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Liu C, Liu J, Shao J, Huang C, Dai X, Shen Y, Hou W, Shen Y, Yu Y. MAGED4B Promotes Glioma Progression via Inactivation of the TNF-α-induced Apoptotic Pathway by Down-regulating TRIM27 Expression. Neurosci Bull 2023; 39:273-291. [PMID: 35986882 PMCID: PMC9905453 DOI: 10.1007/s12264-022-00926-6] [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: 03/04/2022] [Accepted: 06/09/2022] [Indexed: 10/15/2022] Open
Abstract
MAGED4B belongs to the melanoma-associated antigen family; originally found in melanoma, it is expressed in various types of cancer, and is especially enriched in glioblastoma. However, the functional role and molecular mechanisms of MAGED4B in glioma are still unclear. In this study, we found that the MAGED4B level was higher in glioma tissue than that in non-cancer tissue, and the level was positively correlated with glioma grade, tumor diameter, Ki-67 level, and patient age. The patients with higher levels had a worse prognosis than those with lower MAGED4B levels. In glioma cells, MAGED4B overexpression promoted proliferation, invasion, and migration, as well as decreasing apoptosis and the chemosensitivity to cisplatin and temozolomide. On the contrary, MAGED4B knockdown in glioma cells inhibited proliferation, invasion, and migration, as well as increasing apoptosis and the chemosensitivity to cisplatin and temozolomide. MAGED4B knockdown also inhibited the growth of gliomas implanted into the rat brain. The interaction between MAGED4B and tripartite motif-containing 27 (TRIM27) in glioma cells was detected by co-immunoprecipitation assay, which showed that MAGED4B was co-localized with TRIM27. In addition, MAGED4B overexpression down-regulated the TRIM27 protein level, and this was blocked by carbobenzoxyl-L-leucyl-L-leucyl-L-leucine (MG132), an inhibitor of the proteasome. On the contrary, MAGED4B knockdown up-regulated the TRIM27 level. Furthermore, MAGED4B overexpression increased TRIM27 ubiquitination in the presence of MG132. Accordingly, MAGED4B down-regulated the protein levels of genes downstream of ubiquitin-specific protease 7 (USP7) involved in the tumor necrosis factor-alpha (TNF-α)-induced apoptotic pathway. These findings indicate that MAGED4B promotes glioma growth via a TRIM27/USP7/receptor-interacting serine/threonine-protein kinase 1 (RIP1)-dependent TNF-α-induced apoptotic pathway, which suggests that MAGED4B is a potential target for glioma diagnosis and treatment.
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Affiliation(s)
- Can Liu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
| | - Jun Liu
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Juntang Shao
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xingliang Dai
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yujun Shen
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Weishu Hou
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yuxian Shen
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China.
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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Bi SQ, Zhang QM, Zeng X, Liu C, Nong WX, Xie H, Li F, Lin LN, Luo B, Ge YY, Xie XX. Combined treatment with epigenetic agents enhances anti-tumor activity of MAGE-D4 peptide-specific T cells by upregulating the MAGE-D4 expression in glioma. Front Oncol 2022; 12:873639. [PMID: 35992806 PMCID: PMC9382192 DOI: 10.3389/fonc.2022.873639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThe study evaluated the efficacy of combined epigenetic drugs of decitabine (DAC), valproic acid (VPA), and trichostatin A (TSA) on immunotherapy against glioma.MethodsThe expression and prognosis of MAGE-D4 in glioma were analyzed online, and the expression of MAGE-D4 and HLA-A2 in glioma induced by epigenetic drugs was detected by qRT-PCR, Western blot, and flow cytometry. The methylation status of the MAGE-D4 promoter was determined by pyrosequencing. An HLA-A2 restricted MAGE-D4 peptide was predicted and synthesized. An affinity assay and a peptide/HLA complex stability assay were performed to determine the affinity between peptide and HLA. CCK8 assay, CFSE assay, ELISA and ELISPOT were performed to detect the function of MAGE-D4 peptide-specific T cells. Flow cytometry, ELISA, and cytotoxicity assays were used to detect the cytotoxicity effect of MAGE-D4 peptide-specific T cells combined with epigenetic drugs against glioma in vitro. Finally, the glioma-loaded mouse model was applied to test the inhibitory effect of specific T cells on gliomas in vivo.ResultsMAGE-D4 was highly expressed in glioma and correlated with poor prognosis. Glioma cells could be induced to express MAGE-D4 and HLA-A2 by epigenetic drugs. MAGE-D4-associated peptides were found that induce DCs to stimulate the highest T-cell activities of proliferation, IL-2 excretion, and IFN-γ secretion. MAGE-D4 peptide-specific T cells treated with TSA only or combining TSA and DAC had the most cytotoxicity effect, and its cytotoxicity effect on glioma cells decreased significantly after HLA blocking. In vivo experiments also confirmed that MAGE-D4-specific T cells inhibit TSA-treated glioma.ConclusionMAGE-D4 is highly expressed in glioma and correlated with the prognosis of glioma. The novel MAGE-D4 peptide identified was capable of inducing MAGE-D4-specific T cells that can effectively inhibit glioma growth, and the epigenetic drug application can enhance this inhibition.
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Affiliation(s)
- Shui-Qing Bi
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Department of Neurosurgery, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Qing-Mei Zhang
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key laboratory of Preclinical Medicine, Education Department of Guangxi Zhuang Autonomous region, Nanning, China
| | - Xia Zeng
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Chang Liu
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei-Xia Nong
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Huan Xie
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Feng Li
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Li-Na Lin
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Bin Luo
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key laboratory of Preclinical Medicine, Education Department of Guangxi Zhuang Autonomous region, Nanning, China
| | - Ying-Ying Ge
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
- *Correspondence: Ying-Ying Ge, ; Xiao-Xun Xie,
| | - Xiao-Xun Xie
- Department of Histology and Embryology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key laboratory of Preclinical Medicine, Education Department of Guangxi Zhuang Autonomous region, Nanning, China
- *Correspondence: Ying-Ying Ge, ; Xiao-Xun Xie,
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Ouyang J, Hu Z, Tong J, Yang Y, Wang J, Chen X, Luo T, Yu S, Wang X, Huang S. Construction and evaluation of a nomogram for predicting survival in patients with lung cancer. Aging (Albany NY) 2022; 14:2775-2792. [PMID: 35321944 PMCID: PMC9004553 DOI: 10.18632/aging.203974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/28/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Lung cancer is a heterogeneous disease with a severe disease burden. Because the prognosis of patients with lung cancer varies, it is critical to identify effective biomarkers for prognosis prediction. METHODS A total of 2325 lung cancer patients were integrated into four independent sets (training set, validation set I, II and III) after removing batch effects in our study. We applied the microarray data algorithm to screen the differentially expressed genes in the training set. The most robust markers for prognosis were identified using the LASSO-Cox regression model, which was then used to create a Cox model and nomogram. RESULTS Through LASSO and multivariate Cox regression analysis, eight genes were identified as prognosis-associated hub genes, followed by the creation of prognosis-associated risk scores (PRS). The results of the Kaplan-Meier analysis in the three validation sets demonstrate the good predictive performance of PRS, with hazard ratios of 2.38 (95% confidence interval (CI), 1.61-3.53) in the validation set I, 1.35 (95% CI, 1.06-1.71) in the validation set II, and 2.71 (95% CI, 1.77-4.18) in the validation set III. Additionally, the PRS demonstrated superior survival prediction in subgroups by age, gender, p-stage, and histologic type (p < 0.0001). The complex model integrating PRS and clinical risk factors also have a good predictive performance for 3-year overall survival. CONCLUSIONS In this study, we developed a PRS signature to help predict the survival of lung cancer. By combining it with clinical risk factors, a nomogram was established to quantify the individual risk assessments.
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Affiliation(s)
- Jin Ouyang
- Laboratory of Precision Preventive Medicine, Medical School, Jiujiang University, Jiujiang, Jiangxi 332000, PR China.,Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang 330006, PR China.,SpecAlly Life Technology Co. Ltd., Wuhan, Hubei 430075, PR China
| | - Zhijian Hu
- Laboratory Department, Jiujiang University Clinical Medical College, Jiujiang University Hospital, Jiujiang, Jiangxi 332000, PR China
| | - Jianlin Tong
- Laboratory Department, Jiujiang University Clinical Medical College, Jiujiang University Hospital, Jiujiang, Jiangxi 332000, PR China
| | - Yong Yang
- SpecAlly Life Technology Co. Ltd., Wuhan, Hubei 430075, PR China
| | - Juan Wang
- SpecAlly Life Technology Co. Ltd., Wuhan, Hubei 430075, PR China
| | - Xi Chen
- SpecAlly Life Technology Co. Ltd., Wuhan, Hubei 430075, PR China
| | - Ting Luo
- Laboratory of Precision Preventive Medicine, Medical School, Jiujiang University, Jiujiang, Jiangxi 332000, PR China
| | - Shiqun Yu
- Laboratory of Precision Preventive Medicine, Medical School, Jiujiang University, Jiujiang, Jiangxi 332000, PR China
| | - Xin Wang
- Laboratory of Precision Preventive Medicine, Medical School, Jiujiang University, Jiujiang, Jiangxi 332000, PR China
| | - Shaoxin Huang
- Laboratory of Precision Preventive Medicine, Medical School, Jiujiang University, Jiujiang, Jiangxi 332000, PR China.,SpecAlly Life Technology Co. Ltd., Wuhan, Hubei 430075, PR China.,School of Public Health, Qingdao University, Qingdao 266100, PR China
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Kondoh N, Mizuno-Kamiya M, Umemura N, Takayama E, Kawaki H, Mitsudo K, Muramatsu Y, Sumitomo S. Immunomodulatory aspects in the progression and treatment of oral malignancy. JAPANESE DENTAL SCIENCE REVIEW 2019; 55:113-120. [PMID: 31660091 PMCID: PMC6806653 DOI: 10.1016/j.jdsr.2019.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/28/2022] Open
Abstract
Inflammation substantially affects the risk of oral malignancy. Pro-inflammatory cytokine, interferon (IFN)-γ, confers anti-tumor activity using several different mechanisms. Conversely, higher expression of interleukin (IL)-17 is associated with worse prognosis. Monocyte chemotactic protein (MCP)-1 correlates positively with poor long-term survival of head and neck squamous cell carcinoma (HNSCC) patients. IL-1α affects cancer associated fibroblasts and macrophages, and promote several malignant phenotypes including immune suppression. Some anti-inflammatory cytokines, including IL-10 and transforming growth factor (TGF)-β, relate to pro-tumoral activities. Among immune checkpoint modulators, programmed death (PD-)1 and PD-ligand (L)1 facilitate oral squamous cell carcinoma (OSCC) cell evasion from immune surveillance, and the expression status of these has a prognostic value. OSCCs contain tumor associated macrophages (TAMs) as major stromal cells of their tumor microenvironment. Among the two distinctive states, M2 macrophages support tumor invasion, metastasis and immune suppression. Crosstalk between TAMs and OSCC or cancer-associated fibroblasts (CAF) plays an important role in the progression of OSCC. Clinical trials with blocking antibodies against IL-1α or melanoma-associated antigens have been reported as therapeutic approaches against OSCCs. The most promising approach activating antitumor immunity is the blockade of PD-1/PD-L1 axis. Manipulating the polarization of pro-tumorigenic macrophages has been reported as a novel therapeutic approach.
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Affiliation(s)
- Nobuo Kondoh
- Department of Oral Biochemistry, Division of Oral Structure, Function and Development, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Masako Mizuno-Kamiya
- Chemistry Laboratory, Department of Business Administration, Asahi University School of Business Administration, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Naoki Umemura
- Department of Oral Biochemistry, Division of Oral Structure, Function and Development, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Eiji Takayama
- Department of Oral Biochemistry, Division of Oral Structure, Function and Development, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Harumi Kawaki
- Department of Oral Biochemistry, Division of Oral Structure, Function and Development, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Kenji Mitsudo
- Department of Oral and Maxillofacial Surgery, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Yasunori Muramatsu
- Department of Oral and Maxillofacial Surgery, Division of Oral Pathogenesis and Disease Control, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Shinichiro Sumitomo
- Department of Oral and Maxillofacial Surgery, Division of Oral Pathogenesis and Disease Control, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu, 501-0296, Japan
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Yan J, Wen J, Wei ZD, Li XS, Li P, Xiao SW. Prognostic and clinicopathological value of melanoma-associated antigen D4 in patients with glioma. Oncol Lett 2018. [PMID: 29541180 PMCID: PMC5835852 DOI: 10.3892/ol.2018.7884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to evaluate the clinical importance of melanoma-associated antigen D4 (MAGE-D4) expression in glioma, and to identify it as a valuable prognostic biomarker and therapeutic target. To achieve this, the expression of MAGE-D4 protein in 124 tumor tissues from patients with glioma was measured using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC), and the associations between MAGE-D4expression and clinicopathological factors were evaluated. The survival analysis demonstrated the significant prognostic value of MAGE-D4 in glioma using follow-up data. RT-qPCR and IHC analysis confirmed that MAGE-D4 mRNA and protein expression levels were significantly increased in glioma tissues compared with those in normal brain tissues. The present study demonstrated that the percentage of glioma tissues with high expression of MAGE-D4 mRNA was 67.74%, and the percentage positive for MAGE-D4 protein expression was 78.23%. All patients with high MAGE-D4 expression in cancerous tissues experienced significantly reduced median overall survival (OS; 18.00 vs. 33.29 months; P<0.001) and recurrence-free survival (RFS; 12.7 vs. 28.3 months; P<0.001) times compared with those with low MAGE-D4 expression. In the patients with lower grade glioma [World Health Organization (WHO), I–II], similar results were obtained for the OS (26.11 vs. 57.85 months; P=0.013) and RFS (22.7 vs. 55.3 months; P=0.010) times; however, in patients with high-grade glioma (WHO, III–IV), there were no significant differences between high and low MAGE-D4 expression levels with regard to OS and RFS times (P>0.05). Multivariate analysis indicated that high MAGE-D4 protein expression was an important independent prognostic factor for patients with glioma (hazard ratio, 2.384; P=0.005), and was significantly associated with higher grade glioma (P<0.001). These results indicated that MAGE-D4 may be a potential biomarker for glioma and an important prognostic factor for patients with new or recurring glioma.
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Affiliation(s)
- Jun Yan
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jing Wen
- Department of Rheumatism, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zong-Dang Wei
- Department of Neurosurgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xi-Sheng Li
- Department of Neurosurgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Ping Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Shao-Wen Xiao
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.,Department of Neurosurgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Oya H, Kanda M, Koike M, Iwata N, Niwa Y, Shimizu D, Takami H, Sueoka S, Hashimoto R, Ezaka K, Nomoto S, Yamada S, Fujii T, Nakayama G, Sugimoto H, Fujiwara M, Kodera Y. Detection of serum melanoma-associated antigen D4 in patients with squamous cell carcinoma of the esophagus. Dis Esophagus 2016; 29:663-9. [PMID: 25951896 DOI: 10.1111/dote.12373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite improvements in surgical techniques, perioperative management, and multidisciplinary therapy, treatment outcomes of patients with esophageal squamous cell carcinoma (ESCC) remain poor. Therefore, development of novel molecular biomarkers, which either predict patient survival or become therapeutic targets, is urgently required. In the present study, to facilitate early detection of ESCC and predict its clinical course, we investigated the relationship of the serum level of melanoma-associated antigen (MAGE)-D4 to patients' clinicopathological characteristics. Using quantitative real-time reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assays, we determined the levels of MAGE-D4 mRNA and protein in cell lysates and conditioned medium of cultures, respectively, of nine ESCC cell lines. Further, we determined MAGE-D4 levels in serum samples collected from 44 patients with ESCC who underwent radical esophagectomy without neoadjuvant therapy as well as from 40 healthy volunteers. Samples of conditioned medium and cell lysates contained comparable levels of MAGE-D4 that correlated closely with the levels of MAGE-D4 mRNA. Preoperative MAGE-D4 levels in the sera of 44 patients with ESCC, which varied from 0 to 2,354 pg/mL (314 ± 505 pg/mL, mean ± standard deviation), were significantly higher compared with those of healthy volunteers. By setting the cutoff at the highest value for healthy volunteers (50 pg/mL), the MAGE-D4-positive group of patients was more likely to have shorter disease-specific and disease-free survival compared with those of the MAGE-D4-negative group, although the differences were not statistically significant. Our results indicate that the elevation of preoperative serum MAGE-D4 levels in some patients with ESCC was possibly caused by excess production of MAGE-D4 by tumor cells followed by its release into the circulation. Clinical implications of serum MAGE-D4 levels should be validated in a large population of patients with ESCC.
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Affiliation(s)
- H Oya
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Kanda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Koike
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - N Iwata
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Niwa
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Shimizu
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Takami
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Sueoka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - R Hashimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ezaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Nomoto
- Department of Surgery, Aichi-Gakuin University School of Dentistry, Nagoya, Japan
| | - S Yamada
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Fujii
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - G Nakayama
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Sugimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Fujiwara
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Kodera
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
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Hu S, Li B, Shen X, Zhang R, Gao D, Guo Q, Jin Y, Fei Z. Induction of antigen-specific cytotoxic T-cell response by dendritic cells generated from ecto-mesenchymal stem cells infected with an adenovirus containing the MAGE-D4a gene. Oncol Lett 2016; 11:2886-2892. [PMID: 27073570 DOI: 10.3892/ol.2016.4306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 01/11/2016] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate the feasibility of using ecto-mesenchymal stem cell (EMSC)-derived dendritic cells (DCs) for glioma immunotherapy following infection by a recombinant adenovirus containing the melanoma-associated antigen D4a (MAGE-D4a) gene. The ex vivo cultured EMSCs were infected by the adenoviral plasmid containing MAGE-D4a (pAd/MAGE-D4a). Efficiency of transfection was evaluated through the detection of green fluorescent protein-marked MAGE-D4a. The MAGE-EMSCs were induced to differentiate into DCs, termed as MAGE-EMSCs-DCs. The morphology was subsequently analyzed under a microscope, and methyl thiazolyl tetrazolium (MTT) and interferon-γ (IFN-γ) assays were performed to analyze the cytotoxicity of the MAGE-EMSC-DCs on the human glioma U251 cell line. Following purification by magnetic-activated cell sorting, the EMSCs grew into swirls, with a long spindle shape and were fibroblast-like. The gene transfected with recombinant adenovirus vectors maintained high and stable expression levels of MAGE-D4a, and its efficiency was increased in a multiplicity of infection-dependent manner. The results of the MTT assay indicated that the T cells, primed by the recombinant MAGE-D4a-infected EMSC-DCs in vitro, recognized MAGE-D4a-expressing tumor cell lines in a human leukocyte antigen class I-restricted manner, and evoked a higher cytotoxic T cell (CTL) response. The CTL response induced by the MAGE-EMSC-DCs, co-cultured with the U251 cells for 24 h, produced 765.0 pg/ml IFN-γ, which was significantly greater when compared to the control wells. T lymphocytes stimulated by MAGE-EMSC-DCs evoke a higher CTL response to human glioma cell lines, and may serve as a promising therapeutic modality for the treatment of MAGE-D4a-expressing glioma.
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Affiliation(s)
- Shijie Hu
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Bing Li
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xuefeng Shen
- Department of Occupational and Environmental Health and The Ministry of Education Key Laboratory of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Rui Zhang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Dakuan Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Qingdong Guo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yan Jin
- Department of Oral Histology and Pathology, Research and Development Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Zhou Fei
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Transmembrane-4-L-six-family-1, a potential predictor for poor prognosis, overexpressed in human glioma. Neuroreport 2016; 26:455-61. [PMID: 25855954 DOI: 10.1097/wnr.0000000000000370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transmembrane-4-L-six-family-1 (TM4SF1), a tumor-associated antigen, is expressed in various human epithelial malignancies including breast, ovarian, lung, and colon carcinomas. The aim of the present study was to measure TM4SF1 gene expression in human glioma tissues and to investigate its relationship with patient outcome. We measured TM4SF1 expression in tumor tissue from 72 patients with glioma and in eight control brain tissues by means of quantitative reverse transcription-PCR, western blotting, and immunohistochemistry. The survival data including age, sex, Karnofsky performance scores, epilepsy, size of tumor, extent of resection, pathological grade, and TM4SF1 expression were analyzed using Kaplan-Meier analysis and the multivariate test method (Cox's proportional hazards model). We observed a higher level of TM4SF1 expression in human glioma tissues than in control brain tissues. Furthermore, TM4SF1 expression increased with ascending tumor grade (rs=0.950, P<0.05). Kaplan-Meier analysis with the log-rank test indicated that high TM4SF1 expression had a significant negative impact on overall survival (P<0.001). Moreover, multivariate Cox regression analysis revealed that TM4SF1 was an independent prognostic marker in glioma patients. These findings indicate that (a) TM4SF1 is overexpressed in human gliomas in general and (b) the precise level of expression might predict outcome and could be of clinical value.
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Lim KP, Chun NAL, Gan CP, Teo SH, Rahman ZAA, Abraham MT, Zain RB, Ponniah S, Cheong SC. Identification of immunogenic MAGED4B peptides for vaccine development in oral cancer immunotherapy. Hum Vaccin Immunother 2015; 10:3214-23. [PMID: 25483651 DOI: 10.4161/hv.29226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ever-increasing number of tumor-associated antigens has provided a major stimulus for the development of therapeutic peptides vaccines. Tumor-associated peptides can induce high immune response rates and have been developed as vaccines for several types of solid tumors, and many are at various stages of clinical testing. MAGED4B, a melanoma antigen, is overexpressed in oral squamous cell carcinoma (OSCC) and this expression promotes proliferation and cell migration. In this study, we have identified 9 short peptides derived from MAGED4B protein that are restricted in binding to the HLA subtypes common in the Asian population (HLA-A2, A11, and A24). The peptides had good binding affinity with the MHC-Class I molecules and stimulated ex-vivo IFN-gamma and Granzyme-B production in blood samples from OSCC patients, suggesting that they are immunogenic. Further, T cells stimulated with peptide-pulsed dendritic cells showed enhanced T-cell cytotoxic activity against MAGED4B-overexpressing OSCC cell lines. In summary, we have identified MAGED4B peptides that induce anti-tumor immune responses advocating that they could be further developed as vaccine candidates for the treatment of OSCC.
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Affiliation(s)
- Kue Peng Lim
- a Oral Cancer Research Team; Cancer Research Initiatives Foundation (CARIF) ; Subang Jaya , Selangor , Malaysia
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10
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Yang XN, Huang L, Chen Y, An SJ, Zhang XC, Liao RQ, Su J, Wu YL. Single nucleotide polymorphisms of MAGE-A3 gene and its clinical implications in Chinese patients with non-small cell lung cancer (NSCLC). Chin J Cancer Res 2015; 27:301-8. [PMID: 26157327 DOI: 10.3978/j.issn.1000-9604.2014.11.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/15/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Available study revealed advanced tumors have a higher expression rate of MAGE-A3 gene which has a lot of single nucleotide polymorphism (SNP) loci with polymorphisms. This study aimed to analyze the allele frequency of SNP loci in MAGE-A3 gene and investigate the relationship between MAGE-A3 gene polymorphisms and clinical factors. METHODS Tumor samples of a cohort of 191 NSCLC patients were collected. EGFR mRNA expression were detected by qRT-PCR. SNPs in whole length of MAGE-A3 gene were detected by direct sequencing. Frequencies of the SNPs were correlated to gene expression, mutation status of EGFR and clinical factors. RESULTS Sequencing analysis confirmed that allele frequencies of genotypes on SNP loci rs5970360, rs5925210, rs5970361, rs5925211 and rs35123853 were CC (0.681)/CT (0.319), CC (0.660)/CG (0.340), CC (0.681)/CA (0.319), AA (0.984)/AT (0.016) and GG (1.000)/GA (0.000), respectively, which were different from the frequencies and genotypes of MAGE-A3 in SNP database. Chi-square tests showed the EGFR mRNA expression level had significant correlation with the genotypes of SNP loci rs5970360 and rs5925210. But all frequencies of each MAGE-A3 SNPs were not found significantly different between EGFR mutant and wild type patients. MAGE-A3 gene polymorphisms had no significant effects on survival of NSCLC patients. CONCLUSIONS Chinese patients with NSCLC had different SNP patterns of MAGE-A3 in comparison with those in international SNP database. These MAGE-A3 SNP loci might have not prognostic significance. MAGE-A3 SNP loci rs5970360 and rs5925210 might be predictive for EGFR mRNA expression levels and helpful to the selection of patients for epidermal growth factor receptor (EGFR) targeted immunotherapy.
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Affiliation(s)
- Xue-Ning Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ling Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yu Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - She-Juan An
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ri-Qiang Liao
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
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11
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Zhang QM, Shen N, Xie S, Bi SQ, Luo B, Lin YD, Fu J, Zhou SF, Luo GR, Xie XX, Xiao SW. MAGED4 expression in glioma and upregulation in glioma cell lines with 5-aza-2'-deoxycytidine treatment. Asian Pac J Cancer Prev 2015; 15:3495-501. [PMID: 24870746 DOI: 10.7314/apjcp.2014.15.8.3495] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Melanoma-associated antigen (MAGE) family genes have been considered as potentially promising targets for anticancer immunotherapy. MAGED4 was originally identified as a glioma-specific antigen. Current knowledge about MAGED4 expression in glioma is only based on mRNA analysis and MAGED4 protein expression has not been elucidated. In the present study, we investigated this point and found that MAGED4 mRNA and protein were absent or very lowly expressed in various normal tissues and glioma cell line SHG44, but overexpressed in glioma cell lines A172,U251,U87-MG as well as glioma tissues, with significant heterogeneity. Furthermore, MAGED4 protein expression was positively correlated with the glioma type and grade. We also found that the expression of MAGED4 inversely correlated with the overall methylation status of the MAGED4 promoter CpG island. Furthermore, when SHG44 and A172 with higher methylation were treated with the DNA demethylating agent 5-aza-2'-deoxycytidine (5-AZA-CdR) reactivation of MAGED4 mRNA was mediated by significant demethylation in SHG44 instead of A172. However, 5-AZA-CdR treatment had no effect on MAGED4 protein in both SHG44 and A172 cells. In conclusion, MAGED4 is frequently and highly expressed in glioma and is partly regulated by DNA methylation. The results suggest that MAGED4 might be a promising target for glioma immunotherapy combined with 5-AZA-CdR to enhance its expression and eliminate intratumor heterogeneity.
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Affiliation(s)
- Qing-Mei Zhang
- Department of Histology and Embryology, School of Pre-clinical Medicine, Guangxi Medical University, Guangxi, China E-mail :
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Zhan C, Zhang Y, Ma J, Wang L, Jiang W, Shi Y, Wang Q. Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-Seq. Acta Biochim Biophys Sin (Shanghai) 2014; 46:330-7. [PMID: 24457517 DOI: 10.1093/abbs/gmt153] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the accuracy of quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on the reliable reference genes, many commonly used reference genes are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. The aim of this study was to identify novel reliable reference genes in lung squamous-cell carcinoma. We used RNA sequencing (RNA-Seq) to survey the whole genome expression in 5 lung normal samples and 44 lung squamous-cell carcinoma samples. We evaluated the expression profiles of 15 commonly used reference genes and identified five additional candidate reference genes. To validate the RNA-Seq dataset, we used qRT-PCR to verify the expression levels of these 20 genes in a separate set of 100 pairs of normal lung tissue and lung squamous-cell carcinoma samples, and then analyzed these results using geNorm and NormFinder. With respect to 14 of the 15 common reference genes (B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, and YWHAZ), the expression levels were either too low to be easily detected, or exhibited a high degree of variability either between lung normal and squamous-cell carcinoma samples, or even among samples of the same tissue type. In contrast, 1 of the 15 common reference genes (ACTB) and the 5 additional candidate reference genes (EEF1A1, FAU, RPS9, RPS11, and RPS14) were stably and constitutively expressed at high levels in all the samples tested. ACTB, EEF1A1, FAU, RPS9, RPS11, and RPS14 are ideal reference genes for qRT-PCR analysis of lung squamous-cell carcinoma, while 14 commonly used qRT-PCR reference genes are less appropriate in this context.
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Affiliation(s)
- Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200031, China
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13
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Takami H, Kanda M, Oya H, Hibino S, Sugimoto H, Suenaga M, Yamada S, Nishikawa Y, Asai M, Fujii T, Nomoto S, Kodera Y. Evaluation of MAGE-D4 expression in hepatocellular carcinoma in Japanese patients. J Surg Oncol 2013; 108:557-62. [PMID: 24068544 DOI: 10.1002/jso.23440] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/28/2013] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVES Though Melanoma-associated antigen (MAGE) family genes have received lots of attention as cancer-related genes and targets for immunotherapy, MAGE-D4 expression in hepatocellular carcinoma (HCC) has not yet been evaluated. METHODS MAGE-D4 mRNA expression was assayed in nine HCC cell lines and 94 HCC surgical specimens obtained from Japanese patients by quantitative real-time reverse transcription polymerase chain reaction, and the correlations between MAGE-D4 mRNA expression and clinicopathological factors were evaluated. The expression and distribution of MAGE-D4b protein were evaluated immunohistochemically. RESULTS MAGE-D4 mRNA was overexpressed in five of nine HCC cell lines and 34 of 94 primary HCCs (36.2%). Median overall survival (14.8 vs. 118 months, P < 0.001) and relapse-free survival (2.7 vs. 18.3 months, P < 0.001) were significantly shorter in patients with high than with low-moderate MAGE-D4 expression. Multivariate analysis for overall survival showed that MAGE-D4 overexpression was independently prognostic for survival (hazard ratio 2.88, P = 0.009) and significantly associated with high alpha-fetoprotein concentration (P < 0.001), poor tumor differentiation (P = 0.003) and vascular invasion (P = 0.021). MAGE-D4b protein expression patterns were consistent with those of MAGE-D4 mRNA. CONCLUSIONS Overexpression of MAGE-D4 may be a predictive marker of early recurrence and mortality in patients with HCC.
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Affiliation(s)
- Hideki Takami
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
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Chong CE, Lim KP, Gan CP, Marsh CA, Zain RB, Abraham MT, Prime SS, Teo SH, Silvio Gutkind J, Patel V, Cheong SC. Over-expression of MAGED4B increases cell migration and growth in oral squamous cell carcinoma and is associated with poor disease outcome. Cancer Lett 2012; 321:18-26. [DOI: 10.1016/j.canlet.2012.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/21/2012] [Accepted: 03/21/2012] [Indexed: 11/16/2022]
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15
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Ma QY, Pang LW, Chen ZM, Zhu YJ, Chen G, Chen J. The significance of MAGED4 expression in non-small cell lung cancer as analyzed by real-time fluorescence quantitative PCR. Oncol Lett 2012. [PMID: 23205092 DOI: 10.3892/ol.2012.786] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to detect differences in the expression levels of melanoma-associated antigen D4 (MAGED4) mRNA between non-small cell lung cancer (NSCLC) tissues and normal tissues, and to compare differences in the expression levels of MAGED4 in tumor patients. Patients were grouped according to age, gender, smoking history, tumor size, pathological classification, degree of lung cancer cell differentiation and presence of lymph node metastasis. The expression levels of MAGED4 were detected using real-time fluorescence quantitative PCR. MAGED4 expression was higher in squamous cell carcinomas compared to adenocarcinomas (P<0.05), in poorly differentiated tissues compared to well-differentiated tissues (P<0.05), and in patients with lymph node metastasis compared to patients without lymph node metastasis (P<0.05). MAGED4 may be used as a specific antigen for NSCLC to influence the improvement of diagnosis, prognosis and immunological therapy outcomes in lung cancer patients.
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Affiliation(s)
- Qin-Yun Ma
- Department of Thoracic Surgery, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, P.R. China
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Liu Y, Yang S, Yang J, Que H, Liu S. Relative expression of type II MAGE genes during retinoic acid-induced neural differentiation of mouse embryonic carcinoma P19 cells: a comparative real-time PCR analysis. Cell Mol Neurobiol 2012; 32:1059-68. [PMID: 22410673 DOI: 10.1007/s10571-012-9826-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/28/2012] [Indexed: 02/05/2023]
Abstract
In mammals, the type II melanoma antigen (MAGE) protein family is constituted by at least ten closely related members, but our understanding of their function in the developing nervous system remains poor. To systematically study the expression pattern of type II MAGE genes during neurogenesis, we employed mouse embryonic carcinoma P19 cells as an in vitro model for neural differentiation by retinoic acid (RA) induction. The expression of type II MAGE genes was investigated under distinct steps of differentiation by a comparative ΔΔC (T) paradigm of real-time quantitative reverse-transcription PCR (qRT-PCR). The relative levels of each gene expression at various steps of differentiation were expressed as a fold change compared with that in RA-untreated P19 cells. The results revealed that: (1) the expression of MAGE-E1, E2, and Necdin transcripts was steadily increased, and the relative levels of MAGE-D1, D2, D3, F1, G1, and H1 mRNA were fluctuantly elevated after the RA-treatment at embryoid body and neural stages; (2) during RA-treatment and subsequent differentiation, the expression of MAGE-L2 mRNA was decreased. Therefore, our results suggested that MAGE-D1, D2, D3, E1, E2, F1, G1, H1, and Necdin might be involved in the early process of neurogenesis, and MAGE-L2 connected with maintenance of pluripotency of stem cells. These studies may present some clues for a better understanding of the fundamental aspects of type II MAGE genes during neurogenesis.
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Affiliation(s)
- Yong Liu
- State Key Laboratory of Proteomics, Department of Neurobiology, Institute of Basic Medical Sciences, Beijing, People's Republic of China.
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Chakraborty S, Datta S, Datta S. Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies. ACTA ACUST UNITED AC 2012; 28:799-806. [PMID: 22238271 DOI: 10.1093/bioinformatics/bts022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
MOTIVATION In a typical gene expression profiling study, our prime objective is to identify the genes that are differentially expressed between the samples from two different tissue types. Commonly, standard analysis of variance (ANOVA)/regression is implemented to identify the relative effects of these genes over the two types of samples from their respective arrays of expression levels. But, this technique becomes fundamentally flawed when there are unaccounted sources of variability in these arrays (latent variables attributable to different biological, environmental or other factors relevant in the context). These factors distort the true picture of differential gene expression between the two tissue types and introduce spurious signals of expression heterogeneity. As a result, many genes which are actually differentially expressed are not detected, whereas many others are falsely identified as positives. Moreover, these distortions can be different for different genes. Thus, it is also not possible to get rid of these variations by simple array normalizations. This both-way error can lead to a serious loss in sensitivity and specificity, thereby causing a severe inefficiency in the underlying multiple testing problem. In this work, we attempt to identify the hidden effects of the underlying latent factors in a gene expression profiling study by partial least squares (PLS) and apply ANCOVA technique with the PLS-identified signatures of these hidden effects as covariates, in order to identify the genes that are truly differentially expressed between the two concerned tissue types. RESULTS We compare the performance of our method SVA-PLS with standard ANOVA and a relatively recent technique of surrogate variable analysis (SVA), on a wide variety of simulation settings (incorporating different effects of the hidden variable, under situations with varying signal intensities and gene groupings). In all settings, our method yields the highest sensitivity while maintaining relatively reasonable values for the specificity, false discovery rate and false non-discovery rate. Application of our method to gene expression profiling for acute megakaryoblastic leukemia shows that our method detects an additional six genes, that are missed by both the standard ANOVA method as well as SVA, but may be relevant to this disease, as can be seen from mining the existing literature.
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Affiliation(s)
- Sutirtha Chakraborty
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
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Germano S, Kennedy S, Rani S, Gleeson G, Clynes M, Doolan P, McDonnell S, Hughes L, Crown J, O'Driscoll L. MAGE-D4B is a novel marker of poor prognosis and potential therapeutic target involved in breast cancer tumorigenesis. Int J Cancer 2011; 130:1991-2002. [PMID: 21618523 DOI: 10.1002/ijc.26200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 05/02/2011] [Indexed: 11/07/2022]
Abstract
Melanoma-associated antigen (MAGE) family members are generally described as tumor-specific antigens. An association between MAGE-D4B and breast cancer has yet to be reported and the functional role of the encoded protein has never been established. We performed microarray analysis of 104 invasive breast tumors and matched non-cancerous breast biopsies. qPCR was used for validation in an independent biobank. To investigate the biological relevance of MAGE-D4B in breast tumorigenesis, its phenotypic effects were assessed in vitro. Overall, MAGE-D4B was detected in 43% of tumors while undetected in normal breast tissue. MAGE-D4B was found to correlate with tumor progression and to be an independent prognostic marker for poor outcome in term of relapse-free and overall survival, with potential predictive relevance in relation to response to chemotherapy. RNA interference-mediated knockdown of MAGE-D4B significantly hampered the invasive properties of Hs578T cells by affecting anchorage-independent growth, adhesion, migration and invasion affecting anchorage-independent growth, adhesion, migration and invasion and by modulating expression of invasion-suppressor gene E-cadherin.
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Affiliation(s)
- Serena Germano
- School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
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A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biol Direct 2011; 6:30. [PMID: 21668950 PMCID: PMC3142252 DOI: 10.1186/1745-6150-6-30] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 06/13/2011] [Indexed: 01/07/2023] Open
Abstract
Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR), a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA) was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80%) of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy (http://main.g2.bx.psu.edu/). Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT) were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius); Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi).
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Chung FY, Cheng TL, Chang HJ, Chiu HH, Huang MY, Chang MS, Chen CC, Yang MJ, Wang JY, Lin SR. Differential gene expression profile of MAGE family in taiwanese patients with colorectal cancer. J Surg Oncol 2010; 102:148-53. [PMID: 20648585 DOI: 10.1002/jso.21580] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The melanoma-associated antigen (MAGE) gene family consists of different expression patterns in various tumor types. They are considered tumor-specific antigens and are ideal targets for cancer immunotherapy. The purpose of this study is to identify the expression profiles of the MAGE family genes in Taiwanese colorectal cancer patients. METHODS In this study, a well-constructed chip array platform was used to analyze the expression of the MAGE family genes of 100 colorectal cancer tissues. Statistical analysis of the experimental results and patients' clinical manifestations were also conducted. RESULTS The results showed MAGE-A2 (87%), -A7 (83%), -A8 (75%), -A12 (71%), -B2 (75%), -B3 (79%), -D2 (75%), -F1 (79%), and -H1 (70%) were significantly overexpressed genes in colorectal cancer tissues. MAGE-A2 was the most highly overexpressed gene among the MAGE family. MAGE-B3 gene expression is statistically correlated with tumor size, lymph node, and UICC stage. In addition, the overexpression of MAGE-D2 and -H1 genes are statistically correlated to the tumor size and depth, respectively (P < 0.05). CONCLUSIONS This is the first comprehensive report to clarify the differential expression profile of whole MAGE family in CRCs, and it might provide some crucial information about the carcinogenesis and progression in Taiwanese patients with CRC.
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Affiliation(s)
- Fu-Yen Chung
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Kim SH, Lee S, Lee CH, Lee MK, Kim YD, Shin DH, Choi KU, Kim JY, Park DY, Sol MY. Expression of Cancer-Testis Antigens MAGE-A3/6 and NY-ESO-1 in Non-Small-Cell Lung Carcinomas and Their Relationship with Immune Cell Infiltration. Lung 2009; 187:401-11. [DOI: 10.1007/s00408-009-9181-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 09/10/2009] [Indexed: 11/29/2022]
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22
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Cheong SC, Chandramouli GVR, Saleh A, Zain RB, Lau SH, Sivakumaren S, Pathmanathan R, Prime SS, Teo SH, Patel V, Gutkind JS. Gene expression in human oral squamous cell carcinoma is influenced by risk factor exposure. Oral Oncol 2009; 45:712-9. [PMID: 19147396 DOI: 10.1016/j.oraloncology.2008.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 11/04/2008] [Accepted: 11/04/2008] [Indexed: 10/21/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a world health problem and is associated with exposure to different risk factors. In the west, smoking and alcohol consumption are considered to be the main risk factors whilst in India and southeast Asia, betel quid (BQ) chewing is predominant. In this study, we compared the gene expression patterns of oral cancers associated with BQ chewing to those caused by smoking using Affymetrix microarrays. We found that 281 genes were differentially expressed between OSCC and normal oral mucosa regardless of aetiological factors including MMP1, PLAU, MAGE-D4, GNA12, IFITM3 and NMU. Further, we identified 168 genes that were differentially expressed between the BQ and smoking groups including CXCL-9, TMPRSS2, CA12 and RNF24. The expression of these genes was validated using qPCR using independent tissue samples. The results demonstrate that whilst common genes/pathways contribute to the development of oral cancer, there are also other gene expression changes that are specific to certain risk factors. The findings suggest that different carcinogens activate or inhibit specific pathways during cancer development and progression. These unique gene expression profiles should be taken into consideration when developing biomarkers for future use in prognostic or therapeutic applications.
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Affiliation(s)
- S C Cheong
- Cancer Research Initiatives Foundation, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia.
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Kim S, Kim H, Kwon OJ, Chung MP, Suh GY, Koh WJ, Ham CR, Nam HS, Um SW, Kwon YS, Park S. The Utility of MAGE Gene Detection in Bronchial Washing Fluid for Patients with Peripheral NSCLC. Tuberc Respir Dis (Seoul) 2008. [DOI: 10.4046/trd.2008.64.1.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Suhyun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Man Pyo Chung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Gee Young Suh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Cho Rom Ham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hae Seong Nam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yong Soo Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sunghoon Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Tsai JR, Chong IW, Chen YH, Yang MJ, Sheu CC, Chang HC, Hwang JJ, Hung JY, Lin SR. Differential expression profile of MAGE family in non-small-cell lung cancer. Lung Cancer 2007; 56:185-92. [PMID: 17208331 DOI: 10.1016/j.lungcan.2006.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 11/20/2006] [Accepted: 12/01/2006] [Indexed: 11/16/2022]
Abstract
The expression of the melanoma-associated antigen (MAGE) genes consists of variables in all tumor types, such as lung cancer, which are relevant to be silent in all normal tissues except germ cells. They are considered as tumor-specific antigens, and are ideal targets for cancer immunotherapy. A complete MAGE genes differential expression profile analysis of lung cancer can provide this study not only various target genes for immunotherapy, but also valuable markers for further diagnosis and prognosis. This research has constructed a membrane array, which was consisted 32 MAGE genes, to detect whether the differential expression profile occurred in 52 pairs of non-small-cell lung cancer (NSCLC) samples. Nearly 32 MAGE genes have been differential expressed in NSCLC except MAGE-B1 and -E2. MAGE-B, -C, -D, and subgroup -B6, -D4 have showed prominences in lung adenocarcinoma. High-frequent expression of MAGE-D, and subgroup -A2, -D2 has also been discovered in non-metastasis group (p<0.05). However, there is no significant difference of MAGE genes differential expression shown among different primary tumor (T), nodal involvement (N) and overall stages. Several MAGE subgroup genes, such as MAGE-A5, -A7, -A8, -A9, -A11, -B3, -B4, -B10, -D2, -D3, -F1, -G1, -H1, and -L2, have been first discovered to show differential expression in NSCLC. Although the small size of the sample may limit the diagnostic and prognostic value of MAGE genes, the function of the membrane array can provide this study a high-throughput method to detect the whole MAGE genes differential expression profile.
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Affiliation(s)
- Jong-Rung Tsai
- Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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