic index (NPI), and Scarff-Bloom-Richardson (SBR) grade in breast cancer, whereas it was positively linked to basal-like and triple negative breast cancer status. Ectopic expression of CLIP4 was related with poor prognosis. In the analysis of genes co-expressed with CLIP4, GSEA showed that the Hedgehog (Hh), JAK-STAT, ERBB, Wnt signaling pathway, cell adhesion molecules, and pathways in cancer were dissimilarly enriched in the CLIP4 expression high phenotype. Analysis of the genetics and epigenetics of CLIP4 indicated that its expression was negatively correlated with DNA methylation. Conclusion: Methylated CLIP4 may be a novel prognostic and therapeutic biomarker for breast cancer.
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Affiliation(s)
- Yu Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Lijia He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yu Wang
- Health Management Department, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shaozhi Fu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yunwei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Juan Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
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15
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Luo D, Yang Q, Wang H, Tan M, Zou Y, Liu J. A predictive model for assessing prognostic risks in gastric cancer patients using gene expression and methylation data. BMC Med Genomics 2021; 14:14. [PMID: 33407483 PMCID: PMC7789242 DOI: 10.1186/s12920-020-00856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The role(s) of epigenetic reprogramming in gastric cancer (GC) remain obscure. This study was designed to identify methylated gene markers with prognostic potential for GC. METHODS Five datasets containing gene expression and methylation profiles from GC samples were collected from the GEO database, and subjected to meta-analysis. All five datasets were subjected to quality control and then differentially expressed genes (DEGs) and differentially expressed methylation genes (DEMGs) were selected using MetaDE. Correlations between gene expression and methylation status were analysed using Pearson coefficient correlation. Then, enrichment analyses were conducted to identify signature genes that were significantly different at both the gene expression and methylation levels. Cox regression analyses were performed to identify clinical factors and these were combined with the signature genes to create a prognosis-related predictive model. This model was then evaluated for predictive accuracy and then validated using a validation dataset. RESULTS This study identified 1565 DEGs and 3754 DEMGs in total. Of these, 369 were differentially expressed at both the gene and methylation levels. We identified 12 signature genes including VEGFC, FBP1, NR3C1, NFE2L2, and DFNA5 which were combined with the clinical data to produce a novel prognostic model for GC. This model could effectively split GC patients into two groups, high- and low-risk with these observations being confirmed in the validation dataset. CONCLUSION The differential methylation of the 12 signature genes, including VEGFC, FBP1, NR3C1, NFE2L2, and DFNA5, identified in this study may help to produce a functional predictive model for evaluating GC prognosis in clinical samples.
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Affiliation(s)
- Dan Luo
- Department of General Surgery, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
| | - QingLing Yang
- Department of Pulmonary and Critical Care Medicine, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
| | - HaiBo Wang
- Department of General Surgery, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
| | - Mao Tan
- Department of General Surgery, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
| | - YanLei Zou
- Department of General Surgery, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
| | - Jian Liu
- Department of General Surgery, Chengdu Fifth People’s Hospital, 33 Mashi St, Chengdu, 610000 Sichuan China
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16
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Nie K, Zheng Z, Wen Y, Shi L, Xu S, Wang X, Zhou Y, Fu B, Li X, Deng Z, Pan J, Jiang X, Jiang K, Yan Y, Zhuang K, Huang W, Liu F, Li P. Construction and validation of a TP53-associated immune prognostic model for gastric cancer. Genomics 2020; 112:4788-4795. [PMID: 32858135 DOI: 10.1016/j.ygeno.2020.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023]
Abstract
Increasing evidence indicates that TP53 mutation impacts the patients' prognosis by regulating the gastric cancer (GC) immunophenotype. An immune prognostic signature (IPS) was constructed based on TP53 status. The effects of the IPS on the immune microenvironment of GC were analyzed. We also constructed a nomogram integrating the IPS and other clinical factors. An IPS was constructed in the TCGA cohort and validated in the meta-GEO cohort. TP53 mutation resulted in the downregulation of the immune response in GC. Concretely, high-risk patients were characterized by increased monocyte, macrophage M0 and T cell follicular helper infiltration; increased stromal score, ESTIMATE score and immune score; higher TIM3 and BTLA expression; and decreased dendritic cell and T cell CD4 memory-activated infiltration and tumor purity. The nomogram also showed good predictive performance. These results suggest that the IPS is an effective prognostic indicator for GC patients, which might provide a theoretical foundation for immunotherapy.
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Affiliation(s)
- Kechao Nie
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China; Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhihua Zheng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yi Wen
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Laner Shi
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Shjie Xu
- Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Xueqi Wang
- Department of The Spleen and Stomach, Qingyuan Traditional Chinese Medicine Hospital, Qingyuan 511500, Guangdong, China
| | - Yingsheng Zhou
- University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Bin Fu
- Hospital of Traditional Chinese Medicine of Zhongshan, Zhongshan 528400, China
| | - Xiushen Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Zhitong Deng
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Jinglin Pan
- Department of Gastroenterology, Hainan Provincial Hospital of Traditional Chinese Medicine, Haikou, Hainan, China
| | - Xiaotao Jiang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Kailin Jiang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yanhua Yan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Kunhai Zhuang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China.
| | - Wei Huang
- Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Fengbin Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China.
| | - Peiwu Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China.
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17
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Bacolod MD, Mirza AH, Huang J, Giardina SF, Feinberg PB, Soper SA, Barany F. Application of Multiplex Bisulfite PCR-Ligase Detection Reaction-Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer. J Mol Diagn 2020; 22:885-900. [PMID: 32407802 DOI: 10.1016/j.jmoldx.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The analysis of CpG methylation in circulating tumor DNA fragments has emerged as a promising approach for the noninvasive early detection of solid tumors, including colorectal cancer (CRC). The most commonly employed assay involves bisulfite conversion of circulating tumor DNA, followed by targeted PCR, then real-time quantitative PCR (alias methylation-specific PCR). This report demonstrates the ability of a multiplex bisulfite PCR-ligase detection reaction-real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. This scalable assay is designed for multiplexing and incorporates steps for improved sensitivity and specificity, including the enrichment of methylated CpG fragments, ligase detection reaction, the incorporation of ribose bases in primers, and use of uracil DNA glycosylase. Six of the seven CpG markers (located in promoter regions of PPP1R16B, KCNA3, CLIP4, GDF6, SEPT9, and GSG1L) were identified through integrated analyses of genome-wide methylation data sets for 31 different types of cancer. These markers were mapped to CpG sites at the promoter region of VIM; VIM and SEPT9 are established epigenetic markers of CRC. Additional bioinformatics analyses show that the methylation at these CpG sites negatively correlates with the transcription of their corresponding genes.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.
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18
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Rajamanickam V, Yan T, Wu L, Zhao Y, Xu X, Zhu H, Chen X, Wang M, Liu Z, Liu Z, Liang G, Wang Y. Allylated Curcumin Analog CA6 Inhibits TrxR1 and Leads to ROS-Dependent Apoptotic Cell Death in Gastric Cancer Through Akt-FoxO3a. Cancer Manag Res 2020; 12:247-263. [PMID: 32021440 PMCID: PMC6968823 DOI: 10.2147/cmar.s227415] [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: 08/15/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background Gastric cancer is one of the leading causes of cancer-related deaths. Allylated monocarbonyl analogs of curcumin (MACs) have been reported to selectively inhibit a broad range of human cancers including gastric cancer. However, the precise molecular mechanisms underlying the inhibitory activities of MACs are not fully known. Methods In this study, we examined the anti-tumor activities of an allylated MAC, CA6, on gastric cancer cells and gastric cancer xenograft mouse model. The potential molecular anti-tumor mechanisms of CA6 were also elucidated. Results Our data show that CA6 exhibited significant cytotoxicity in gastric cancer cells, which was seen as an induction of G2/M cell cycle arrest and apoptosis. These activities were mediated through an elaboration of ROS levels in gastric cancer cells and induction of endoplasmic reticulum stress. CA6 increased ROS levels through directly binding to and inhibiting thioredoxin reductase R1 (TrxR1). Also, CA6-generated ROS inhibited Akt and activated forkhead O3A (FoxO3a), causing cytotoxicity in gastric cancer cells. Finally, CA6 treatment dose-dependently reduced the growth of gastric cancer xenografts in tumor-bearing mice, which was associated with reduced TrxR1 activity and increased ROS in the tumor. Conclusion In summary, our studies demonstrate that CA6 inhibited gastric cancer growth by inhibiting TrxR1 and increasing ROS, which in turn activated FoxO3a through suppressing Akt. CA6 is a potential candidate for the treatment of gastric cancer.
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Affiliation(s)
- Vinothkumar Rajamanickam
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Tao Yan
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Liangrong Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Yanni Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Xiaohong Xu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Heping Zhu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Xi Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Meihong Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Zhoudi Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Zhiguo Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Yi Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
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19
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: https:/doi.org/10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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20
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: 10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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21
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Fang WL, Chen MH, Huang KH, Chang SC, Lin CH, Chao Y, Lo SS, Li AFY, Wu CW, Shyr YM. Analysis of the clinical significance of DNA methylation in gastric cancer based on a genome-wide high-resolution array. Clin Epigenetics 2019; 11:154. [PMID: 31675985 PMCID: PMC6824057 DOI: 10.1186/s13148-019-0747-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation is involved in gastric carcinogenesis and may serve as a useful biomarker in the diagnosis and detection of gastric cancer (GC) recurrence. RESULTS A total of 157 patients who received surgery for GC were enrolled in the present study. A genome-wide methylation analysis was performed in tumor and adjacent normal tissues for the discovery set of 16 GC patients; the top three hypermethylated CpG sites of DNA promoters were selected for validation in tissue and plasma samples for the validation set of 141 GC patients. The frequencies of the top three hypermethylated genes in available patient tissues (n = 141) and plasma samples (n = 106) were 41.8% and 38.7%, respectively, for ADAM19; 40.4% and 42.5%, respectively, for FLI1; and 56.7% and 50.9%, respectively, for MSC. In both tissue and plasma samples, FLI1 hypermethylation was associated with more advanced GC and liver and distant lymphatic metastasis, and ADAM19 hypermethylation was associated with more stage IV GC. In plasma samples, MSC hypermethylation was more common in non-superficial type GC than samples without MSC hypermethylation. In both tissue and plasma samples, patients with methylation of all the three genes had significantly more liver metastases, distant lymphatic metastases, and paraaortic lymph node metastases than patients with two or fewer hypermethylated genes. The survival analysis showed that only for stage III GC, patients with hypermethylation of two or three genes had a worse 5-year disease-free survival rate than those with hypermethylation of one or none of the three genes. Subgroup analysis showed that FLI1 hypermethylation in both tissue and plasma samples was associated with liver metastasis in MSI-/EBV- GC, and MSC hypermethylation in tissue samples was correlated with liver metastasis in MSI+ or EBV+ GC. Patients with FLI1 hypermethylation in plasma samples had a significantly worse 5-year disease-free survival rate than those without FLI1 hypermethylation in MSI-/EBV- GC. FLI1 hypermethylation was an independent prognostic factor affecting the overall survival and disease-free survival in both tissue and plasma samples. CONCLUSIONS DNA methylation is a useful biomarker for predicting tumor recurrence patterns and GC patient survival.
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Affiliation(s)
- Wen-Liang Fang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217. .,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.
| | - Ming-Huang Chen
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Kuo-Hung Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Shih-Ching Chang
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Chien-Hsing Lin
- Genome Research Center, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Yee Chao
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Su-Shun Lo
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,National Yang-Ming University Hospital, Yilan County, Taiwan, 26058
| | - Anna Fen-Yau Li
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Pathology, Taipei Veterans General Hospital, Taipei City, 11217, Taiwan
| | - Chew-Wun Wu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Yi-Ming Shyr
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
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22
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Song J, Li P, Yuan GH, Jia Z, Zhang RL, Wang FB, Zhong GB, Li YN, Zhong DJ. Value of of ELMO1 gene methylation detection in early diagnosis of gastric cancer. Shijie Huaren Xiaohua Zazhi 2019; 27:1055-1061. [DOI: 10.11569/wcjd.v27.i17.1055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is a malignant tumor that seriously endangers human health. Its morbidity and mortality rank second and first, respectively, among malignant tumors in China. It is difficult to diagnose early. Therefore, finding new markers for GC diagnosis is very important to improve the early detection rate and prognosis of GC. At present, there are few reports on the diagnostic value of engulfment and cell motility 1 (ELMO1) gene methylation in GC.
AIM To explore the relationship between the methylation of ELMO1 gene and GC in order to provide new ideas for early diagnosis of this malignancy.
METHODS From January 2017 to August 2018, 20 cases of chronic superficial gastritis, 20 cases of chronic atrophic gastritis, and 37 cases of GC (15 cases of early GC and 22 cases of advanced GC) were selected. The gastric juice and biopsy were collected at the same time. Methylation-specific polymerase chain reaction was used to detect the methylation level of ELMO1 gene in the three groups, and the correlation between ELMO1 gene methylation and the occurrence, stage, and metastasis of GC was analyzed.
RESULTS The methylation rate of ELMO1 gene in tissues and gastric juice of chronic superficial gastritis, chronic atrophic gastritis, and GC were 0%, 20.5%, and 93.3% (P < 0.01), and 0%, 12.3%, and 76.7% (P < 0.05), respectively. The methylation rate of ELMO1 gene in adjacent tissue DNA was 96.7%, which was not significantly different from that in the GC group (P > 0.05). The methylation rates of ELMO1 gene in gastric juice of patients with early GC and advanced GC were 73.3% and 80.0%, respectively. The methylation rates of ELMO1 gene in the two tissues were 86.7% and 100%, respectively. There was no significant difference between them in both gastric juice and tissues (P > 0.05).
CONCLUSION The promoter region of ELMO1 gene in gastric juice DNA and pathological tissues of patients with GC is hypermethylated, which has high consistency. ELMO1 gene methylation can be used as a molecular target for early diagnosis of GC, and gastric juice can be used as a good clinical sample for detection of ELMO1 gene methylation.
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Affiliation(s)
- Jian Song
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Ping Li
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Gui-Hong Yuan
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Zhen Jia
- Department of Anesthesiology, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Rong-Lin Zhang
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Fa-Bao Wang
- Department of Pathology, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Guo-Bing Zhong
- Central Laboratory of Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Yi-Ni Li
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
| | - Dun-Jing Zhong
- Department of Digestive Endoscopy, Hainan Cancer Hospital, Haikou 570123, Hainan Province, China
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23
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Amini M, Foroughi K, Talebi F, Aghagolzade Haji H, Kamali F, Jandaghi P, Hoheisel JD, Manoochehri M. GHSR DNA hypermethylation is a new epigenetic biomarker for gastric adenocarcinoma and beyond. J Cell Physiol 2019; 234:15320-15329. [PMID: 30677130 DOI: 10.1002/jcp.28179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Aberrations of DNA methylation are early events in the development of tumors. In this study, we investigated the DNA methylation status of growth hormone secretagogue receptor (GHSR), a promising pan-cancer biomarker, in gastric cancer (GC). Initially, data sets from DNA methylation and gene expression studies available at Gene Expression Omnibus (GEO) were analyzed. Confirmation was done on primary tumor specimens and adjacent normal stomach tissue samples. Both analyses showed significant hypermethylation of GHSR. For further validation, The Cancer Genome Atlas data on stomach cancer was used. A receiver operating characteristic curve analysis yielded an area under the curve value of 0.85, corroborating its usefulness as a diagnostic marker. A genome-wide comethylation analysis revealed several correlated genes. CREB1 was found to act as an upstream regulator of this gene network. Furthermore, GHSR methylation was found to be a biomarker in several other tumor entities, namely cancers of the bladder, endometrium, esophagus, head and neck, liver, thyroid, kidney, and ovary. Our findings along with previous reports on other types of cancer suggest a high potential of GHSR gene methylation as a pan-cancer biomarker, which could be considered for liquid biopsy applications.
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Affiliation(s)
- Mohammad Amini
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Kobra Foroughi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Fatemeh Talebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Hemat Aghagolzade Haji
- Department of Biochemistry, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Kamali
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran, Iran
| | - Pouria Jandaghi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mehdi Manoochehri
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.,Molecular Genetics of Breast Cancer (B072), German Cancer Research Center (DKFZ), Heidelberg, Germany
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24
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Zhang L, Li W, Cao L, Xu J, Qian Y, Chen H, Zhang Y, Kang W, Gou H, Wong CC, Yu J. PKNOX2 suppresses gastric cancer through the transcriptional activation of IGFBP5 and p53. Oncogene 2019; 38:4590-4604. [PMID: 30745575 PMCID: PMC6756047 DOI: 10.1038/s41388-019-0743-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/31/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023]
Abstract
Promoter methylation plays a vital role in tumorigenesis through transcriptional silencing of tumor suppressive genes. Using genome-wide methylation array, we first identified PBX/Knotted Homeobox 2 (PKNOX2) as a candidate tumor suppressor in gastric cancer. PKNOX2 mRNA expression is largely silenced in gastric cancer cell lines and primary gastric cancer via promoter methylation. Promoter methylation of PKNOX2 was associated with poor survival in gastric cancer patients. A series of in vitro and in vivo functional studies revealed that PKNOX2 functions as a tumor suppressor. Ectopic PKNOX2 expression inhibited cell proliferation in GC cell lines and suppressed growth of tumor xenografts in mice via induction of apoptosis and cell cycle arrest; and suppressed cell migration and invasion by blocking epithelial-to-mesenchymal transition. On the other hand, knockdown PKNOX2 in normal gastric epithelial cells triggered diverse malignant phenotypes. Mechanistically, PKNOX2 exerts its tumor suppressive effect by promoting the up-regulation of Insulin like Growth Factor Binding Protein 5 (IGFBP5) and TP53. PKNOX2 binds to the promoter regions of IGFBP5 and TP53 and transcriptionally activated their expression by chromatin immunoprecipitation (ChIP)-PCR assay. IGFBP5 knockdown partly abrogated tumor suppressive effect of PKNOX2, indicating that the function(s) of PKNOX2 are dependent on IGFBP5. IGFBP5 promoted PKNOX2-mediated up-regulation of p53. As a consequence, p53 transcription target genes were coordinately up-regulated in PKNOX2-expressing GC cells, leading to tumor suppression. In summary, our results identified PKNOX2 as a tumor suppressor in gastric cancer by activation of IGFBP5 and p53 signaling pathways. PKNOX2 promoter hypermethylation might be a biomarker for the poor survival of gastric cancer patients.
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Affiliation(s)
- Li Zhang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong.,Department of Surgery, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Lei Cao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Jiaying Xu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Yun Qian
- Department of Gastroenterology, Shenzhen University Hospital, Shenzhen, China
| | - Huarong Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Yanquan Zhang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Hongyan Gou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong.
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong.
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25
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Guio H, Poterico JA, Levano KS, Cornejo‐Olivas M, Mazzetti P, Manassero‐Morales G, Ugarte‐Gil MF, Acevedo‐Vásquez E, Dueñas‐Roque M, Piscoya A, Fujita R, Sanchez C, Casavilca‐Zambrano S, Jaramillo‐Valverde L, Sullcahuaman‐Allende Y, Iglesias‐Pedraz JM, Abarca‐Barriga H. Genetics and genomics in Peru: Clinical and research perspective. Mol Genet Genomic Med 2018; 6:873-886. [PMID: 30584990 PMCID: PMC6305655 DOI: 10.1002/mgg3.533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022] Open
Abstract
Peruvians currently preserve in their DNA the history of 2.5 million years of human evolution and 150,000 years of migration from Africa to Peru or the Americas. The development of Genetics and Genomics in the clinical and academic field is shown in this review.
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Affiliation(s)
- Heinner Guio
- Instituto Nacional de Salud del PerúLimaPerú
- Universidad Científica del SurLimaPerú
| | - Julio A. Poterico
- Instituto Nacional de Salud del PerúLimaPerú
- Servicio de GenéticaInstituto Nacional de Salud del Niño San Borja (INSN‐SB)LimaPeru
| | | | - Mario Cornejo‐Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias NeurológicasLimaPerú
| | - Pilar Mazzetti
- Neurogenetics Research Center, Instituto Nacional de Ciencias NeurológicasLimaPerú
- School of MedicineUniversidad Nacional Mayor de San MarcosLimaPerú
| | | | - Manuel F. Ugarte‐Gil
- Universidad Científica del SurLimaPerú
- Rheumatology Department. Hospital Guillermo Almenara Irigoyen. EsSaludLimaPerú
| | - Eduardo Acevedo‐Vásquez
- School of MedicineUniversidad Nacional Mayor de San MarcosLimaPerú
- Clínica San FelipeLimaPerú
| | - Milagros Dueñas‐Roque
- Servicio de GenéticaHospital Nacional Edgardo Rebagliati MartinsLimaPerú
- Sociedad de Genética Médica del PerúLimaPeru
| | - Alejandro Piscoya
- Universidad San Ignacio de LoyolaLimaPerú
- Hospital Guillermo Kaelin de la FuenteLimaPerú
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Universidad de San Martín de PorresLimaPerú
| | | | - Sandro Casavilca‐Zambrano
- Banco de Tejidos Tumorales, Instituto Nacional de Enfermedades NeoplásicasBanco de Tejidos TumoralesLimaPerú
- Instituto Nacional de Enfermedades NeoplásicasLimaPerú
| | | | | | - Juan M. Iglesias‐Pedraz
- Universidad Científica del SurLimaPerú
- Laboratorio de Genética Molecular y Bioquímica, Departamento de Investigación, Desarrollo e InnovaciónUniversidad Científica del SurLimaPerú
| | - Hugo Abarca‐Barriga
- Servicio de Genética & EIMInstituto Nacional de Salud del Niño Breña (INSN)LimaPeru
- Facultad de EstomatologíaUniversidad Científica del SurLimaPerú
- Facultad de Medicina HumanaUniversidad Ricardo PalmaLimaPerú
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26
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Dos Santos MP, Sallas ML, Zapparoli D, Orcini WA, Chen E, Smith MDAC, Payão SLM, Rasmussen LT. Lack of Association between IL-6 Polymorphisms and Haplotypes with Gastric Cancer. J Cell Biochem 2018; 120:9448-9454. [PMID: 30525242 DOI: 10.1002/jcb.28220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/15/2018] [Indexed: 12/24/2022]
Abstract
The process of combating neoplasms and mononuclear cells, and during H. pylori infection, several pro-inflammatory and anti-inflammatory cytokines are synthesized. In view of the involvement of the IL-6 law and the presence of H. pylori in the development of gastric diseases, the present study aimed to characterize the promoter-region polymorphism -597 (G/A) (rs1800797), -572 (C/G) (rs1800796), and -174 (G/C) (rs1800795) by PCR-RFLP in 375 gastric biopsy specimens from patients with peptic symptoms. A total of 375 samples were analyzed: 87 patients (without lesion without gastric tissue); 236 patients with gastritis and 52 patients with gastric cancer analyzed the PCR-RFLP techniques. All the results were normalized in relation to the presence of H. pylori. The frequencies of the three polymorphisms were compared in the Control vs Gastritis groups and a statistically significant test observed: -174 (G/C) (OR: 1.27; 95% CI: 0.84-1.93; P = 0.26), 572 (C/G) (OR: 1.42; 95% CI: 0.78-2.59; P = 0.25), and 597 (G/A) (OR: 0.98; 95% CI, 0.64-1.52; P = 0.94). Similar results were obtained when the gastric cancer group was compared to the control group: -174 (G/C) (OR: 1.27; 95% CI: 0.66-2.47; P = 0.47), -572 (C/G) (OR: 1.07; 95% CI: 0.43-2.68; P = 0.88), and -597 (G/A) (OR: 1.01; 95% CI, 0.5-0.9; P = 0.99). The haplotypes were and were not observed statistically significant differences. In conclusion, we found no correlations between any of the three polymorphisms in the IL-6 gene analyzed in this study and a higher risk of gastritis or gastric cancer.
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Affiliation(s)
| | | | - Diana Zapparoli
- Universidade do Sagrado Coração (USC), Bauru, São Paulo, Brazil
| | | | - Elizabeth Chen
- Universidade Federal de São Paulo, (UNIFESP), São Paulo, Brazil
| | | | | | - Lucas Trevizani Rasmussen
- Universidade do Sagrado Coração (USC), Bauru, São Paulo, Brazil.,Faculdade de Medicina de Marilia (FAMEMA) - Hemocentro, Marília, São Paulo, Brazil
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27
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Tsygankov AY. TULA-family proteins: Jacks of many trades and then some. J Cell Physiol 2018; 234:274-288. [PMID: 30076707 DOI: 10.1002/jcp.26890] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/13/2018] [Indexed: 12/17/2022]
Abstract
UBASH3/STS/TULA is a novel two-member family, which exerts several key regulatory effects in multiple cell types. UBASH3B/STS-1/TULA-2 is a highly active protein tyrosine phosphatase; its major target appears to be a specific regulatory site of protein tyrosine kinases of the Syk family, dephosphorylation of which inhibits Syk and Zap-70 kinases and suppresses receptor signaling mediated by these kinases. UBASH3A/STS-2/TULA exhibits substantial homology to UBASH3B/STS-1/TULA-2, but possesses only a small fraction of phosphatase activity of UBASH3B/STS-1/TULA-2, and thus, its regulatory effect may be based also on the phosphatase-independent mechanisms. Critical physiologic effects of these proteins have been demonstrated in T lymphocytes, platelets, stem cells, and other important cell types. These proteins have also been shown to play a key role in such pathologic conditions as autoimmunity, cancer, and thrombosis. The review focuses on the recent studies of this important family of cellular regulators.
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Affiliation(s)
- Alexander Y Tsygankov
- Department of Microbiology and Immunology, Fels Institute for Cancer Research and Molecular Biology and Sol Sherry Thrombosis Center, Temple University School of Medicine, Philadelphia, Pennsylvania
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Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
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Hu C, Zhou Y, Liu C, Kang Y. A novel scoring system for gastric cancer risk assessment based on the expression of three CLIP4 DNA methylation-associated genes. Int J Oncol 2018; 53:633-643. [PMID: 29901187 PMCID: PMC6017186 DOI: 10.3892/ijo.2018.4433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/26/2018] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-associated mortality worldwide. In the current study, comprehensive bioinformatic analyses were performed to develop a novel scoring system for GC risk assessment based on CAP-Gly domain containing linker protein family member 4 (CLIP4) DNA methylation status. Two GC datasets with methylation sequencing information and mRNA expression profiling were downloaded from the The Cancer Genome Atlas and Gene Expression Omnibus databases. Differentially expressed genes (DEGs) between the CLIP4 hypermethylation and CLIP4 hypomethylation groups were screened using the limma package in R 3.3.1, and survival analysis of these DEGs was performed using the survival package. A risk scoring system was established via regression factor-weighted gene expression based on linear combination to screen the most important genes associated with CLIP4 methylation and prognosis. Genes associated with high/low-risk value were selected using the limma package. Functional enrichment analysis of the top 500 DEGs that positively and negatively associated with risk values was performed using DAVID 6.8 online and the gene set enrichment analysis (GSEA) software. In total, 35 genes were identified to be that significantly associated with prognosis and CLIP4 DNA methylation, and three prognostic signature genes, claudin-11 (CLDN11), apolipoprotein D (APOD), and chordin like 1 (CHRDL1), were used to establish a risk assessment system. The prognostic scoring system exhibited efficiency in classifying patients with different prognoses, where the low-risk groups had significantly longer overall survival times than those in the high-risk groups. CLDN11, APOD and CHRDL1 exhibited reduced expression in the hypermethylation and low-risk groups compare with the hypomethylation and high-risk groups, respectively. Multivariate Cox analysis indicated that risk value could be used as an independent prognostic factor. In functional analysis, six functional gene ontology terms and five GSEA pathways were associated with CLDN11, APOD and CHRDL1. The results established the credibility of the scoring system in this study. Additionally, these three genes, which were significantly associated with CLIP4 DNA methylation and GC risk assessment, were identified as potential prognostic biomarkers.
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Affiliation(s)
- Chenggong Hu
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yongfang Zhou
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chang Liu
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yan Kang
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Anderson BW, Suh YS, Choi B, Lee HJ, Yab TC, Taylor WR, Dukek BA, Berger CK, Cao X, Foote PH, Devens ME, Boardman LA, Kisiel JB, Mahoney DW, Slettedahl SW, Allawi HT, Lidgard GP, Smyrk TC, Yang HK, Ahlquist DA. Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma. Clin Cancer Res 2018; 24:5724-5734. [PMID: 29844130 DOI: 10.1158/1078-0432.ccr-17-3364] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/09/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022]
Abstract
Purpose: Gastric adenocarcinoma is the third most common cause of cancer mortality worldwide. Accurate and affordable noninvasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDM) for gastric adenocarcinoma, validate their discrimination for gastric adenocarcinoma in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from gastric adenocarcinoma cases and normal controls.Experimental Design: Following discovery by unbiased whole-methylome sequencing, candidate MDMs were validated by blinded methylation-specific PCR in archival case-control tissues from U.S. and South Korean patients. Top MDMs were then assayed by an analytically sensitive method (quantitative real-time allele-specific target and signal amplification) in a blinded pilot study on archival plasma from gastric adenocarcinoma cases and normal controls.Results: Whole-methylome discovery yielded novel and highly discriminant candidate MDMs. In tissue, a panel of candidate MDMs detected gastric adenocarcinoma in 92% to 100% of U.S. and South Korean cohorts at 100% specificity. Levels of most MDMs increased progressively from normal mucosa through metaplasia, adenoma, and gastric adenocarcinoma with variation in points of greatest marker acquisition. In plasma, a 3-marker panel (ELMO1, ZNF569, C13orf18) detected 86% (95% CI, 71-95) of gastric adenocarcinomas at 95% specificity.Conclusions: Novel MDMs appear to accurately discriminate gastric adenocarcinoma from normal controls in both tissue and plasma. The point of aberrant methylation during oncogenesis varies by MDM, which may have relevance to marker selection in clinical applications. Further exploration of these MDMs for gastric adenocarcinoma screening and surveillance is warranted. Clin Cancer Res; 24(22); 5724-34. ©2018 AACR.
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Affiliation(s)
- Bradley W Anderson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Boram Choi
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyuk-Joon Lee
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Mary E Devens
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Information, Mayo Clinic, Rochester, Minnesota
| | - Seth W Slettedahl
- Department of Biomedical Statistics and Information, Mayo Clinic, Rochester, Minnesota
| | | | | | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Han-Kwang Yang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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DNA Methylation Levels of the ELMO Gene Promoter CpG Islands in Human Glioblastomas. Int J Mol Sci 2018; 19:ijms19030679. [PMID: 29495584 PMCID: PMC5877540 DOI: 10.3390/ijms19030679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 02/07/2023] Open
Abstract
Complete surgical resection of glioblastoma is difficult due to the invasive nature of this primary brain tumor, for which the molecular mechanisms behind remain poorly understood. The three human ELMO genes play key roles in cellular motility, and have been linked to metastasis and poor prognosis in other cancer types. The aim of this study was to investigate methylation levels of the ELMO genes and their correlation to clinical characteristics and outcome in patients diagnosed with glioblastoma. To measure DNA methylation levels we designed pyrosequencing assays targeting the promoter CpG island of each the ELMO genes. These were applied to diagnostic tumor specimens from a well-characterized cohort of 121 patients who received standard treatment consisting of surgery, radiation therapy, plus concomitant and adjuvant chemotherapy. The promoter methylation levels of ELMO1 and ELMO2 were generally low, whereas ELMO3 methylation levels were high, in the tumor biopsies. Thirteen, six, and 18 biopsies were defined as aberrantly methylated for ELMO1, ELMO2, and ELMO3, respectively. There were no significant associations between the methylation status of any of the ELMO gene promoter CpG islands and overall survival, progression-free survival, and clinical characteristics of the patients including intracranial tumor location. Therefore, the methylation status of the ELMO gene promoter CpG islands is unlikely to have prognostic value in glioblastoma.
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Fu H, Wang C, Yang D, Wei Z, Xu J, Hu Z, Zhang Y, Wang W, Yan R, Cai Q. Curcumin regulates proliferation, autophagy, and apoptosis in gastric cancer cells by affecting PI3K and P53 signaling. J Cell Physiol 2018; 233:4634-4642. [PMID: 28926094 DOI: 10.1002/jcp.26190] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/12/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Hongbing Fu
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Changming Wang
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Dejun Yang
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Ziran Wei
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Jiapeng Xu
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Zunqi Hu
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Yu Zhang
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Weimin Wang
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Ronglin Yan
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
| | - Qingping Cai
- Department of Gastrointestinal Surgery; Changzheng Hospital; Second Military Medical University; Shanghai P.R. China
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