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Liu T, Ji W, Cheng X, Lv L, Yu X, Wang N, Li M, Hu T, Shi Z. Revealing a Novel Methylated Integrin Alpha-8 Related to Extracellular Matrix and Anoikis Resistance Using Proteomic Analysis in the Immune Microenvironment of Lung Adenocarcinoma. Mol Biotechnol 2024:10.1007/s12033-024-01114-9. [PMID: 38514598 DOI: 10.1007/s12033-024-01114-9] [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: 09/15/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Genomic epigenetics of extracellular matrix (ECM) play an important role in lung adenocarcinoma (LUAD). Our study identified a signature of potential prognostic genes associated with ECM and constructed immune risk-related prognosis model in LUAD. We downloaded mRNAs transcriptome data, miRNAs expression data, and clinical patient information for LUAD based on The Cancer Genome Atlas. "Limma, clusterProfiler, ggplot2" R packages and GSEA were used to analyze meaningful genes and explore potential biological function. A competing endogenous RNA network was constructed to reveal the mechanism of ECM-related genes. Combined with clinical LUAD patients' characteristics, univariate and multivariate Cox regression analyses were used to build prognostic immune risk model. Next, we calculated AUC value of ROC curve, and explored survival probability of different risk groups. A total of 2966 mRNAs were differently expressed in LUAD samples and normal samples. Function enrichment analyses proved mRNAs were associated with many tumor pathways, such as cell adhesion, vascular smooth muscle contraction, and cell cycle. There were 18 mRNAs related to ECM receptor signaling pathway, and 7 mRNAs expressions were correlated with EGFR expression, but only 5mRNAs were associated with the long-term prognosis. Based on Integrin alpha-8 (ITGA8) molecule, we identified potential 3 miRNAs from several databases. The promoter of ITGA8 was higher-methylated and lower-expressed in LUAD. And lower-expressed group has poor prognosis for patients. 66 immunomodulators related to ITGA8 were performed to construct immune correlation prediction model (p < 0.05). Comprehensive analyses of ITGA8 revealed it combined focal adhesion kinase to activate PI3K/AKT signaling pathway to influence the occurrence and development of LUAD. A novel immune prognostic model about ITGA8 was constructed and verified in LUAD patients. Combined with non-coding genes and genomic epigenetics, identification of potential biomarkers provided new light on therapeutic strategy for clinical patients.
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Affiliation(s)
- Tingting Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Wen Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xue Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Lin Lv
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xiaohui Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Na Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Mengcong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Tinghua Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Zhihong Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China.
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Öling S, Struck E, Noreen-Thorsen M, Zwahlen M, von Feilitzen K, Odeberg J, Pontén F, Lindskog C, Uhlén M, Dusart P, Butler LM. A human stomach cell type transcriptome atlas. BMC Biol 2024; 22:36. [PMID: 38355543 PMCID: PMC10865703 DOI: 10.1186/s12915-024-01812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. RESULTS Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. CONCLUSIONS We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.
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Affiliation(s)
- S Öling
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - E Struck
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Noreen-Thorsen
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Zwahlen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - K von Feilitzen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - J Odeberg
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- The University Hospital of North Norway (UNN), 9019, Tromsø, Norway
- Department of Haematology, Coagulation Unit, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - F Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - C Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - M Uhlén
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - P Dusart
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - L M Butler
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway.
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden.
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden.
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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Shi S, Zhong J, Peng W, Yin H, Zhong D, Cui H, Sun X. System analysis based on the migration- and invasion-related gene sets identifies the infiltration-related genes of glioma. Front Oncol 2023; 13:1075716. [PMID: 37091145 PMCID: PMC10117932 DOI: 10.3389/fonc.2023.1075716] [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: 10/20/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The current database has no information on the infiltration of glioma samples. Here, we assessed the glioma samples' infiltration in The Cancer Gene Atlas (TCGA) through the single-sample Gene Set Enrichment Analysis (ssGSEA) with migration and invasion gene sets. The Weighted Gene Co-expression Network Analysis (WGCNA) and the differentially expressed genes (DEGs) were used to identify the genes most associated with infiltration. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the major biological processes and pathways. Protein-protein interaction (PPI) network analysis and the least absolute shrinkage and selection operator (LASSO) were used to screen the key genes. Furthermore, the nomograms and receiver operating characteristic (ROC) curve were used to evaluate the prognostic and predictive accuracy of this clinical model in patients in TCGA and the Chinese Glioma Genome Atlas (CGGA). The results showed that turquoise was selected as the hub module, and with the intersection of DEGs, we screened 104 common genes. Through LASSO regression, TIMP1, EMP3, IGFBP2, and the other nine genes were screened mostly in correlation with infiltration and prognosis. EMP3 was selected to be verified in vitro. These findings could help researchers better understand the infiltration of gliomas and provide novel therapeutic targets for the treatment of gliomas.
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Affiliation(s)
- Shuang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiacheng Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen Peng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Haoyang Yin
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Tan X, Liu Z, Wang Y, Wu Z, Zou Y, Luo S, Tang Y, Chen D, Yuan G, Yao K. miR-138-5p-mediated HOXD11 promotes cell invasion and metastasis by activating the FN1/MMP2/MMP9 pathway and predicts poor prognosis in penile squamous cell carcinoma. Cell Death Dis 2022; 13:816. [PMID: 36151071 PMCID: PMC9508180 DOI: 10.1038/s41419-022-05261-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 01/23/2023]
Abstract
The presence and extent of regional lymph node and distant metastasis are the most fatal prognostic factors in penile squamous cell carcinoma (PSCC). However, the available biomarkers and detailed mechanisms underlying the metastasis of PSCC remain elusive. Here, we explored the expression landscape of HOX genes in twelve paired PSCC tissues, including primary tumors, metastatic lymph nodes and corresponding normal tissues, and highlighted that HOXD11 was indispensable in the progression of PSCC. HOXD11 was upregulated in PSCC cell lines and tumors, especially in metastatic lymph nodes. High HOXD11 expression was associated with aggressive features, such as advanced pN stages, extranodal extension, pelvic lymph node and distant metastasis, and predicted poor survival. Furthermore, tumorigenesis assays demonstrated that knockdown of HOXD11 not only inhibited the capability of cell proliferation, invasion and tumor growth but also reduced the burden of metastatic lymph nodes. Further mechanistic studies indicated that miR-138-5p was a tumor suppressor in PSCC by inhibiting the translation of HOXD11 post-transcriptionally through binding to the 3' untranslated region. Furthermore, HOXD11 activated the transcription of FN1 to decompose the extracellular matrix and to promote epithelial mesenchymal transition-like phenotype metastasis via FN1/MMP2/MMP9 pathways. Our study revealed that HOXD11 is a promising prognostic biomarker and predicts advanced disease with poor outcomes, which could serve as a potential therapeutic target for PSCC.
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Affiliation(s)
- Xingliang Tan
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zhenhua Liu
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yanjun Wang
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zhiming Wu
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yuantao Zou
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Sihao Luo
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yi Tang
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Dong Chen
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Gangjun Yuan
- grid.190737.b0000 0001 0154 0904Department of Urology Oncological Surgery, Chongqing University Cancer Hospital, Chongqing, China ,grid.190737.b0000 0001 0154 0904Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Kai Yao
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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Wang L, Qiao C, Cao L, Cai S, Ma X, Song X, Jiang Q, Huang C, Wang J. Significance of HOXD transcription factors family in progression, migration and angiogenesis of cancer. Crit Rev Oncol Hematol 2022; 179:103809. [PMID: 36108961 DOI: 10.1016/j.critrevonc.2022.103809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 10/31/2022] Open
Abstract
The transcription factors (TFs) of the HOX family play significant roles during early embryonic development and cellular processes. They also play a key role in tumorigenesis as tumor oncogenes or suppressors. Furthermore, TFs of the HOXD geFIne cluster affect proliferation, migration, and invasion of tumors. Consequently, dysregulated activity of HOXD TFs has been linked to clinicopathological characteristics of cancer. HOXD TFs are regulated by non-coding RNAs and methylation of DNA on promoter and enhancer regions. In addition, HOXD genes modulate the biological function of cancer cells via the MEK and AKT signaling pathways, thus, making HOXD TFs, a suitable molecular marker for cancer prognosis and therapy. In this review, we summarized the roles of HOXD TFs in different cancers and highlighted its potential as a diagnostic and therapeutic target.
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Affiliation(s)
- Lumin Wang
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China; Institute of precision medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Chenyang Qiao
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Li Cao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Shuang Cai
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Xiaoping Ma
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Xinqiu Song
- Department of Cell Biology and Genetics, Medical College of Yan'an University, Yan'an, Shaanxi, PR China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China.
| | - Jinhai Wang
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China; Institute of precision medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
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7
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Wang J, Liu Z, Zhang C, Wang H, Li A, Liu B, Lian X, Ren Z, Zhang W, Wang Y, Zhang B, Pang B, Gao Y. Abnormal expression of HOXD11 promotes the malignant behavior of glioma cells and leads to poor prognosis of glioma patients. PeerJ 2021; 9:e10820. [PMID: 33614284 PMCID: PMC7877241 DOI: 10.7717/peerj.10820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/02/2021] [Indexed: 12/13/2022] Open
Abstract
Background Homeobox D11 (HOXD11) plays an important role in a variety of cancers, but its precise role in gliomas remains unclear. This study aimed to explore the relationship between HOXD11 and gliomas by combining bioinformatics methods with basic experimental validation. Materials and methods Obtain gene expression information and clinical information of glioma and non-tumor brain tissue samples from multiple public databases such as TCGA (666 glioma samples), CGGA (749 glioma samples), GEPIA(163 glioblastoma samples and 207 normal control samples), GEO (GSE4290 and GSE15824). Nine cases of glioma tissue and five cases of normal control brain tissue were collected from the clinical department of Henan Provincial People’s Hospital for further verification. A series of bioinformatic analysis methods were used to confirm the relationship between HOXD11 expression and overall survival and clinical molecular characteristics of patients with glioma. RT-qPCR was used to verify the change of expression level of HOXD11 in glioma cells and tissues. MTT assay, colony formation assay, wound-healing assay, immunofluorescence staining, flow cytometry and western blotting were used to detect the effect of HOXD11 on the biological behavior of glioma cell line U251. Results The high expression of HOXD11 was significantly related to age, World Health Organization (WHO) grade, chemotherapy status, histological type, and even 1p19q codeletion data and isocitrate dehydrogenase (IDH) mutation. HOXD11, as an independent risk factor, reduces the overall survival of glioma patients and has diagnostic value for the prognosis of glioma. Gene Set Enrichment Analysis (GSEA) showed that HOXD11 was significantly enriched in cell signaling pathway such as cell cycle, DNA replication and so on. Finally, we confirmed that the knockout of HOXD11 can inhibit the proliferation and invasion of U251 glioma cells, and change the biological behavior of tumor cells by preventing the progression of cell cycle. Conclusions HOXD11 may be used as a candidate biomarker for the clinical application of targeted drug and prognostic assessment treatment of glioma. In addition, This study will help to explore the pathological mechanism of glioma.
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Affiliation(s)
- Jialin Wang
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan, China
| | - Cheng Zhang
- North Broward Preparatory School, Nord Anglia Education, Coconut Creek, FL, United States of America
| | - Hongbo Wang
- Henan University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Ang Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan, China
| | - Binfeng Liu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xiaoyu Lian
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Zhishuai Ren
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Wang Zhang
- Department of Neurosurgery of the First Affiliate Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanbiao Wang
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Bo Zhang
- Henan University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Bo Pang
- Department of Neurosurgery, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan, China
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Wan L, Tan N, Zhang N, Xie X. Establishment of an immune microenvironment-based prognostic predictive model for gastric cancer. Life Sci 2020; 261:118402. [DOI: 10.1016/j.lfs.2020.118402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 02/08/2023]
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Wu J, Cheng J, Zhang F, Luo X, Zhang Z, Chen S. Estrogen receptor α is involved in the regulation of ITGA8 methylation in estrogen receptor-positive breast cancer. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:993. [PMID: 32953793 PMCID: PMC7475494 DOI: 10.21037/atm-20-5220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Integrin subunit α 8 (ITGA8) methylation has been associated with the development of several cancers, but its contribution to breast cancer remains unclear. The present study aimed to investigate the methylation status of ITGA8, and the underlying regulatory mechanisms of ITGA8 methylation in breast cancer. Methods ITGA8 expression was investigated using the Gene Expression Profiling Interactive Analysis 2 (GEPIA2) database and the Breast Cancer Gene-Expression Miner v.4.4 (bc-GenExMiner v4.4). The association between ITGA8 expression levels and the survival rate of breast cancer patients was evaluated using The Cancer Genome Atlas (TCGA) database and Gene Expression-based Outcome for Breast Cancer Online (GOBO): Gene Set Analysis. Methylation-specific PCR (MSP) was used to detect the methylation of ITGA8. Protein level of ITGA8 was determined by Western blot analysis. Results ITGA8 was expressed at low levels in human breast cancer cells compared to non-tumorigenic breast cells and breast tissue, and was upregulated in estrogen receptor (ER)-positive tissue compared with ER-negative tissue (P<0.01). ITGA8 gene expression was negatively associated with breast tumor stage and survival rate in all breast cancer patients. However, ER-positive patients with low ITGA8 expression showed poorer distant metastasis-free survival (DMFS) and recurrence-free survival (RFS) rates than patients with high ITGA8 expression. This was not observed in the ER-negative population. Mechanistically speaking, hypermethylation of ITGA8 was discovered in ER-positive breast cancer cells. Administration of the methylation inhibitor, 5-aza-2’-deoxycytidine (5-aza-dC), significantly elevated protein expression of ITGA8 in ER-positive breast cancer cells compared to ER-negative cells. The positive association between ITGA8 status and methylation was also observed in clinical tissue specimens. When treated with 17-beta-estradiol, an antagonist of ERα, 5-aza-dC-induced upregulation of ITGA8 in ER-positive breast cancer cells was no longer observed. Conclusions Low ITGA8 expression in ER-positive breast cancer might be caused by the hypermethylation of ITGA8, a process dependent on ERα. Our findings provide an important foundation for investigations into ITGA8-targeted treatment strategies for ER-positive breast cancer.
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Affiliation(s)
- Jingxun Wu
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jianghong Cheng
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical University, Xi'an, China
| | - Fuxing Zhang
- Department of General Surgery, The First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Xianyang Luo
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Otolaryngology Head and Neck Surgery, Xiamen, China.,Teaching Hospital of Fujian Medical University, Fuzhou, China
| | - Zhiming Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Teaching Hospital of Fujian Medical University, Fuzhou, China
| | - Shuai Chen
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical University, Xi'an, China.,Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Otolaryngology Head and Neck Surgery, Xiamen, China.,Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
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Bai G, Song J, Yuan Y, Chen Z, Tian Y, Yin X, Niu Y, Liu J. Systematic analysis of differentially methylated expressed genes and site-specific methylation as potential prognostic markers in head and neck cancer. J Cell Physiol 2019; 234:22687-22702. [PMID: 31131446 PMCID: PMC6772109 DOI: 10.1002/jcp.28835] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC) remains one of the most malignant tumors with a significantly high mortality. DNA methylation exerts a vital role in the prognosis of HNC. In this study, we try to screen abnormal differential methylation genes (DMGs) and pathways in Head-Neck Squamous Cell Carcinoma via integral bioinformatics analysis. Data of gene expression microarrays and gene methylation microarrays were obtained from the Cancer Genome Atlas database. Aberrant DMGs were identified by the R Limma package. We conducted the Cox regression analysis to select the prognostic aberrant DMGs and site-specific methylation. Five aberrant DMGs were recognized that significantly correlated with overall survival. The prognostic model was constructed based on five DMGs (PAX9, STK33, GPR150, INSM1, and EPHX3). The five DMG models acted as prognostic biomarkers for HNC. The area under the curve based on the five DMGs predicting 5-year survival is 0.665. Moreover, the correlation between the DMGs/site-specific methylation and gene expression was also explored. The findings demonstrated that the five DMGs can be used as independent prognostic biomarkers for predicting the prognosis of patients with HNC. Our study might lay the groundwork for further mechanism exploration in HNC and may help identify diagnostic biomarkers for early stage HNC.
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Affiliation(s)
- Guohui Bai
- Zunyi Medical UniversityZunyiGuizhouChina
- Special Key Laboratory of Oral Diseases ResearchStomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial SurgeryGuizhou Provincial People's HospitalGuizhouChina
| | | | - Zhu Chen
- Guiyang Hospital of StomatologyGuizhouChina
| | - Yuan Tian
- Stomatology Colledge Affiliated to Zunyi Medical UniversityZunyiGuizhouChina
| | - Xinhai Yin
- Department of Oral and Maxillofacial SurgeryGuizhou Provincial People's HospitalGuizhouChina
| | - Yuming Niu
- Department of Stomatology and Center for Evidence‐Based Medicine and Clinical Research, Taihe HospitalHubei University of MedicineShiyanChina
| | - Jianguo Liu
- Zunyi Medical UniversityZunyiGuizhouChina
- Special Key Laboratory of Oral Diseases ResearchStomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
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11
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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12
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Unverricht-Yeboah M, Giesen U, Kriehuber R. Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation-potential biomarkers for the discrimination of radiation qualities. JOURNAL OF RADIATION RESEARCH 2018; 59:411-429. [PMID: 29800458 PMCID: PMC6054186 DOI: 10.1093/jrr/rry038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/29/2017] [Indexed: 05/27/2023]
Abstract
Gene expression analysis was carried out in Jurkat cells in order to identify candidate genes showing significant gene expression alterations allowing robust discrimination of the Auger emitter 123I, incorporated into the DNA as 123I-iododeoxyuridine (123IUdR), from α- and γ-radiation. The γ-H2AX foci assay was used to determine equi-effect doses or activity, and gene expression analysis was carried out at similar levels of foci induction. Comparative gene expression analysis was performed employing whole human genome DNA microarrays. Candidate genes had to show significant expression changes and no altered gene regulation or opposite regulation after exposure to the radiation quality to be compared. The gene expression of all candidate genes was validated by quantitative real-time PCR. The functional categorization of significantly deregulated genes revealed that chromatin organization and apoptosis were generally affected. After exposure to 123IUdR, α-particles and γ-rays, at equi-effect doses/activity, 155, 316 and 982 genes were exclusively regulated, respectively. Applying the stringent requirements for candidate genes, four (PPP1R14C, TNFAIP8L1, DNAJC1 and PRTFDC1), one (KLF10) and one (TNFAIP8L1) gene(s) were identified, respectively allowing reliable discrimination between γ- and 123IUdR exposure, γ- and α-radiation, and α- and 123IUdR exposure, respectively. The Auger emitter 123I induced specific gene expression patterns in Jurkat cells when compared with γ- and α-irradiation, suggesting a unique cellular response after 123IUdR exposure. Gene expression analysis might be an effective tool for identifying biomarkers for discriminating different radiation qualities and, furthermore, might help to explain the varying biological effectiveness at the mechanistic level.
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Affiliation(s)
- Marcus Unverricht-Yeboah
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich, Jülich, Germany
| | - Ulrich Giesen
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, Braunschweig, Germany
| | - Ralf Kriehuber
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich, Jülich, Germany
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HOX genes: potential candidates for the progression of laryngeal squamous cell carcinoma. Tumour Biol 2016; 37:15087-15096. [PMID: 27658780 DOI: 10.1007/s13277-016-5356-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a very aggressive cancer, considered to be a subtype of the head and neck squamous cell carcinoma (HNSCC). Despite significant advances in the understanding and treatment of cancer, prognosis of patients with LSCC has not improved recently. In the present study, we sought to understand better the genetic mechanisms underlying LSCC development. Thirty-two tumor samples were collected from patients undergoing surgical resection of LSCC. The samples were submitted to whole-genome cDNA microarray analysis aiming to identify genetic targets in LSCC. We also employed bioinformatic approaches to expand our findings using the TCGA database and further performed functional assays, using human HNSCC cell lines, to evaluate viability, cell proliferation, and cell migration after silencing of selected genes. Eight members of the homeobox gene family (HOX) were identified to be overexpressed in LSCC samples when compared to normal larynx tissue. Quantitative RT-PCR analysis validated the overexpression of HOX gene family members in LSCC. Receiver operating characteristic (ROC) statistical method curve showed that the expression level of seven members of HOX gene family can distinguish tumor from nontumor tissue. Correlation analysis of clinical and gene expression data revealed that HOXC8 and HOXD11 genes were associated with the differentiation degree of tumors and regional lymph node metastases, respectively. Additionally, siRNA assays confirmed that HOXC8, HOXD10, and HOXD11 genes might be critical for cell colony proliferation and cell migration. According to our findings, several members of the HOX genes were overexpressed in LSCC samples and seem to be required in biological processes involved in tumor development. This suggests that HOX genes might play a critical role in the physiopathology of LSCC tumors.
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Miller KR, Patel JN, Ganapathi MK, Tait DL, Ganapathi RN. Biological role and clinical implications of homeobox genes in serous epithelial ovarian cancer. Gynecol Oncol 2016; 141:608-615. [DOI: 10.1016/j.ygyno.2016.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/30/2023]
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Kok-Sin T, Mokhtar NM, Ali Hassan NZ, Sagap I, Mohamed Rose I, Harun R, Jamal R. Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data. Oncol Rep 2015; 34:22-32. [PMID: 25997610 PMCID: PMC4484611 DOI: 10.3892/or.2015.3993] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/30/2015] [Indexed: 12/12/2022] Open
Abstract
Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) p-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that contribute to colorectal carcinogenesis.
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Affiliation(s)
- Teow Kok-Sin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nur Zarina Ali Hassan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Roslan Harun
- Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Pua HH, Krishnamurthi S, Farrell J, Margeta M, Ursell PC, Powers M, Slavotinek AM, Jeng LJB. Novel interstitial 2.6 Mb deletion on 9q21 associated with multiple congenital anomalies. Am J Med Genet A 2015; 164A:237-42. [PMID: 24501764 DOI: 10.1002/ajmg.a.36230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Array comparative genomic hybridization (aCGH) is now commonly used to identify copy number changes in individuals with developmental delay, intellectual disabilities, autism spectrum disorders, and/or multiple congenital anomalies. We report on an infant with multiple congenital anomalies and a novel 2.6 Mb interstitial deletion within 9q21.32q21.33 detected by aCGH. Her clinical presentation included dysmorphic craniofacial features, cleft palate, atrial septal defect, bicornuate uterus, bilateral hip dislocation, hypotonia, and recurrent pneumonia. Parental aCGH studies were negative for copy loss in this region. To our knowledge, no similar deletions have been reported in available databases or published literature. This deletion encompasses 12 genes, and prediction algorithms as well as experimental data suggest that a subset is likely to be haploinsufficient. Included are a neurotrophin receptor (NKG2D), a gene implicated in cilia function (KIF27), an adaptor protein important for ubiquitin-dependent protein quality control (UBQLN1), a gene important for transcription and signaling (HNRNPK), and a gene involved in maintaining genomic stability (RMI1). Identifying additional patients with similar copy losses and further study of these genes will contribute to a better understanding of the pathophysiology of multiple congenital anomalies.
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Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crécy-Lagard V. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol 2014; 9:1812-25. [PMID: 24911101 PMCID: PMC4136680 DOI: 10.1021/cb500278k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Queuosine (Q) is a modification found
at the wobble position of
tRNAs with GUN anticodons. Although Q is present in most eukaryotes
and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or
microflora, making q an important but under-recognized micronutrient
for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases
(eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous
accessory subunit (QTRTD1) forming a complex that catalyzes q insertion
into target tRNAs. Phylogenetic analysis of eTGT subunits revealed
a patchy distribution pattern in which gene losses occurred independently
in different clades. Searches for genes co-distributing with eTGT
family members identified DUF2419 as a potential Q salvage protein
family. This prediction was experimentally validated in Schizosaccharomyces
pombe by confirming that Q was present by analyzing tRNAAsp with anticodon GUC purified from wild-type cells and by
showing that Q was absent from strains carrying deletions in the QTRT1
or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya
with a few possible cases of horizontal gene transfer to bacteria.
The universality of the DUF2419 function was confirmed by complementing
the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues.
The enzymatic function of this family is yet to be determined, but
structural similarity with DNA glycosidases suggests a ribonucleoside
hydrolase activity.
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Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Céline Brochier-Armanet
- Université
Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie
Evolutive, Université de Lyon, 69622 Villeurbanne, France
| | - Kirk W. Gaston
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Farhad Forouhar
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - John F. Hunt
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Genetics Institute, Gainesville, Florida 32611, United States
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A 92-gene cancer classifier predicts the site of origin for neuroendocrine tumors. Mod Pathol 2014; 27:44-54. [PMID: 23846576 DOI: 10.1038/modpathol.2013.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/08/2013] [Accepted: 05/11/2013] [Indexed: 01/04/2023]
Abstract
A diagnosis of neuroendocrine carcinoma is often morphologically straight-forward; however, the tumor site of origin may remain elusive in a metastatic presentation. Neuroendocrine tumor subtyping has important implications for staging and patient management. In this study, the novel use and performance of a 92-gene molecular cancer classifier for determination of the site of tumor origin are described in a series of 75 neuroendocrine tumors (44 metastatic, 31 primary; gastrointestinal (n=12), pulmonary (n=22), Merkel cell (n=10), pancreatic (n=10), pheochromocytoma (n=10), and medullary thyroid carcinoma (n=11)). Formalin-fixed, paraffin-embedded samples passing multicenter pathologist adjudication were blinded and tested by a 92-gene molecular assay that predicts tumor type/subtype based upon relative quantitative PCR expression measurements for 87 tumor-related and 5 reference genes. The 92-gene assay demonstrated 99% (74/75; 95% confidence interval (CI) 0.93-0.99) accuracy for classification of neuroendocrine carcinomas and correctly subtyped the tumor site of origin in 95% (71/75; 95% CI 0.87-0.98) of cases. Analysis of gene expression subsignatures within the 92-gene assay panel showed 4 genes with promising discriminatory value for tumor typing and 15 genes for tumor subtyping. The 92-gene classifier demonstrated excellent accuracy for classifying and determining the site of origin in tumors with neuroendocrine differentiation. These results show promise for use of this test to aid in classifying neuroendocrine tumors of indeterminate primary site, particularly in the metastatic setting.
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Abstract
BACKGROUND A remarkable correspondence exists between the cytogenetic locations of the known fragile sites and frequently reported sites of hypermethylation. The best-known features of fragile sites are sequence motifs that are prone to the spontaneous formation of a non-B DNA structure. These facts, coupled with the known enzymological specificities of DNA methyltransferase 1 (DNMT1), the ATP-dependent and actin-dependent helicases, and the ten-eleven translocation (TET) dioxygenases, suggest that these enzymes are involved in an epigenetic cycle that maintains the unmethylated state at these sites by resolving non-B structure, preventing both the sequestration of DNA methyltransferases (DNMTs) and hypermethylation in normal cells. PRESENTATION OF THE HYPOTHESIS The innate tendency of DNA sequences present at fragile sites to form non-B DNA structures results in de novo methylation of DNA at these sites that is held in check in normal cells by the action of ATP-dependent and actin-dependent helicases coupled with the action of TET dioxygenases. This constitutes a previously unrecognized epigenetic repair cycle in which spontaneously forming non-B DNA structures formed at fragile sites are methylated by DNMTs as they are removed by the action of ATP-dependent and actin-dependent helicases, with the resulting nascent methylation rendered non-transmissible by TET dioxygenases. TESTING THE HYPOTHESIS A strong prediction of the hypothesis is that knockdown of ATP-dependent and actin-dependent helicases will result in enhanced bisulfite sensitivity and hypermethylation at non-B structures in multiple fragile sites coupled with global hypomethylation. IMPLICATIONS OF THE HYPOTHESIS A key implication of the hypothesis is that helicases, like the lymphoid-specific helicase and alpha thalassemia/mental retardation syndrome X-linked helicase, passively promote accurate maintenance of DNA methylation by preventing the sequestration of DNMTs at sites of unrepaired non-B DNA structure. When helicase action is blocked due to mutation or downregulation of the respective genes, DNMTs stall at unrepaired non-B structures in fragile sites after methylating them and are unable to methylate other sites in the genome, resulting in hypermethylation at non-B DNA-forming sites, along with hypomethylation elsewhere.
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Affiliation(s)
- Steven S Smith
- City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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Pashai N, Hao H, All A, Gupta S, Chaerkady R, De Los Angeles A, Gearhart JD, Kerr CL. Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells. PLoS One 2012; 7:e39088. [PMID: 22737227 PMCID: PMC3380858 DOI: 10.1371/journal.pone.0039088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
Human embryonic germ cells (EGCs) provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs), and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA) reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs), induced pluripotent stem cells (IPSCs), and embryonal carcinoma cells (ECCs). Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency.
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Affiliation(s)
- Nikta Pashai
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haiping Hao
- Deep Sequencing and Microarray Core, High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Angelo All
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Siddharth Gupta
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Raghothama Chaerkady
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alejandro De Los Angeles
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children’s Hospital Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - John D. Gearhart
- Department of Cell and Developmental Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Animal Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Candace L. Kerr
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Pandiri AR, Sills RC, Ziglioli V, Ton TVT, Hong HHL, Lahousse SA, Gerrish KE, Auerbach SS, Shockley KR, Bushel PR, Peddada SD, Hoenerhoff MJ. Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer. Toxicol Pathol 2012; 40:1141-59. [PMID: 22688403 DOI: 10.1177/0192623312447543] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lung cancer is the leading cause of cancer-related death in people and is mainly due to environmental factors such as smoking and radon. The National Toxicology Program (NTP) tests various chemicals and mixtures for their carcinogenic hazard potential. In the NTP chronic bioassay using B6C3F1 mice, the incidence of lung tumors in treated and control animals is second only to the liver tumors. In order to study the molecular mechanisms of chemically induced lung tumors, an understanding of the genetic changes that occur in spontaneous lung (SL) tumors from untreated control animals is needed. The authors have evaluated the differential transcriptomic changes within SL tumors compared to normal lungs from untreated age-matched animals. Within SL tumors, several canonical pathways associated with cancer (eukaryotic initiation factor 2 signaling, RhoA signaling, PTEN signaling, and mammalian target of rapamycin signaling), metabolism (Inositol phosphate metabolism, mitochondrial dysfunction, and purine and pyramidine metabolism), and immune responses (FcγR-mediated phagocytosis, clathrin-mediated endocytosis, interleukin 8 signaling, and CXCR4 signaling) were altered. Meta-analysis of murine SL tumors and human non-small cell lung cancer transcriptomic data sets revealed a high concordance. These data provide important information on the differential transcriptomic changes in murine SL tumors that will be critical to our understanding of chemically induced lung tumors and will aid in hazard analysis in the NTP 2-year carcinogenicity bioassays.
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Affiliation(s)
- Arun R Pandiri
- Cellular and Molecular Pathology Branch, National Toxicology Program-NTP, National Institute of Environmental Health Sciences-NIEHS, Research Triangle Park, North Carolina, USA.
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Rodini CO, Xavier FCA, Paiva KBS, De Souza Setúbal Destro MF, Moyses RA, Michaluarte P, Carvalho MB, Fukuyama EE, Tajara EH, Okamoto OK, Nunes FD. Homeobox gene expression profile indicates HOXA5 as a candidate prognostic marker in oral squamous cell carcinoma. Int J Oncol 2011; 40:1180-8. [PMID: 22227861 PMCID: PMC3584618 DOI: 10.3892/ijo.2011.1321] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 11/11/2011] [Indexed: 12/18/2022] Open
Abstract
The search for molecular markers to improve diagnosis, individualize treatment and predict behavior of tumors has been the focus of several studies. This study aimed to analyze homeobox gene expression profile in oral squamous cell carcinoma (OSCC) as well as to investigate whether some of these genes are relevant molecular markers of prognosis and/or tumor aggressiveness. Homeobox gene expression levels were assessed by microarrays and qRT-PCR in OSCC tissues and adjacent non-cancerous matched tissues (margin), as well as in OSCC cell lines. Analysis of microarray data revealed the expression of 147 homeobox genes, including one set of six at least 2-fold up-regulated, and another set of 34 at least 2-fold down-regulated homeobox genes in OSCC. After qRT-PCR assays, the three most up-regulated homeobox genes (HOXA5, HOXD10 and HOXD11) revealed higher and statistically significant expression levels in OSCC samples when compared to margins. Patients presenting lower expression of HOXA5 had poorer prognosis compared to those with higher expression (P=0.03). Additionally, the status of HOXA5, HOXD10 and HOXD11 expression levels in OSCC cell lines also showed a significant up-regulation when compared to normal oral keratinocytes. Results confirm the presence of three significantly upregulated (>4-fold) homeobox genes (HOXA5, HOXD10 and HOXD11) in OSCC that may play a significant role in the pathogenesis of these tumors. Moreover, since lower levels of HOXA5 predict poor prognosis, this gene may be a novel candidate for development of therapeutic strategies in OSCC.
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Affiliation(s)
- Camila Oliveira Rodini
- Laboratory of Molecular Pathology, Department of Oral Pathology, School of Dentistry, University of São Paulo, Cidade Universitária, 05508-000 São Paulo, Brazil
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Keebaugh AC, Mitchell HA, Gaval-Cruz M, Freeman KG, Edwards GL, Weinshenker D, Thomas JW. PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse. PLoS One 2011; 6:e22381. [PMID: 21818316 PMCID: PMC3144895 DOI: 10.1371/journal.pone.0022381] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/20/2011] [Indexed: 11/19/2022] Open
Abstract
Lesch-Nyhan disease (LND) is a severe X-linked neurological disorder caused by a deficiency of hypoxanthine phosphoribosyltransferase (HPRT). In contrast, HPRT-deficiency in the mouse does not result in the profound phenotypes such as self-injurious behavior observed in humans, and the genetic basis for this phenotypic disparity between HPRT-deficient humans and mice is unknown. To test the hypothesis that HPRT deficiency is modified by the presence/absence of phosphoribosyltransferase domain containing 1 (PRTFDC1), a paralog of HPRT that is a functional gene in humans but an inactivated pseudogene in mice, we created transgenic mice that express human PRTFDC1 in wild-type and HPRT-deficient backgrounds. Male mice expressing PRTFDC1 on either genetic background were viable and fertile. However, the presence of PRTFDC1 in the HPRT-deficient, but not wild-type mice, increased aggression as well as sensitivity to a specific amphetamine-induced stereotypy, both of which are reminiscent of the increased aggressive and self-injurious behavior exhibited by patients with LND. These results demonstrate that PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse and could therefore have important implications for unraveling the molecular etiology of LND.
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Affiliation(s)
- Alaine C. Keebaugh
- Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Heather A. Mitchell
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Meriem Gaval-Cruz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kimberly G. Freeman
- Department of Physiology and Pharmacology, University of Georgia, Atlanta, Georgia, United States of America
| | - Gaylen L. Edwards
- Department of Physiology and Pharmacology, University of Georgia, Atlanta, Georgia, United States of America
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - James W. Thomas
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 2011; 13:541-9. [PMID: 21499256 DOI: 10.1038/ncb2239] [Citation(s) in RCA: 451] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/16/2011] [Indexed: 02/07/2023]
Abstract
Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming.
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Abstract
Ovarian cancer is the leading cause of death among gynecological cancers. It is now recognized that in addition to genetic alterations, epigenetic mechanisms, such as DNA methylation, histone modifications and nucleosome remodeling, play an important role in the development and progression of ovarian cancer by modulating chromatin structure, and gene and miRNA expression. Furthermore, epigenetic alterations have been recognized as useful tools for the development of novel biomarkers for diagnosis, prognosis, therapeutic prediction and monitoring of diseases. Moreover, new epigenetic therapies, such as DNA methyltransferase inhibitors and histone deacetylase inhibitors, have been found to be a potential therapeutic option, especially when used in combination with other agents. Here we discuss current developments in ovarian carcinoma epigenome research, the importance of the ovarian carcinoma epigenome for development of diagnostic and prognostic biomarkers, and the current epigenetic therapies used in ovarian cancer.
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Affiliation(s)
- Leonel Maldonado
- Department of Otolaryngology & Head & Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, USA
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Welin M, Egeblad L, Johansson A, Stenmark P, Wang L, Flodin S, Nyman T, Trésaugues L, Kotenyova T, Johansson I, Eriksson S, Eklund H, Nordlund P. Structural and functional studies of the human phosphoribosyltransferase domain containing protein 1. FEBS J 2010; 277:4920-30. [PMID: 21054786 DOI: 10.1111/j.1742-4658.2010.07897.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human hypoxanthine-guanine phosphoribosyltransferase (HPRT) (EC 2.4.2.8) catalyzes the conversion of hypoxanthine and guanine to their respective nucleoside monophosphates. Human HPRT deficiency as a result of genetic mutations is linked to both Lesch-Nyhan disease and gout. In the present study, we have characterized phosphoribosyltransferase domain containing protein 1 (PRTFDC1), a human HPRT homolog of unknown function. The PRTFDC1 structure has been determined at 1.7 Å resolution with bound GMP. The overall structure and GMP binding mode are very similar to that observed for HPRT. Using a thermal-melt assay, a nucleotide metabolome library was screened against PRTFDC1 and revealed that hypoxanthine and guanine specifically interacted with the enzyme. It was subsequently confirmed that PRTFDC1 could convert these two bases into their corresponding nucleoside monophosphate. However, the catalytic efficiency (k(cat)/K(m)) of PRTFDC1 towards hypoxanthine and guanine was only 0.26% and 0.09%, respectively, of that of HPRT. This low activity could be explained by the fact that PRTFDC1 has a Gly in the position of the proposed catalytic Asp of HPRT. In PRTFDC1, a water molecule at the position of the aspartic acid side chain position in HPRT might be responsible for the low activity observed by acting as a weak base. The data obtained in the present study indicate that PRTFDC1 does not have a direct catalytic role in the nucleotide salvage pathway.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Aberrant promoter methylation of SPARC in ovarian cancer. Neoplasia 2009; 11:126-35. [PMID: 19177197 DOI: 10.1593/neo.81146] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 10/24/2008] [Accepted: 10/27/2008] [Indexed: 12/31/2022] Open
Abstract
Epigenetic silencing of tumor suppressor genes is a new focus of investigation in the generation and proliferation of carcinomas. Secreted protein acidic and rich in cysteine (SPARC) is reportedly detrimental to the growth of ovarian cancer cells and has been shown to be epigenetically silenced in several cancers. We hypothesized that SPARC is downregulated in ovarian cancer through aberrant promoter hypermethylation. To that end, we analyzed SPARC expression in ovarian cancer cell lines and investigated the methylation status of the Sparc promoter using methylation-specific polymerase chain reaction. Our results show that SPARC mRNA expression is decreased in three (33%) and absent in four (44%) of the nine ovarian cancer cell lines studied, which correlated with hypermethylation of the Sparc promoter. Treatment with the demethylating agent 5-aza-2'-deoxycytidine rescued SPARC mRNA and protein expression. Addition of exogenous SPARC, as well as ectopic expression by an adenoviral vector, resulted in decreased proliferation of ovarian cancer cell lines. Investigation of primary tumors revealed that the Sparc promoter is methylated in 68% of primary ovarian tumors and that the levels of SPARC protein decrease as the disease progresses from low to high grade. Lastly, de novo methylation of Sparc promoter was shown to be mediated by DNA methyltransferase 3a. These results implicate Sparc promoter methylation as an important factor in the genesis and survival of ovarian carcinomas and provide new insights into the potential use of SPARC as a novel biomarker and/or treatment modality for this disease.
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Barton CA, Hacker NF, Clark SJ, O'Brien PM. DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment. Gynecol Oncol 2008; 109:129-39. [PMID: 18234305 DOI: 10.1016/j.ygyno.2007.12.017] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/07/2007] [Accepted: 12/10/2007] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To review epigenetic changes identified in ovarian cancer, focusing on their potential as clinical markers for detection, monitoring of disease progression and as markers of therapeutic response. METHODS A comprehensive review of English language scientific literature on the topics of methylation and ovarian cancer was conducted. RESULTS Genome-wide demethylation of normally methylated and silenced chromosomal regions, and hypermethylation and silencing of genes including tumor suppressors are common features of cancer cells. Epigenetic alterations, including CpG island DNA methylation, occur in ovarian cancer and the identification of specific genes that are altered by epigenetic events is an area of intense research. Aberrant DNA methylation in ovarian cancer is observed in early cancer development, can be detected in DNA circulating in the blood and hence provides the promise of a non-invasive cancer detection test. In addition, identification of ovarian cancer-specific epigenetic changes has promise in molecular classification and disease stratification. CONCLUSIONS The detection of cancer-specific DNA methylation changes heralds an exciting new era in cancer diagnosis as well as evaluation of prognosis and therapeutic responsiveness and warrants further investigation.
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Affiliation(s)
- Caroline A Barton
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia
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