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Guo S, Wang E, Wang B, Xue Y, Kuang Y, Liu H. Comprehensive Multiomics Analyses Establish the Optimal Prognostic Model for Resectable Gastric Cancer : Prognosis Prediction for Resectable GC. Ann Surg Oncol 2024; 31:2078-2089. [PMID: 37996637 DOI: 10.1245/s10434-023-14249-x] [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: 06/12/2023] [Accepted: 08/14/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Prognostic models based on multiomics data may provide better predictive capability than those established at the single-omics level. Here we aimed to establish a prognostic model for resectable gastric cancer (GC) with multiomics information involving mutational, copy number, transcriptional, methylation, and clinicopathological alterations. PATIENTS AND METHODS The mutational, copy number, transcriptional, methylation data of 268, 265, 226, and 252 patients with stages I-III GC were downloaded from the TCGA database, respectively. Alterations from all omics were characterized, and prognostic models were established at the individual omics level and optimized at the multiomics level. All models were validated with a cohort of 99 patients with stages I-III GC. RESULTS TTN, TP53, and MUC16 were among the genes with the highest mutational frequency, while UBR5, ZFHX4, PREX2, and ARID1A exhibited the most prominent copy number variations (CNVs). Upregulated COL10A1, CST1, and HOXC10 and downregulated GAST represented the biggest transcriptional alterations. Aberrant methylation of some well-known genes was revealed, including CLDN18, NDRG4, and SDC2. Many alterations were found to predict the patient prognosis by univariate analysis, while four mutant genes, two CNVs, five transcriptionally altered genes, and seven aberrantly methylated genes were identified as independent risk factors in multivariate analysis. Prognostic models at the single-omics level were established with these alterations, and optimized combination of selected alterations with clinicopathological factors was used to establish a final multiomics model. All single-omics models and the final multiomics model were validated by an independent cohort. The optimal area under the curve (AUC) was 0.73, 0.71, 0.71, and 0.85 for mutational, CNV, transcriptional, and methylation models, respectively. The final multiomics model significantly increased the AUC to 0.92 (P < 0.05). CONCLUSIONS Multiomics model exhibited significantly better capability in predicting the prognosis of resectable GC than single-omics models.
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Affiliation(s)
- Shaohua Guo
- Department of General Surgery, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Erpeng Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Baishi Wang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yonggan Xue
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yanshen Kuang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Hongyi Liu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China.
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Bioinformatics Prediction and Machine Learning on Gene Expression Data Identifies Novel Gene Candidates in Gastric Cancer. Genes (Basel) 2022; 13:genes13122233. [PMID: 36553500 PMCID: PMC9778573 DOI: 10.3390/genes13122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Gastric cancer (GC) is one of the five most common cancers in the world and unfortunately has a high mortality rate. To date, the pathogenesis and disease genes of GC are unclear, so the need for new diagnostic and prognostic strategies for GC is undeniable. Despite particular findings in this regard, a holistic approach encompassing molecular data from different biological levels for GC has been lacking. To translate Big Data into system-level biomarkers, in this study, we integrated three different GC gene expression data with three different biological networks for the first time and captured biologically significant (i.e., reporter) transcripts, hub proteins, transcription factors, and receptor molecules of GC. We analyzed the revealed biomolecules with independent RNA-seq data for their diagnostic and prognostic capabilities. While this holistic approach uncovered biomolecules already associated with GC, it also revealed novel system biomarker candidates for GC. Classification performances of novel candidate biomarkers with machine learning approaches were investigated. With this study, AES, CEBPZ, GRK6, HPGDS, SKIL, and SP3 were identified for the first time as diagnostic and/or prognostic biomarker candidates for GC. Consequently, we have provided valuable data for further experimental and clinical efforts that may be useful for the diagnosis and/or prognosis of GC.
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3
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Li R, He C, Shen L, Wang S, Shen Y, Feng F, Zhang J, Zheng J. NDRG4 sensitizes CRC cells to 5-FU by upregulating DDIT3 expression. Oncol Lett 2021; 22:782. [PMID: 34594423 PMCID: PMC8456512 DOI: 10.3892/ol.2021.13043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/13/2021] [Indexed: 11/05/2022] Open
Abstract
The incidence of colorectal cancer (CRC) has remained high in recent years, and 5-fluorouracil (5-FU) is a vital chemotherapeutic agent for its treatment. Our previous study reported that N-myc downstream-regulated gene 4 (NDRG4) plays a tumor-suppressive role in CRC, but the mechanisms associated with NDRG4 and 5-FU chemosensitivity remain unclear. The results of the present study demonstrate that NDRG4 sensitized CRC cells to 5-FU by upregulating DNA damage inducible transcript 3 (DDIT3). NDRG4 inhibited the proliferation of CRC cells and the activation of PI3K/AKT and ERK signaling. Furthermore, NDRG4 promoted CRC cell apoptosis induced by 5-FU. Mechanistic analyses revealed that NDRG4 upregulated DDIT3 expression, and that the proapoptotic effect of NDRG4 under 5-FU treatment conditions was dependent on DDIT3. These findings support the biological value of the association between NDRG4, DDIT3 and 5-FU chemosensitivity in CRC, and may advance the clinical treatment of CRC in the future.
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Affiliation(s)
- Ruikai Li
- Department of Gastrointestinal Surgery, Xijing Hospital, Xi'an, Shaanxi 710032, P.R. China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Chenxiang He
- Department of General Surgery, Shanghai Fourth People's Hospital Affiliated to Tongji University of Medicine, Shanghai 200080, P.R. China
| | - Liangliang Shen
- State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China.,Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Shuai Wang
- Department of Gastrointestinal Surgery, Xijing Hospital, Xi'an, Shaanxi 710032, P.R. China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yao Shen
- State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China.,Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Fan Feng
- Department of Gastrointestinal Surgery, Xijing Hospital, Xi'an, Shaanxi 710032, P.R. China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jian Zhang
- State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China.,Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jianyong Zheng
- Department of Gastrointestinal Surgery, Xijing Hospital, Xi'an, Shaanxi 710032, P.R. China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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4
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Liu N, Wu Y, Cheng W, Wu Y, Wang L, Zhuang L. Identification of novel prognostic biomarkers by integrating multi-omics data in gastric cancer. BMC Cancer 2021; 21:460. [PMID: 33902514 PMCID: PMC8073914 DOI: 10.1186/s12885-021-08210-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Gastric cancer is a fatal gastrointestinal cancer with high morbidity and poor prognosis. The dismal 5-year survival rate warrants reliable biomarkers to assess and improve the prognosis of gastric cancer. Distinguishing driver mutations that are required for the cancer phenotype from passenger mutations poses a formidable challenge for cancer genomics. METHODS We integrated the multi-omics data of 293 primary gastric cancer patients from The Cancer Genome Atlas (TCGA) to identify key driver genes by establishing a prognostic model of the patients. Analyzing both copy number alteration and somatic mutation data helped us to comprehensively reveal molecular markers of genomic variation. Integrating the transcription level of genes provided a unique perspective for us to discover dysregulated factors in transcriptional regulation. RESULTS We comprehensively identified 31 molecular markers of genomic variation. For instance, the copy number alteration of WASHC5 (also known as KIAA0196) frequently occurred in gastric cancer patients, which cannot be discovered using traditional methods based on significant mutations. Furthermore, we revealed that several dysregulation factors played a hub regulatory role in the process of biological metabolism based on dysregulation networks. Cancer hallmark and functional enrichment analysis showed that these key driver (KD) genes played a vital role in regulating programmed cell death. The drug response patterns and transcriptional signatures of KD genes reflected their clinical application value. CONCLUSIONS These findings indicated that KD genes could serve as novel prognostic biomarkers for further research on the pathogenesis of gastric cancers. Our study elucidated a multidimensional and comprehensive genomic landscape and highlighted the molecular complexity of GC.
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Affiliation(s)
- Nannan Liu
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yun Wu
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Weipeng Cheng
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yuxuan Wu
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Liguo Wang
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China.
| | - Liwei Zhuang
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, 150001, Heilongjiang, China.
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Tang J, Pan R, Xu L, Ma Q, Ying X, Zhao J, Zhao H, Miao L, Xu Y, Duan S, Wang J. IL10 hypomethylation is associated with the risk of gastric cancer. Oncol Lett 2021; 21:241. [PMID: 33664805 PMCID: PMC7882872 DOI: 10.3892/ol.2021.12502] [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: 12/02/2018] [Accepted: 09/10/2020] [Indexed: 12/17/2022] Open
Abstract
Interleukin-10 (IL10), a pleiotropic cytokine secreted by type-2 helper (Th2) T cells, contributes to the oncogenic activation or inactivation of tumor-suppressor genes. The present study investigated whether hypomethylation of IL10 CpG island (CGI) was associated with the risk of developing gastric cancer (GC) and the prognosis of patients with GC. A fragment (hg18, chr1: 206945638-206945774) at the CGI of IL10 was selected for the present methylation assay. Quantitative methylation-specific PCR was used to evaluate the methylation of IL10 CGI in 117 tumor samples from patients with GC. The results demonstrated that IL10 CGI methylation was significantly lower in the tumor tissues compared with that in the paired adjacent non-tumor tissues (median percentage of methylated reference, 29.16 vs. 42.82%, respectively; P=4×10−8). Furthermore, results from receiver operating characteristic curve analysis identified a significant area under the curve of 0.706, with a sensitivity and a specificity of 77.8 and 58.1%, respectively, between cancer tissues and paired adjacent non-tumor tissues. Furthermore, the methylation of IL10 CGI was significantly associated with patients' age at diagnosis (r=−0.201; P=0.03). Subgroup analyses demonstrated that the association between IL10 CGI hypomethylation and the risk of GC was specific for patients with low differentiation (P=1×10−7) and Borrmann types III+IV (P=1×10−7). In addition, IL10 CGI hypomethylation was significantly associated with the risk of GC for patients without smoking history (P=3×10−7) or a family history of cancer (P=2×10−7). The results from Kaplan-Meier survival analysis demonstrated that IL10 CGI hypomethylation was associated with a significantly shorter overall survival of patients with GC (P=0.041). Similar results were identified for patients with GC who did not have smoking history (P=0.037) or a family history of cancer (P=0.049). The results from this study demonstrated that IL10 CGI hypomethylation may be considered as a potential biomarker for the diagnosis and prognosis of patients with GC in the Chinese population.
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Affiliation(s)
- Junjian Tang
- Department of Vascular Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214000, P.R. China.,Department of Vascular Surgery, Taihu Hospital, Wuxi, Jiangsu 214004, P.R. China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Lele Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215200, P.R. China
| | - Qinghua Ma
- Department of Preventive Health, The Third People's Hospital of Xiangcheng District, Suzhou, Jiangsu 215134, P.R. China
| | - Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jun Zhao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Haibin Zhao
- Department of Pathology, Taihu Hospital, Wuxi, Jiangsu 214004, P.R. China
| | - Li Miao
- Department of Pediatrics, Xuzhou Medical University Affiliated Hospital of Lianyungang, Xuzhou, Jiangsu 222002, P.R. China
| | - Yue Xu
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, Jiangsu 215007, P.R. China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jinzhi Wang
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, Jiangsu 215007, P.R. China
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Shi HH, Liu HE, Luo XJ. Hypermethylation-mediated silencing of NDRG4 promotes pancreatic ductal adenocarcinoma by regulating mitochondrial function. BMB Rep 2020. [PMID: 33298240 PMCID: PMC7781911 DOI: 10.5483/bmbrep.2020.53.12.168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The N-myc downstream regulated gene (NDRG) family members are dysregulated in several tumors. Functionally, NDRGs play an important role in the malignant progression of cancer cells. However, little is known about the potential implications of NDRG4 in pancreatic ductal adenocarcinoma (PDAC). The aim of the current study was to elucidate the expression pattern of NDRG4 in PDAC and evaluate its potential cellular biological effects. Here, we firstly report that epigenetic-mediated silencing of NDRG4 promotes PDAC by regulating mitochondrial function. Data mining demonstrated that NDRG4 was significantly down-regulated in PDAC tissues and cells. PDAC patients with low NDRG4 expression showed poor prognosis. Epigenetic regulation by DNA methylation was closely associated with NDRG4 down-regulation. NDRG4 overexpression dramatically suppressed PDAC cell growth and metastasis. Further functional analysis demonstrated that up-regulated NDRG4 in SW1990 and Canpan1 cells resulted in attenuated mitochondrial function, including reduced ATP production, decreased mitochondrial membrane potential, and increased fragmented mitochondria. However, opposite results were obtained for HPNE cells with NDRG4 knockdown. These results indicate that hypermethylation-driven silencing of NDRG4 can promote PDAC by regulating mitochondrial function and that NDRG4 could be as a potential biomarker for PDAC patients.
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Affiliation(s)
- Hao-Hong Shi
- Department of Anesthesia, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Hai-E Liu
- Department of Anesthesia, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Xing-Jing Luo
- Department of Anesthesia, Children’s Hospital of Fudan University, Shanghai 201102, China
- Department of Anesthesia, Anhui Provincial Children’s Hospital, Hefei, Anhui 230022, China
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7
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Li X, Bu S, Pan RR, Zhou C, Qu K, Ying X, Zhong J, Xiao J, Yuan Q, Zhang S, Tipton L, Wang Y, Deng Y, Duan S. The values of AHCY and CBS promoter methylation on the diagnosis of cerebral infarction in Chinese Han population. BMC Med Genomics 2020; 13:163. [PMID: 33138824 PMCID: PMC7607831 DOI: 10.1186/s12920-020-00798-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/16/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The goal of our study is to investigate whether the methylation levels of AHCY and CBS promoters are related to the risk of cerebral infarction by detecting the methylation level of AHCY and CBS genes. METHODS We extracted peripheral venous blood from 152 patients with cerebral infarction and 152 gender- and age-matched healthy controls, and determined methylation levels of AHCY and CBS promoters using quantitative methylation-specific polymerase chain reaction. We used the percentage of methylation reference (PMR) to indicate gene methylation level. RESULTS We compared the promoter methylation levels of two genes (AHCY and CBS) in peripheral blood DNA between the cerebral infarction case group and the control group. Our study showed no significant difference in AHCY promoter methylation between case and control. Subgroup analysis by gender showed that the methylation level of AHCY in males in the case group was lower than that in the control group, but the difference was not statistically significant in females. In a subgroup analysis by age, there was no significant difference in the AHCY methylation level between the case and control in the young group (≤44 years old). However, the level of AHCY gene methylation in the middle-aged group (45-59 years old) was significantly higher and the aged group (≥60 years old) was significantly lower than that in the control groups. However, CBS promoter methylation levels were significantly lower in the case group than in the control group (median PMR: 70.20% vs 104.10%, P = 3.71E-10). In addition, the CBS methylation levels of males and females in the case group were significantly lower than those in the control group (male: 64.33% vs 105%, P = 2.667E-08; female: 78.05% vs 102.8%, P = 0.003). We also found that the CBS levels in the young (23-44), middle-aged (45-59), and older (60-90) groups were significantly lower than those in the control group (young group: 69.97% vs 114.71%; P = 0.015; middle-aged group: 56.04% vs 91.71%; P = 6.744E-06; older group: 81.6% vs 119.35%; P = 2.644E-04). Our ROC curve analysis of CBS hypomethylation showed an area under the curve of 0.713, a sensitivity of 67.4%, and a specificity of 74.0%. CONCLUSION Our study suggests that hypomethylation of the CBS promoter may be closely related to the risk of cerebral infarction and may be used as a non-invasive diagnostic biomarker for cerebral infarction.
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Affiliation(s)
- Xiaodong Li
- Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450006, Henan, China
| | - Shufang Bu
- Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450006, Henan, China
| | - Ran Ran Pan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Cong Zhou
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Kun Qu
- Department of Neurology, the 960th of Hospital of PLA, Zibo, 255330, Shandong, China
| | - Xiuru Ying
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jie Zhong
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jianhao Xiao
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Qian Yuan
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Simiao Zhang
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Laura Tipton
- Bioinformatics Core, Department of Complementary and Integrative Medicine and John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China.
| | - Youping Deng
- Bioinformatics Core, Department of Complementary and Integrative Medicine and John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96822, USA.
| | - Shiwei Duan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
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Cao L, Hu T, Lu H, Peng D. N-MYC Downstream Regulated Gene 4 ( NDRG4), a Frequent Downregulated Gene through DNA Hypermethylation, plays a Tumor Suppressive Role in Esophageal Adenocarcinoma. Cancers (Basel) 2020; 12:cancers12092573. [PMID: 32927604 PMCID: PMC7565689 DOI: 10.3390/cancers12092573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Esophageal adenocarcinoma has become a major clinical challenge in the western world due to its rapid increasing incidence and poor overall prognosis. Understanding the molecular events of its tumorigenesis is the key to better diagnosis and development of better therapeutic strategies. In the current study we aimed to identify epigenetic alteration targets in esophageal adenocarcinoma. We focused on a candidate gene, NDRG4 (N-myc downregulated gene 4). We found that NDRG4 was frequent downregulated in esophageal adenocarcinoma through DNA hypermethylation of its promoter region. Re-expression of NRDG4 in cancer cells significantly suppressed tumor growth via inhibition of cell proliferation. These results will improve our understanding on how dysfunction of NDRG4 contributes to esophageal adenocarcinoma. DNA hypermethylation of NDRG4 may be a useful biomarker in clinical monitoring of esophageal adenocarcinoma patients. Abstract The incidence of esophageal adenocarcinoma (EAC) has been rising dramatically in the past few decades in the United States and Western world. The N-myc downregulated gene 4 (NDRG4) belongs to the human NDRG family. In this study, we aimed to identify the expression levels, regulation, and functions of NDRG4 in EAC. Using an integrative epigenetic approach, we identified genes showing significant downregulation in EAC and displaying upregulation after 5-Aza-deoxycitidine. Among these genes, likely to be regulated by DNA methylation, NDRG4 was among the top 10 candidate genes. Analyses of TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) data sets and EAC tissue samples demonstrated that NDRG4 was significantly downregulated in EAC (p < 0.05). Using Pyrosequencing technology for quantification of DNA methylation, we detected that NDRG4 promoter methylation level was significantly higher in EAC tissue samples, as compared to normal esophagus samples (p < 0.01). A strong inverse correlation between NDRG4 methylation and its gene expression levels (r = −0.4, p < 0.01) was observed. Treatment with 5-Aza restored the NDRG4 expression, confirming that hypermethylation is a driving force for NDRG4 silencing in EAC. Pathway and gene set enrichment analyses of TCGA data suggested that NDRG4 is strongly associated with genes related to cell cycle regulation. Western blotting analysis showed significant downregulation of Cyclin D1, CDK4 and CDK6 in EAC cells after overexpression of NDRG4. Functionally, we found that the reconstitution of NDRG4 resulted in a significant reduction in tumor cell growth in two-dimensional (2D) and three-dimensional (3D) organotypic culture models and inhibited tumor cell proliferation as indicated by the EdU (5-ethynyl-2′-deoxyuridine) proliferation assay.
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Affiliation(s)
- Longlong Cao
- Department of Surgery, Miller School of Medicine, Miami, FL 33136, USA; (L.C.); (T.H.); (H.L.)
| | - Tianling Hu
- Department of Surgery, Miller School of Medicine, Miami, FL 33136, USA; (L.C.); (T.H.); (H.L.)
| | - Heng Lu
- Department of Surgery, Miller School of Medicine, Miami, FL 33136, USA; (L.C.); (T.H.); (H.L.)
| | - Dunfa Peng
- Department of Surgery, Miller School of Medicine, Miami, FL 33136, USA; (L.C.); (T.H.); (H.L.)
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
- Correspondence: ; Tel.: 305-243-3989
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9
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Romero-Garcia S, Prado-Garcia H, Carlos-Reyes A. Role of DNA Methylation in the Resistance to Therapy in Solid Tumors. Front Oncol 2020; 10:1152. [PMID: 32850327 PMCID: PMC7426728 DOI: 10.3389/fonc.2020.01152] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the recent advances in chemotherapeutic treatments against cancer, some types of highly aggressive and invasive cancer develop drug resistance against conventional therapies, which continues to be a major problem in the fight against cancer. In recent years, studies of alterations of DNA methylome have given us a better understanding of the role of DNA methylation in the development of tumors. DNA methylation (DNAm) is an epigenetic change that promotes the covalent transfer of methyl groups to DNA. This process suppresses gene expression through the modulation of the transcription machinery access to the chromatin or through the recruitment of methyl binding proteins. DNAm is regulated mainly by DNA methyltransferases. Aberrant DNAm contributes to tumor progression, metastasis, and resistance to current anti-tumoral therapies. Aberrant DNAm may occur through hypermethylation in the promoter regions of tumor suppressor genes, which leads to their silencing, while hypomethylation in the promoter regions of oncogenes can activate them. In this review, we discuss the impact of dysregulated methylation in certain genes, which impact signaling pathways associated with apoptosis avoidance, metastasis, and resistance to therapy. The analysis of methylome has revealed patterns of global methylation, which regulate important signaling pathways involved in therapy resistance in different cancer types, such as breast, colon, and lung cancer, among other solid tumors. This analysis has provided gene-expression signatures of methylated region-specific DNA that can be used to predict the treatment outcome in response to anti-cancer therapy. Additionally, changes in cancer methylome have been associated with the acquisition of drug resistance. We also review treatments with demethylating agents that, in combination with standard therapies, seem to be encouraging, as tumors that are in early stages can be successfully treated. On the other hand, tumors that are in advanced stages can be treated with these combination schemes, which could sensitize tumor cells that are resistant to the therapy. We propose that rational strategies, which combine specific demethylating agents with conventional treatment, may improve overall survival in cancer patients.
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Affiliation(s)
- Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Heriberto Prado-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
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10
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Tepus M, Yau TO. Non-Invasive Colorectal Cancer Screening: An Overview. Gastrointest Tumors 2020; 7:62-73. [PMID: 32903904 DOI: 10.1159/000507701] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Colorectal cancer (CRC) follows a protracted stepwise progression, from benign adenomas to malignant adenocarcinomas. If detected early, 90% of deaths are preventable. However, CRC is asymptomatic in its early-stage and arises sporadically within the population. Therefore, CRC screening is a public health priority. Summary Faecal immunochemical test (FIT) is gradually replacing guaiac faecal occult blood test and is now the most commonly used screening tool for CRC screening program globally. However, FIT is still limited by the haemoglobin degradation and the intermittent bleeding patterns, so that one in four CRC cases are still diagnosed in a late stage, leading to poor prognosis. A multi-target stool DNA test (Cologuard, a combination of NDRG4 and BMP3 DNA methylation, KRAS mutations, and haemoglobin) and a plasma SEPT9 DNA methylation test (Epi proColon) are non-invasive tools also approved by the US FDA, but those screening approaches are not cost-effective, and the detection accuracies remain unsatisfactory. In addition to the approved tests, faecal-/blood-based microRNA and CRC-related gut microbiome screening markers are under development, with work ongoing to find the best combination of molecular biomarkers which maximise the screening sensitivity and specificity. Key Message Maximising the detection accuracy with a cost-effective approach for non-invasive CRC screening is urgently needed to further reduce the incidence of CRC and associated mortality rates.
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Affiliation(s)
- Melanie Tepus
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Tung On Yau
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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11
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Network Structure Analysis Identifying Key Genes of Autism and Its Mechanism. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:3753080. [PMID: 32273901 PMCID: PMC7125446 DOI: 10.1155/2020/3753080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/04/2019] [Accepted: 02/22/2020] [Indexed: 01/16/2023]
Abstract
Identifying the key genes of autism is of great significance for understanding its pathogenesis and improving the clinical level of medicine. In this paper, we use the structural parameters (average degree) of gene correlation networks to identify genes related to autism and study its pathogenesis. Based on the gene expression profiles of 82 autistic patients (the experimental group, E) and 64 healthy persons (the control group, C) in NCBI database, spearman correlation networks are established, and their average degrees under different thresholds are analyzed. It is found that average degrees of C and E are basically separable at the full thresholds. This indicates that there is a clear difference between the network structures of C and E, and it also suggests that this difference is related to the mechanism of disease. By annotating and enrichment analysis of the first 20 genes (MD-Gs) with significant difference in the average degree, we find that they are significantly related to gland development, cardiovascular development, and embryogenesis of nervous system, which support the results in Alter et al.'s original research. In addition, FIGF and CSF3 may play an important role in the mechanism of autism.
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Li Y, Liu H, Chen H, Shao J, Su F, Zhang S, Cai X, He X. DERL3 functions as a tumor suppressor in gastric cancer. Comput Biol Chem 2020; 84:107172. [DOI: 10.1016/j.compbiolchem.2019.107172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/13/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023]
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Liu X, Fu J, Bi H, Ge A, Xia T, Liu Y, Sun H, Li D, Zhao Y. DNA methylation of SFRP1, SFRP2, and WIF1 and prognosis of postoperative colorectal cancer patients. BMC Cancer 2019; 19:1212. [PMID: 31830937 PMCID: PMC6909551 DOI: 10.1186/s12885-019-6436-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/05/2019] [Indexed: 12/24/2022] Open
Abstract
Background As biomarkers, DNA methylation is used to detect colorectal cancer (CRC) and make assessment of CRC prognosis. The published findings showed the association between the methylation of SFRP1, SFRP2, and WIF1, located in the Wnt signaling pathway, and the prognosis of CRC were not consistent. Our study aimed to explore the potential possibility of SFRP1, SFRP2, and WIF1 concomitant promoter methylation as prognostic biomarkers of postoperative CRC patients. Methods As a total of 307 sporadic postoperative CRC patients were followed up, we detected SFRP1, SFRP2, and WIF1 methylation obtained from tumor tissues and adjacent non-tumor tissues respectively on the basis of methylation-sensitive high resolution melting analysis. Univariate and multivariate Cox regressions were carried out so as to assess the potential possibility of SFRP1, SFRP2, and WIF1 promoter methylation as predictors of prognosis. Confounders in our study were controlled by Propensity Score (PS) analysis. Results The SFRP1, SFRP2, and WIF1 methylation levels in tumor tissues were significantly higher than that in adjacent non-tumor tissues (P < 0.001). SFRP2 hypermethylation was significantly associated with a favorable clinical outcome at the hazard ratio (HR) of 0.343 [95% confidence intervals (CI): 0.164–0.718, P = 0.005] and 0.410 (95% CI: 0.200–0.842, P = 0.015) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1 and SFRP2 was significantly associated with a favorable clinical outcome at the HR of 0.333 (95% CI: 0.159–0.694, P = 0.003) and 0.398 (95% CI: 0.192–0.821, P = 0.013) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1, SFRP2 and WIF1 was significantly associated with a favorable clinical outcome at the HR of 0.326 (95% CI: 0.117–0.908, P = 0.032) and 0.401 (95% CI: 0.146–1.106, P = 0.077) in multivariate Cox regression and PS analysis, respectively. Conclusions SFRP1, SFRP2, and WIF1 were frequently hypermethylated in CRC tumor tissues. It was apparent that the promoter hypermethylation of SFRP2 and co-hypermethylation of SFRP1 and SFRP2 might be considered as independent prognostic predictors for survival advantage of postoperative CRC patients.
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Affiliation(s)
- Xinyan Liu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Jinming Fu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Haoran Bi
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Anqi Ge
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China.
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Ying X, Pan R, Zhong J, Wu B, Jiang Y, Ying J, Zhou C, Dai J, Zhao S, Shen Y, Zhang W, Duan S. Significant association of EED promoter hypomethylation with colorectal cancer. Oncol Lett 2019; 18:1564-1570. [PMID: 31423224 DOI: 10.3892/ol.2019.10432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/12/2019] [Indexed: 01/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common and serious types of malignancy worldwide. The embryonic ectoderm development (EED) gene is important to maintain transcriptional repressive states of genes over successive cell generations. The present study aimed to investigate the association between EED methylation and CRC. A total of 111 CRC tissue samples, 111 paired para-tumor tissues and 20 colorectal normal tissues were obtained for EED methylation assay, which was performed using a quantitative methylation-specific polymerase chain reaction. The percentage of methylated reference was calculated to represent the DNA methylation level. A dual-luciferase reporter gene assay was used to detect the gene promoter activity of a EED fragment. The current results revealed a significant difference in the EED methylation levels among tumor, para-tumor and normal colorectal tissues (tumor vs. para-tumor vs. normal, 5.03±4.61 vs. 8.65±11.50 vs. 40.12±45.31; F=45.014; P<0.0001). The dual-luciferase reporter gene assay demonstrated that the transcriptional activity of recombinant pGL3-EED plasmid was significantly higher compared with that of the pGL3-Basic control vector (fold-change, 3.15; P=0.014), which suggests the EED fragment can promote gene expression. In conclusion, the present study demonstrated that EED hypomethylation may be an important factor associated with CRC.
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Affiliation(s)
- Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Boyi Wu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yuting Jiang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shuangying Zhao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yinan Shen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Wei Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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Yu C, Hao X, Zhang S, Hu W, Li J, Sun J, Zheng M. Characterization of the prognostic values of the NDRG family in gastric cancer. Therap Adv Gastroenterol 2019; 12:1756284819858507. [PMID: 31384305 PMCID: PMC6647212 DOI: 10.1177/1756284819858507] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 05/07/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The N-myc downstream-regulated gene (NDRG) family, NDRG1-4, has been involved in a wide spectrum of biological functions in multiple cancers. However, their prognostic values remain sparse in gastric cancer (GC). Therefore, it is crucial to systematically investigate the prognostic values of the NDRG family in GC. METHODS The prognostic values of the NDRG family were evaluated by Kaplan-Meier Plotter and SurvExpress. The mRNA of the NDRG family was investigated in The Cancer Genome Atlas (TCGA). Transcription factors (TFs) and miRNAs associated with the NDRG family were predicted by NetworkAnalysis. The prognostic values of DNA methylation levels were analyzed by MethSurv. The correlation between immune cells and the NDRG family was evaluated by the Tumor Immune Estimation Resource (TIMER) database. RESULTS High levels of mRNA expression of NDRG2 and NDRG3 were associated with a favorable prognosis in all GCs. In HER2 - GC, NDRG1 was significantly associated with a poor prognosis of GC [hazard ratio (HR) = 1.65, 95% confidence interval (CI) = 1.16-2.33, p = 0.0046]. In HER2 + GC, NDRG4 showed a poor prognosis (HR = 1.4, 95% CI: 1.06-1.85, p = 0.017). NDRG4 was an independent prognostic factor in recurrence-free survival by TCGA cohort. The low-risk NDRG-signature group displayed a significantly favorable survival outcome than the high-risk group (HR = 1.76, 95% CI: 1.2-2.59, p = 0.00385). The phosphorylated protein NDRG1 (NDRG1_pT346) displayed a favorable overall survival and was significantly associated with HER2 and phosphorylated HER2. Epidermis development was the top biological process (BP) for coexpressed genes associated with NDRG1 and NDRG4, while mitotic nuclear division and mitotic cell processes were the top BPs for NDRG2 and NDRG3, respectively. Overall, 6 CpGs of NDRG1, 4 CpGs of NDRG2, 3 CpGs of NDRG3 and 24 CpGs of NDRG4 were associated with significant prognosis. CD4+ T-cells showed the highest correlation with NDRG4 (correlation = 0.341, p = 2.14e-11). Furthermore, BCL6 in follicular helper T-cells (Tfh) cells showed the highest association with NDRG4 (correlation = 0.438, p = 00e+00). CONCLUSIONS This study analyzed the multilevel prognostic values and biological roles of the NDRG family in GC.
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Affiliation(s)
- Chaoran Yu
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
| | - Xiaohui Hao
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
| | - Sen Zhang
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
| | - Wenjun Hu
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
| | - Jianwen Li
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
| | - Jing Sun
- Department of Gastrointestinal Surgery, Ruijin
Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai,
China
- Shanghai Minimally Invasive Surgery Center,
Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,
Shanghai, China
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Jandrey EHF, Moura RP, Andrade LNS, Machado CL, Campesato LF, Leite KRM, Inoue LT, Asprino PF, da Silva APM, de Barros ACSD, Carvalho A, de Lima VC, Carraro DM, Brentani HP, da Cunha IW, Soares FA, Parmigiani RB, Chammas R, Camargo AA, Costa ÉT. NDRG4 promoter hypermethylation is a mechanistic biomarker associated with metastatic progression in breast cancer patients. NPJ Breast Cancer 2019; 5:11. [PMID: 30963110 PMCID: PMC6450950 DOI: 10.1038/s41523-019-0106-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/11/2019] [Indexed: 01/27/2023] Open
Abstract
The risk of developing metastatic disease in breast cancer patients is traditionally predictable based on the number of positive axillary lymph nodes, complemented with additional clinicopathological factors. However, since lymph node-negative patients have a 20-30% probability of developing metastatic disease, lymph node information alone is insufficient to accurately assess individual risk. Molecular approaches, such as multigene expression panels, analyze a set of cancer-related genes that more accurately predict the early risk of metastasis and the treatment response. Here, we present N-Myc downstream-regulated gene 4 (NDRG4) epigenetic silencing as a mechanistic biomarker of metastasis in ductal invasive breast tumors. While aberrant NDRG4 DNA hypermethylation is significantly associated with the development of metastatic disease, downregulation of NDRG4 transcription and protein expression is functionally associated with enhanced lymph node adhesion and cell mobility. Here, we show that epigenetic silencing of NDRG4 modulates integrin signaling by assembling β1-integrins into large punctate clusters at the leading edge of tumor cells to promote an "adhesive switch," decreasing cell adhesion to fibronectin and increasing cell adhesion and migration towards vitronectin, an important component of human lymph nodes. Taken together, our functional and clinical observations suggest that NDRG4 is a potential mechanistic biomarker in breast cancer that is functionally associated with metastatic disease.
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Affiliation(s)
| | | | - Luciana N. S. Andrade
- Laboratório de Oncologia Experimental, Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, São Paulo, SP Brazil
| | - Camila L. Machado
- Laboratório de Oncologia Experimental, Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, São Paulo, SP Brazil
| | | | | | - Lilian T. Inoue
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP Brazil
| | - Paula F. Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP Brazil
| | | | | | | | - Vladmir C. de Lima
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, Fundação Antônio Prudente, São Paulo, SP Brazil
| | - Dirce M. Carraro
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, Fundação Antônio Prudente, São Paulo, SP Brazil
| | - Helena P. Brentani
- LIM23-Instituto de Psiquiatria, Faculdade de Medicina da Universidade de São Paulo (USP), São Paulo, Brazil
| | | | | | | | - Roger Chammas
- Laboratório de Oncologia Experimental, Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, São Paulo, SP Brazil
| | - Anamaria A. Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP Brazil
- Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - Érico T. Costa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP Brazil
- Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
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Zhang L, Ji H, Huang Y, Hu H, Li B, Yang Y, Yu H, Chen X, Li W, Liu F, Wang S, Wang C, Chen K, Bao Y, Liu H, Duan S. Association of BAX hypermethylation with coronary heart disease is specific to individuals aged over 70. Medicine (Baltimore) 2019; 98:e14130. [PMID: 30681575 PMCID: PMC6358363 DOI: 10.1097/md.0000000000014130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION As a member of B-cell lymphoma-2 (BCL-2) gene family, BCL-2 associated X (BAX) is important for cell apoptosis. In this work, we investigated the association of BAX promoter DNA methylation with coronary heart disease (CHD) in Han Chinese. METHODS A SYBR green-based quantitative methylation specific PCR (qMSP) was used to test BAX methylation levels in 959 CHD cases and 514 controls. RESULTS Although BAX methylation was not associated with CHD in the total samples, further breakdown analysis by age showed that BAX hypermethylation was significantly associated with CHD for individuals aged over 70 (median percentage of methylation ratio [PMR], 10.70% in cases versus (vs) 2.25% in controls, P =.046). Moreover, BAX methylation was associated with smoking and lipoprotein A (Lp(a)) for individuals aged over 70 (CHD: smoking P = .012, Lp(a) P = .001; non-CHD: smoking P = .051, Lp(a) P = .004). Further analysis of Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data showed BAX expression was upregulated by 5-aza-2'-deoxycytidine demethylation agent (fold = 1.66, P = .038) and inversely correlated with BAX methylation (r = -0.428, P = 8E-05). CONCLUSIONS Our study supported that BAX hypermethylation might contribute to CHD risk via downregulation of BAX expression for individuals aged over 70.
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Affiliation(s)
- Limei Zhang
- Department of Cardiology, Yinzhou People's Hospital, Ningbo University, Ningbo
| | - Huihui Ji
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Yi Huang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Haochang Hu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Yong Yang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Xiaoying Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Wenxia Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Fang Liu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
| | - Shi Wang
- Department of Cardiology, Yinzhou People's Hospital, Ningbo University, Ningbo
| | - Chunming Wang
- Department of Cardiology, Yinzhou People's Hospital, Ningbo University, Ningbo
| | - Ke Chen
- Department of Cardiology, Yinzhou People's Hospital, Ningbo University, Ningbo
| | - Yingchun Bao
- Department of Cardiology, Yinzhou People's Hospital, Ningbo University, Ningbo
| | - Haibo Liu
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo
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18
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Pan R, Zhou C, Dai J, Ying X, Yu H, Zhong J, Zhang Y, Wu B, Mao Y, Wu D, Ying J, Zhang W, Duan S. Endothelial PAS domain protein 1 gene hypomethylation is associated with colorectal cancer in Han Chinese. Exp Ther Med 2018; 16:4983-4990. [PMID: 30542453 PMCID: PMC6257466 DOI: 10.3892/etm.2018.6856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/23/2018] [Indexed: 12/17/2022] Open
Abstract
Endothelial PAS domain-containing protein 1 (EPAS1) serves a role in angiogenesis, which is important for the development of tumors, including colorectal cancer (CRC). The current study aimed to estimate whether EPAS1 methylation was associated with CRC. A two-stage association study of EPAS1 methylation and CRC was conducted. In the first phase, EPAS1 methylation was evaluated in the tumor and adjacent non-tumor tissue samples from 41 patients with sporadic CRC in Jiangsu province, China. The diagnostic value of methylation of EPAS1 for CRC in the second phase was evaluated in 79 patients with sporadic CRC and 22 normal individuals in Zhejiang province, China. The methylation assay was performed using a quantitative methylation-specific polymerase chain reaction (qMSP) method. The percentage of methylated reference (PMR) was used to quantify the methylation level. The first-stage results indicated that EPAS1 promoter methylation was significantly lower in CRC tumor tissues compared with 5-cm-para-tumor tissues (median PMR, 0.59 vs. 1.22%; P=0.027) and 10-cm-para-tumor tissues (median PMR, 0.59 vs. 1.89%; P=0.001). In addition, the second-stage results indicated that EPAS1 promoter methylation was significantly lower in tumor tissues compared with 5-cm-para-tumor tissues (median PMR, 1.91 vs. 6.25%; P=3×10−7) and normal intestinal tissues from healthy controls (median PMR, 1.91 vs. 28.4%; P=5×10−7). Receiver Operating Characteristic curve analysis of the second-stage data indicated that the highest area under the curve of EPAS1 hypomethylation was 0.851 between Zhejiang CRC tissues and Zhejiang normal intestinal tissues (sensitivity, 95.5%; specificity, 60.8%).
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Affiliation(s)
- Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yihan Zhang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Boyi Wu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yiyi Mao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Dongping Wu
- Department of Medical Oncology, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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Vedeld HM, Goel A, Lind GE. Epigenetic biomarkers in gastrointestinal cancers: The current state and clinical perspectives. Semin Cancer Biol 2018; 51:36-49. [PMID: 29253542 PMCID: PMC7286571 DOI: 10.1016/j.semcancer.2017.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/17/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
Each year, almost 4.1 million people are diagnosed with gastrointestinal (GI) cancers. Due to late detection of this disease, the mortality is high, causing approximately 3 million cancer-related deaths annually, worldwide. Although the incidence and survival differs according to organ site, earlier detection and improved prognostication have the potential to reduce overall mortality burden from these cancers. Epigenetic changes, including aberrant promoter DNA methylation, are common events in both cancer initiation and progression. Furthermore, such changes may be identified non-invasively with the use of PCR based methods, in bodily fluids of cancer patients. These features make aberrant DNA methylation a promising substrate for the development of disease biomarkers for early detection, prognosis and for predicting response to therapy. In this article, we will provide an update and current clinical perspectives for DNA methylation alterations in patients with colorectal, gastric, pancreatic, liver and esophageal cancers, and discuss their potential role as cancer biomarkers.
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Affiliation(s)
- Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ajay Goel
- Center for Gastrointestinal Research, and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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Sawaki K, Kanda M, Kodera Y. Review of recent efforts to discover biomarkers for early detection, monitoring, prognosis, and prediction of treatment responses of patients with gastric cancer. Expert Rev Gastroenterol Hepatol 2018; 12:657-670. [PMID: 29902383 DOI: 10.1080/17474124.2018.1489233] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gastric cancer (GC) is the leading cause of cancer-related death worldwide. Despite recent advances in diagnosis and therapy, the prognosis of patients with GC is poor. Many patients have inoperable disease upon diagnosis or experience recurrent disease after curative gastrectomy. Unfortunately, tumor markers for GC, such as serum carcinoembryonic antigen and carbohydrate antigen 19-9, lack sufficient sensitivity and specificity. Therefore, effective biomarkers are required to detect early GC and to predict tumor recurrence and chemosensitivity. Areas covered: Here we aimed to review recent developments in techniques that improve the detection of aberrant expression of GC-associated molecules, including protein coding genes, microRNAs, long noncoding RNAs, and methylated promoter DNAs. Expert commentary: Detection of genetic and epigenetic alterations in gastric tissue or in the circulation will likely improve the diagnosis and management of GC to achieve significantly improved outcomes.
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Affiliation(s)
- Koichi Sawaki
- a Department of Gastroenterological Surgery (Surgery II) , Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Mitsuro Kanda
- a Department of Gastroenterological Surgery (Surgery II) , Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yasuhiro Kodera
- a Department of Gastroenterological Surgery (Surgery II) , Nagoya University Graduate School of Medicine , Nagoya , Japan
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Pan R, Yu H, Dai J, Zhou C, Ying X, Zhong J, Zhao J, Zhang Y, Wu B, Mao Y, Wu D, Ying J, Duan S. Significant association of PRMT6 hypomethylation with colorectal cancer. J Clin Lab Anal 2018; 32:e22590. [PMID: 29927001 DOI: 10.1002/jcla.22590] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Protein arginine N-methyltransferase 6 (PRMT6) was deemed to be indispensable in the variety of biological processes. Upregulated PRMT6 was found in various human diseases including cancer. Herein, we investigated the performance of PRMT6 methylation in the diagnosis for CRC. METHODS A quantitative methylation-specific polymerase chain reaction (qMSP) method was used to measure PRMT6 promoter methylation. The percentage of methylated reference (PMR) was applied to represent gene methylation level. RESULTS Our data indicated that PRMT6 promoter methylation levels were significantly lower in CRC tissues than those in paired nontumor tissues (median PMR: 36.93% vs 63.12%, P = 1E-6) and normal intestinal tissues (median PMR: 36.93% vs 506.55%, P = 8E-12). We further examined the potential role of PRMT6 hypomethylation by the receiver operating characteristic (ROC) curve. Our results showed that the area under the curve (AUC) was 0.644 (95% CI = 0.596-0.733) between CRC tissues and paired nontumor tissues, 0.958 (95% CI = 0.919-0.998) between CRC tissues and normal intestinal tissues, and 0.899 (95% CI = 0.825-0.972) between paired nontumor tissues and normal intestinal tissues. CONCLUSION Our study firstly indicated that the hypomethylation of PRMT6 promoter could be a novel diagnostic biomarker for CRC.
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Affiliation(s)
- Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jun Zhao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yihan Zhang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Boyi Wu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yiyi Mao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongping Wu
- Department of Medical Oncology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Ningbo, Zhejiang, China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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Hypermethylation of MDFI promoter with NSCLC is specific for females, non-smokers and people younger than 65. Oncol Lett 2018; 15:9017-9024. [PMID: 29805634 PMCID: PMC5958687 DOI: 10.3892/ol.2018.8535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 01/25/2018] [Indexed: 01/03/2023] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is a major subtype of lung cancer. Aberrant DNA methylation has been frequently observed in NSCLC. The aim of the present study was to investigate the role of MyoD family inhibitor (MDFI) methylation in NSCLC. Formalin-fixed paraffin-embedded tumor tissues and adjacent non-cancerous tissues were collected from a total of 111 patients with NSCLC. A methylation assay was performed using the quantitative methylation-specific polymerase chain reaction method. The percentage of methylated reference was used to represent the methylation level of the MDFI promoter. Data mining of a dataset from The Cancer Genome Atlas (TCGA) demonstrated that MDFI promoter methylation levels were significantly increased in 830 tumor tissues compared with 75 non-tumor tissues (P=0.012). However, the results on tissues obtained in the present study indicated that the MDFI promoter methylation levels in tumor tissues were not significantly different compared with those in the adjacent non-tumor tissues (P=0.159). Subsequent breakdown analysis identified that higher MDFI promoter methylation levels were significantly associated with NSCLC in females (P=0.031), but not in males (P=0.832). Age-based subgroup analysis demonstrated that higher MDFI promoter methylation levels were significantly associated with NSCLC in younger patients (≤65 years; P=0.003), but not in older patients (P=0.327). In addition, the association of MDFI methylation with NSCLC was significant in non-smokers (P=0.014), but not in smokers (P=0.832). Similar results also have been determined from subgroup analysis of the TCGA datasets. The Gene Expression Omnibus database indicated MDFI expression restoration in partial lung cancer cell lines (H1299 and Hotz) following demethylation treatment. However, it was identified that MDFI promoter hypermethylation was not significantly associated with prognosis of NSCLC (P>0.05). In conclusion, the present study indicated that the association of higher methylation of the MDFI promoter with NSCLC may be specific to females, non-smokers and people aged ≤65.
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Liu S, Chen X, Chen R, Wang J, Zhu G, Jiang J, Wang H, Duan S, Huang J. Diagnostic role of Wnt pathway gene promoter methylation in non small cell lung cancer. Oncotarget 2018; 8:36354-36367. [PMID: 28422739 PMCID: PMC5482660 DOI: 10.18632/oncotarget.16754] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Wnt signal pathway genes are known to be involved with cancer development. Here we tested the hypothesis whether DNA methylation of genes part of the Wnt signaling pathway could help the diagnosis of non-small cell lung cancer (NSCLC). The methylation levels of SFRP1, SFRP2, WIF1 and PRKCB in 111 NSCLC patients were evaluated by quantitative methylation-specific PCR (qMSP). Promoter methylation levels of four candidate genes were significantly higher in tumor tissues compared with the adjacent tissues. SFRP1, SFRP2 and PRKCB genes were all shown to be good predictors of NSCLC risk (SFRP1: AUC = 0.711; SFRP2: AUC = 0.631; PRKCB: AUC = 0.650). The combined analysis showed that the methylation status of the four genes had a sensitivity of 70.3% and a specificity of 73.9% in the prediction of NSCLC risk for study cohort. A higher diagnostic value with an AUC of 0.945 (95% CI: 0.923–0.967, sensitivity: 90.6%, specificity: 93.0%) was found in TCGA cohort. In addition, SFRP1 and SFRP2 hypermethylation events were specific to male patients. Further TCGA data mining analysis suggested that SFRP1_cg15839448, SFRP2_cg05774801, and WIF1_cg21383810 were inversely associated with the host gene expression. Moreover, GEO database analysis showed that 5′-Aza-deoxycytidine was able to upregulate gene expression in several lung cancer cell lines. Subsequent dual-luciferase reporter assay showed a crucial regulatory function of PRKCB promoter. In summary, our study showed that a panel of Wnt signal pathway genes (SFRP1, SFRP2, WIF1 and PRKCB) had the potential as methylation biomarkers in the diagnosis of NSCLC.
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Affiliation(s)
- Shunlin Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Xiaoying Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ruhua Chen
- Department of Respiratory Medicine, Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu 214200, China
| | - Jinzhi Wang
- Department of Cell Biology, School of Medicine, Soochow University, Suzhou, Jiangsu 215007, China
| | - Guoliang Zhu
- Department of Pathology, Huzhou First People's Hospital, Huzhou, Zhejiang 313000, China
| | - Jianzhong Jiang
- Department of Geriatrics, Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu 214200, China
| | - Hongwei Wang
- Realgen Biotechnology Co., Ltd. Zhangjiang High Technology Park, Shanghai 201203, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jianan Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
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Zhang Z, She J, Yang J, Bu X, Ji G, Zhu S, He S, Chu D. NDRG4 in gastric cancer determines tumor cell proliferation and clinical outcome. Mol Carcinog 2018; 57:762-771. [PMID: 29500881 DOI: 10.1002/mc.22798] [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: 09/18/2017] [Revised: 01/26/2018] [Accepted: 02/28/2018] [Indexed: 01/04/2023]
Abstract
As a novel candidate tumor suppressor, NDRG4 is largely unstudied in human malignancies. In this study, we investigated the protein expression level of NDRG4 in gastric cancer and its association with outcome of patients. In the present study, we recruited 286 patients with gastric cancer and investigated the protein and mRNA expression of NDRG4 in cancer and adjacent normal specimens by immunohistochemistry assay and real-time PCR. The association of NDRG4 level with clinicopathological characteristics was investigated by appropriate statistical analysis. NDRG4 overexpression and knockdown cell lines were established in order to detect its impact on proliferation and apoptosis. Significant decreased protein and mRNA expression of NDRG4 was found in gastric cancer, compared with adjacent normal specimens. Besides, it was found that NDRG4 protein expression in gastric cancer was significantly associated with tumor differentiation, invasion, metastasis, and stage. Patients with tumors of decreased NDRG4 level were more likely to have unfavorable disease-free and overall survival, in both univariate and multivariate analysis. In addition, overexpression of NDRG4 suppressed cell proliferation of gastric cancer cells in vitro; conversely, the proliferation of gastric cancer cells were enhanced by knockdown of NDRG4. These results proved for the first time that NDRG4 could be a potential tumor suppressor and prognostic marker of gastric cancer.
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Affiliation(s)
- Zixi Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Dermotology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Junjun She
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingyi Yang
- Information Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Bu
- State Key Laboratory of Cancer Biology and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Gang Ji
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shaojun Zhu
- Department of Pathology, Fourth Military Medical University, Xi'an, China
| | - Shuixiang He
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dake Chu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Cheng L, Shen Z, Zhou C. Promoter hypermethylation of PIEZO2 is a risk factor and potential clinical biomarker for laryngeal squamous cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:11635-11643. [PMID: 31966521 PMCID: PMC6966076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/22/2017] [Indexed: 06/10/2023]
Abstract
The aim of this study was to investigate the association between piezo type mechanosensitive ion channel component 2 (PIEZO2)-promoter methylation with and its clinical value for laryngeal squamous cell carcinoma (LSCC). Quantitative methylation-specific polymerase chain reaction technology was applied to measure PIEZO2 promoter methylation levels from 99 LSCC patients. Inclusive in the analysis were 133 (117 LSSC and 16 normal) samples from The Cancer Genome Atlas (TCGA). Our results showed significantly higher levels of PIEZO2 promoter methylation in LSCC than normal tissues (our cohort: P = 2.94E-21; TCGA cohort: P = 1.07E-19). In addition, PIEZO2 methylation was significantly associated with gender, differentiation, tumor (T) stage, lymph node metastasis, and clinical stage. The areas under the receiver characteristic curves (AUCs) based on our cohort and TCGA cohort were 0.917 and 0.978, respectively. Meanwhile, our study confirmed that PIEZO2 promoter hypermethylation could independently predict a poorer overall survival of LSCC patients (hazard ratio = 6.671; 95% confidence interval = 2.087-21.324). In conclusion, our study revealed that PIEZO2 promoter hypermethylation was a risk factor and might be involved in progression and metastasis, as well as serve as a potential clinical biomarker of LSCC.
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Affiliation(s)
- Lixin Cheng
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University Ningbo, Zhejiang, China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University Ningbo, Zhejiang, China
| | - Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University Ningbo, Zhejiang, China
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