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Rajalingam A, Sekar K, Ganjiwale A. Identification of Potential Genes and Critical Pathways in Postoperative Recurrence of Crohn's Disease by Machine Learning And WGCNA Network Analysis. Curr Genomics 2023; 24:84-99. [PMID: 37994325 PMCID: PMC10662376 DOI: 10.2174/1389202924666230601122334] [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: 02/04/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 11/24/2023] Open
Abstract
Background Crohn's disease (CD) is a chronic idiopathic inflammatory bowel disease affecting the entire gastrointestinal tract from the mouth to the anus. These patients often experience a period of symptomatic relapse and remission. A 20 - 30% symptomatic recurrence rate is reported in the first year after surgery, with a 10% increase each subsequent year. Thus, surgery is done only to relieve symptoms and not for the complete cure of the disease. The determinants and the genetic factors of this disease recurrence are also not well-defined. Therefore, enhanced diagnostic efficiency and prognostic outcome are critical for confronting CD recurrence. Methods We analysed ileal mucosa samples collected from neo-terminal ileum six months after surgery (M6=121 samples) from Crohn's disease dataset (GSE186582). The primary aim of this study is to identify the potential genes and critical pathways in post-operative recurrence of Crohn's disease. We combined the differential gene expression analysis with Recursive feature elimination (RFE), a machine learning approach to get five critical genes for the postoperative recurrence of Crohn's disease. The features (genes) selected by different methods were validated using five binary classifiers for recurrence and remission samples: Logistic Regression (LR), Decision tree classifier (DT), Support Vector Machine (SVM), Random Forest classifier (RF), and K-nearest neighbor (KNN) with 10-fold cross-validation. We also performed weighted gene co-expression network analysis (WGCNA) to select specific modules and feature genes associated with Crohn's disease postoperative recurrence, smoking, and biological sex. Combined with other biological interpretations, including Gene Ontology (GO) analysis, pathway enrichment, and protein-protein interaction (PPI) network analysis, our current study sheds light on the in-depth research of CD diagnosis and prognosis in postoperative recurrence. Results PLOD2, ZNF165, BOK, CX3CR1, and ARMCX4, are the important genes identified from the machine learning approach. These genes are reported to be involved in the viral protein interaction with cytokine and cytokine receptors, lysine degradation, and apoptosis. They are also linked with various cellular and molecular functions such as Peptidyl-lysine hydroxylation, Central nervous system maturation, G protein-coupled chemoattractant receptor activity, BCL-2 homology (BH) domain binding, Gliogenesis and negative regulation of mitochondrial depolarization. WGCNA identified a gene co-expression module that was primarily involved in mitochondrial translational elongation, mitochondrial translational termination, mitochondrial translation, mitochondrial respiratory chain complex, mRNA splicing via spliceosome pathways, etc.; Both the analysis result emphasizes that the mitochondrial depolarization pathway is linked with CD recurrence leading to oxidative stress in promoting inflammation in CD patients. Conclusion These key genes serve as the novel diagnostic biomarker for the postoperative recurrence of Crohn's disease. Thus, among other treatment options present until now, these biomarkers would provide success in both diagnosis and prognosis, aiming for a long-lasting remission to prevent further complications in CD.
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Affiliation(s)
- Aruna Rajalingam
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka, 560056, India
| | - Kanagaraj Sekar
- Laboratory for Structural Biology and Bio-computing, Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Anjali Ganjiwale
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka, 560056, India
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Zhao J, Wen D, Zhang S, Jiang H, Di X. The role of zinc finger proteins in malignant tumors. FASEB J 2023; 37:e23157. [PMID: 37615242 DOI: 10.1096/fj.202300801r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/19/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Zinc finger proteins (ZNFs) are the largest family of transcriptional factors in mammalian cells. Recently, their role in the development, progression, and metastasis of malignant tumors via regulating gene transcription and translation processes has become evident. Besides, their possible involvement in drug resistance has also been found, indicating that ZNFs have the potential to become new biological markers and therapeutic targets. In this review, we summarize the oncogenic and suppressive roles of various ZNFs in malignant tumors, including lung, breast, liver, gastric, colorectal, pancreatic, and other cancers, highlighting their role as prognostic markers, and hopefully provide new ideas for the treatment of malignant tumors in the future.
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Affiliation(s)
- Jia Zhao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Doudou Wen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Hao Jiang
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China
| | - Xiaotang Di
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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Yang W, Zhang Z, Li L, Zhang K, Xu Y, Xia M, Zhou J, Gong Y, Chen J, Gong K. ZNF582 overexpression restrains the progression of clear cell renal cell carcinoma by enhancing the binding of TJP2 and ERK2 and inhibiting ERK2 phosphorylation. Cell Death Dis 2023; 14:212. [PMID: 36966163 PMCID: PMC10039855 DOI: 10.1038/s41419-023-05750-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023]
Abstract
Recent evidences have suggested that Zinc finger protein 582 (ZNF582) plays different important roles in various tumors, but its clinical role, biological function and regulatory mechanism in clear cell renal cell carcinoma (ccRCC) are still vague. Through analyzing GEO and TCGA-KIRC data and validation with local samples, we identified the low expression pattern of ZNF582 in ccRCC. Decreased ZNF582 expression is correlated with higher tumor stage and grade, distant metastasis and poor prognosis. By analyzing the DNA methylation data of ccRCC in TCGA-KIRC and using Massarray DNA methylation and demethylation analysis, we confirmed the hypermethylation status of ZNF582 in ccRCC and its negative regulation on ZNF582 expression. Using cell phenotype experiments and orthotopic kidney tumor growth models, we determined the inhibitory effect of ZNF582 overexpression on ccRCC growth and metastasis in vivo and in vitro. Mechanistically, using TMT (Tandem mass tags) quantitative proteomics test, Co-IP (Co-immunoprecipitation) and Western Blot experiments, we clarified that ZNF582 binds to TJP2 and up-regulates TJP2 protein expression. Increased TJP2 protein combines with ERK2 to promote ERK2 protein expression and suppresses the phosphorylation of ERK2, thereby inhibiting the growth and metastasis of ccRCC. In general, our findings provide the first solid theoretical rationale for targeting ZNF582/TJP2/ERK2 axis to improve ccRCC treatment.
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Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Zedan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Lei Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yawei Xu
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Mancheng Xia
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
| | - Jinchao Chen
- Department of Urologic Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, P.R. China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
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Alsadat Mahmoudian R, Amirhosein M, Mahmoudian P, Fardi Golyan F, Mokhlessi L, Maftooh M, Khazaei M, Nassiri M, Mahdi Hassanian S, Ghayour-Mobarhan M, Ferns GA, Shahidsales S, Avan A. The therapeutic potential value of Cancer-testis antigens in immunotherapy of gastric cancer. Gene 2023; 853:147082. [PMID: 36464170 DOI: 10.1016/j.gene.2022.147082] [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: 09/27/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Gastric cancer (GC) is the fourth most common cause of mortality and the fifth for incidence, globally. Diagnosis, early prognosis, and therapy remains challenging for this condition, and new tumor-associated antigens are required for its detection and immunotherapy. Cancer-testis antigens (CTAs) are a subfamily of tumor-associated antigens (TAAs) that have been identified as potential biomarkers and targets for cancer immunotherapy. The CTAs-restricted expression pattern in tumor cells and their potential immunogenicity identify them as attractive target candidates in CTA-based diagnosis or prognosis or immunotherapy. To date, numerous studies have reported the dysregulation of CTAs in GC. Several clinical trials have been done to assess CTA-based immunotherapeutic potential in the treatment of GC patients. NY-ESO-1, MAGE, and KK-LC-1 have been used in GC clinical trials. We review recent studies that have investigated the potential of the CTAs in GC regarding the expression, function, aggressive phenotype, prognosis, and immunological responses as well as their possible clinical significance as immunotherapeutic targets with a focus on challenges and future interventions.
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Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Maharati Amirhosein
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Parvaneh Mahmoudian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Leila Mokhlessi
- Centre for Biomedical Education and Research, Institute of Pharmacology and Toxicology, Witten/Herdecke University, Witten, Germany.
| | - Mina Maftooh
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Khazaei
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Seyed Mahdi Hassanian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Ghayour-Mobarhan
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK.
| | | | - Amir Avan
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Park H, Imoto S, Miyano S. PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinformatics 2022; 23:342. [PMID: 35974335 PMCID: PMC9380306 DOI: 10.1186/s12859-022-04871-z] [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: 01/29/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022] Open
Abstract
Background Gene regulatory networks have garnered a large amount of attention to understand disease mechanisms caused by complex molecular network interactions. These networks have been applied to predict specific clinical characteristics, e.g., cancer, pathogenicity, and anti-cancer drug sensitivity. However, in most previous studies using network-based prediction, the gene networks were estimated first, and predicted clinical characteristics based on pre-estimated networks. Thus, the estimated networks cannot describe clinical characteristic-specific gene regulatory systems. Furthermore, existing computational methods were developed from algorithmic and mathematics viewpoints, without considering network biology. Results To effectively predict clinical characteristics and estimate gene networks that provide critical insights into understanding the biological mechanisms involved in a clinical characteristic, we propose a novel strategy for predictive gene network estimation. The proposed strategy simultaneously performs gene network estimation and prediction of the clinical characteristic. In this strategy, the gene network is estimated with minimal network estimation and prediction errors. We incorporate network biology by assuming that neighboring genes in a network have similar biological functions, while hub genes play key roles in biological processes. Thus, the proposed method provides interpretable prediction results and enables us to uncover biologically reliable marker identification. Monte Carlo simulations shows the effectiveness of our method for feature selection in gene estimation and prediction with excellent prediction accuracy. We applied the proposed strategy to construct gastric cancer drug-responsive networks. Conclusion We identified gastric drug response predictive markers and drug sensitivity/resistance-specific markers, AKR1B10, AKR1C3, ANXA10, and ZNF165, based on GDSC data analysis. Our results for identifying drug sensitive and resistant specific molecular interplay are strongly supported by previous studies. We expect that the proposed strategy will be a useful tool for uncovering crucial molecular interactions involved a specific biological mechanism, such as cancer progression or acquired drug resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04871-z.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Seiya Imoto
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.,Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan
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ZNF165 Is Involved in the Regulation of Immune Microenvironment and Promoting the Proliferation and Migration of Hepatocellular Carcinoma by AhR/CYP1A1. J Immunol Res 2022; 2022:4446805. [PMID: 35692498 PMCID: PMC9177304 DOI: 10.1155/2022/4446805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/27/2023] Open
Abstract
The strong tumorigenic capacity and treatment resistance made hepatocellular carcinoma (HCC) a huge threat to public health. ZNF165, the kruppel family of zinc-finger-containing transcription factors, is expressed in HCC; however, its specific role in HCC and the molecular mechanism are yet to be elucidated. In this study, we observed that ZNF165 was overexpressed in liver cancer tissues and the immune microenvironment; higher ZNF165 expression was correlated with lower overall survival in liver cancer patients. The ZNF165 knockdown in Bel7402 cells revealed the impairment of the tryptophan/kynurenine/AhR/CYP1A1 axis. Moreover, the knockdown of CYP1A1 significantly inhibited the proliferation and migration of HCC cells, and ZNF165 promoted the transcriptional activity of AhR by facilitating the nuclear translocation of CYP1A1. In conclusion, the present study argued that ZNF165 was highly expressed in liver tissues and the immune microenvironment. ZNF165 promoted the proliferation and migration of HCC cells by activating the tryptophan/kynurenine/AhR/CYP1A1 axis and promoting the expression of CYP1A1.
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Liu Q, Shi Z, Liu X, Xiao H. Correlation between the coexpression of zinc finger and SCAN domain-containing protein 31 and transcriptional activator with PDZ-binding motif and prognosis in hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1308. [PMID: 33209888 PMCID: PMC7661889 DOI: 10.21037/atm-20-6373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Transcriptional coactivator with PDZ binding motif (TAZ) regulates multiple biological processes and has been found to be related to hepatocellular carcinoma (HCC). However, common signaling pathways downstream after TAZ knockdown may also be important. Methods TAZ was knocked down in an HCC cell line, and its potential target genes were analyzed. A decrease in the expression of zinc finger and SCAN domain-containing protein 31 (ZSCAN31) was observed. The difference in ZSCAN31 expression was evaluated, and its effect on survival in HCC patients who received surgical resection was determined. Results ZSCAN31 was over-expressed in HCC tissues and was associated with low overall survival (OS) in HCC patients after surgical resection. Analysis of tissue samples from 83 HCC patients who underwent surgical resection in our hospital produced similar results. High ZSCAN31 expression was significantly associated with tumor size. High expression levels of both TAZ and ZSCAN31 were related to poor OS. A positive correlation was identified between ZSCAN31 expression and TAZ expression, and the protein binding of ZSCAN31 and TAZ was confirmed by co-immunoprecipitation (Co-IP) assay using an HCC cell line. Conclusions ZSCAN31 is associated with TAZ expression in HCC cells, and the targeting of ZSCAN31 and TAZ may represent a novel therapeutic approach in HCC.
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Affiliation(s)
- Qiang Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhengrong Shi
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiongwei Liu
- Department of Hepatobiliary Surgery, North-Kuanren General Hospital, Chongqing, China
| | - Heng Xiao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Seifi-Alan M, Shamsi R, Ghafouri-Fard S. Application of cancer-testis antigens in immunotherapy of hepatocellular carcinoma. Immunotherapy 2019; 10:411-421. [PMID: 29473472 DOI: 10.2217/imt-2017-0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a worldwide common malignancy with poor prognosis. Several studies have aimed at identification of appropriate biomarkers for early detection of this cancer. Cancer-testis antigens (CTAs) as a novel group of tumor-associated antigens have been demonstrated to be expressed in HCC samples as well as peripheral blood samples from these patients but not in the corresponding adjacent noncancerous samples. Such pattern of expression has provided them an opportunity to be used as immunotherapeutic targets. The detection of spontaneous immune responses against CTAs in HCC patients has prompted design of CTA-based immunotherapeutic protocols in these patients. The results of some clinical trials have been promising in a subset of patients.
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Affiliation(s)
- Mahnaz Seifi-Alan
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roshanak Shamsi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Huang M, Chen Y, Han D, Lei Z, Chu X. Role of the zinc finger and SCAN domain-containing transcription factors in cancer. Am J Cancer Res 2019; 9:816-836. [PMID: 31218096 PMCID: PMC6556609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/04/2019] [Indexed: 06/09/2023] Open
Abstract
Transcription factors are key determinants of gene expression that recognize and bind to short DNA sequence motifs, thereby regulating many biological processes including differentiation, development, and metabolism. Transcription factors are increasingly recognized for their roles in cancer progression. Here, we describe a subfamily of zinc finger transcription factors named zinc finger and SCAN domain containing (ZSCAN) transcription factors. In this review, we summarize the identified members of the ZSCAN family of transcription factors and their roles in cancer progression. Due to the complex regulation mechanisms, ZSCAN transcription factors may show promotive or prohibitive efforts in angiogenesis, cell apoptosis, cell differentiation, cell migration and invasion, cell proliferation, stem cell properties, and chemotherapy sensitivity. The upstream regulation mechanisms of their varied expression levels may include gene mutation, DNA methylation, alternative splicing, and miRNA regulation. What's more, to clarify their diverse functions, we summarize the modulation mechanisms of their activity in downstream genes transcription, including protein-protein interactions mediated by their SCAN box, recruitment of co-regulating molecules and post-translational modifications. A better understanding of the widespread regulatory mode of these transcription factors will provide further insight into the mechanism of transcriptional regulation and suggest novel therapeutic strategies against tumor progression.
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Affiliation(s)
- Mengxi Huang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing, Jiangsu Province, People’s Republic of China
| | - Yanyan Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing, Jiangsu Province, People’s Republic of China
| | - Dong Han
- Department of Medical Oncology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing, Jiangsu Province, People’s Republic of China
| | - Zengjie Lei
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing, Jiangsu Province, People’s Republic of China
- Department of Medical Oncology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing, Jiangsu Province, People’s Republic of China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing, Jiangsu Province, People’s Republic of China
- Department of Medical Oncology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing, Jiangsu Province, People’s Republic of China
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Astaneh M, Dashti S, Esfahani ZT. Humoral immune responses against cancer-testis antigens in human malignancies. Hum Antibodies 2019; 27:237-240. [PMID: 31006681 DOI: 10.3233/hab-190377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND Cancer-testis antigens (CTAs) are a class of cancer antigens with extensive expression in human cancers. Many researchers have detected antibody responses against these tumor antigens in serum of cancer patients. OBJECTIVES To evaluate the relevance of humoral immune responses against CTAs in clinical outcome of cancer patientsMETHODS: We searched PubMed/Medline with the key words cancer-testis antigen, antibody, humoral response and cancer. RESULTS Humoral immune responses against CTAs have been detected in several human malignancies including skin, breast, brain and ovarian cancers. Some studies have shown associations between the presence of these responses in patients and patients' survival. CONCLUSION Humoral immune responses against CTAs are putative biomarkers for cancer detection and follow-up.
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Zhang HD, Jiang LH, Hou JC, Zhong SL, Zhou SY, Zhu LP, Li J, Wang DD, Sun DW, Ji ZL, Tang JH. Circular RNA hsa_circ_0052112 promotes cell migration and invasion by acting as sponge for miR-125a-5p in breast cancer. Biomed Pharmacother 2018; 107:1342-1353. [PMID: 30257349 DOI: 10.1016/j.biopha.2018.08.030] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Accumulating evidence has been reported that circular RNAs (circRNAs) are a class of relatively stable, non-coding RNAs, which are involved in the progression of many types of diseases. However, the mechanism of hsa_circ_0052112 in breast cancer cells is not entirely clear. Hsa_circ_0052112, generated from the ZNF83 gene, is selected by analyzing circRNA expression profiles of breast cancer cell by using microarray assay. In this study, we will show the role of hsa_circ_0052112 in regulating cell invasion and migration in breast cancer. METHODS The expression level of hsa_circ_0052112 in MCF-7 and MDA-MB-231 cells was detected by RT-qPCR; we performed transwell assay to evaluate breast cancer cells' migration and invasion; predicated circRNA/miRNAs interaction using the miRanda and RNAhybrid software; identified the relationship between hsa_circ_0052112 and miR-125a-5p by luciferase activity assay and show the localization of hsa_circ_0052112 by FISH assay and show the significance of ZNF83 in clinical prognosis by Kaplan-Meier survival analysis. RESULTS Hsa_circ_0052112 expression was significantly higher in MDA-MB-231 cells than that in MCF-7 cells. Overexpression of hsa_circ_0052112 promoted cell migration and invasion in breast cancer. Inversely, down-regulation of hsa_circ_0052112 suppressed breast cancer cells migration and invasion. Hsa_circ_0052112 was mostly located in cytoplasm. Hsa_circ_0052112 could directly sponge to miR-125a-5p; overexpression of miR-125a-5p significantly inhibited breast cancer cells migration and invasion. However, high or low expression of miR-125a-5p was not correlated with relapse free survival (RFS) by TCGA database validation, but high expression of ZNF83 was closely correlated with poor RFS by Kaplan-Meier plotter. CONCLUSIONS These data suggest that hsa_circ_0052112 may be a potent biomarker for breast cancer, and may provide a new perspective on treatment of breast cancer.
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Affiliation(s)
- He-da Zhang
- Department of General Surgery, School of Medicine, Southeast University, Nanjing, Jiangsu, China; Department of General Surgery, Institute for Minimally Invasive Surgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
| | - Lin-Hong Jiang
- Department of Oncology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jun-Chen Hou
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shan-Liang Zhong
- Center of Clinical Laboratory, Cancer Institute of Jiangsu Province, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Si-Ying Zhou
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ling-Ping Zhu
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jian Li
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, Jiangsu, China
| | - Dan-Dan Wang
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Da-Wei Sun
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, Jiangsu, China
| | - Zhen-Ling Ji
- Department of General Surgery, School of Medicine, Southeast University, Nanjing, Jiangsu, China; Department of General Surgery, Institute for Minimally Invasive Surgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China.
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China.
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12
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Hong CF, Chen YC, Chen WC, Tu KC, Tsai MH, Chan YK, Yu SS. Construction of diagnosis system and gene regulatory networks based on microarray analysis. J Biomed Inform 2018; 81:61-73. [PMID: 29550394 DOI: 10.1016/j.jbi.2018.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/30/2018] [Accepted: 03/12/2018] [Indexed: 01/02/2023]
Abstract
A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers. During the first stage, F-statistic, pattern recognition matching, and a two-layer K-means classifier were applied in the system to filter out the 20 critical genes most relevant to ovarian cancer from 9600 genes, and the PDGA was used to decide the fittest values of the parameters for these critical genes. Among the 20 critical genes, 15 are associated with cancer progression. In the second stage, we further employed a GBG selector and the association rule to screen out seven target gene sets, each with only four to six genes, and each of which can precisely identify the malignancy stage of ovarian cancer based on their expression profiles. We further deduced the gene regulatory networks of the 20 critical genes by applying the Pearson correlation coefficient to evaluate the correlationship between the expression of each gene at the same stages and at different stages. Correlationships between gene pairs were calculated, and then, three regulatory networks were deduced. Their correlationships were further confirmed by the Ingenuity pathway analysis. The prognostic significances of the genes identified via regulatory networks were examined using online tools, and most represented biomarker candidates. In summary, our proposed system provides a new strategy to identify critical genes or biomarkers, as well as their regulatory networks, from microarray data.
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Affiliation(s)
- Chun-Fu Hong
- Department of Long-Term Care, National Quemoy University, Kinmen County 892, Taiwan, ROC
| | - Ying-Chen Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Wei-Chun Chen
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Keng-Chang Tu
- Deparment of Computer Science and Engineering, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Meng-Hsiun Tsai
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC.
| | - Yung-Kuan Chan
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC.
| | - Shyr Shen Yu
- Deparment of Computer Science and Engineering, National Chung Hsing University, Taichung City 402, Taiwan, ROC
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13
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Zhang J, Fan J, Zhou C, Qi Y. miR-363-5p as potential prognostic marker for hepatocellular carcinoma indicated by weighted co-expression network analysis of miRNAs and mRNA. BMC Gastroenterol 2017. [PMID: 28637446 PMCID: PMC5480191 DOI: 10.1186/s12876-017-0637-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND This study aimed to investigate potential miRNAs and genes associated with the prognosis of hepatocellular carcinoma (HCC). METHODS Weighted co-expression network analysis was utilized to analyze the mRNA and miRNA sequencing data of HCC from TCGA (The Cancer Genome Atlas) database. Significant network modules were identified, and then functions of genes in the gene network modules and target genes of miRNAs in the miRNA network modules were explored. Additionally, correlations between network modules and prognostic factors of HCC were analyzed. RESULTS In total, 10 mRNA network modules were identified, three of which were significantly related to tumor stage, NAFLD (non-alcoholic fatty liver disease) and patient age. Four miRNA network modules were identified, of which one was associated with tumor stage. Targets of hsa-miR-363-5p were found distributed in the gene network modules, such as RGPD5, RGPD6, ZNF445 and ZNF780B. Kaplan-Meier test revealed that low expression of hsa-miR-363-5p was associated with better overall survival of HCC patients. CONCLUSION hsa-miR-363-5p may be a potential prognostic marker for HCC.
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Affiliation(s)
- Jun Zhang
- Department of Oncology, The third people's hospital of Chengdu, Chengdu, 610031, China.
| | - Jia Fan
- Department of Oncology, The third people's hospital of Chengdu, Chengdu, 610031, China
| | - Chongming Zhou
- Department of Oncology, The third people's hospital of Chengdu, Chengdu, 610031, China
| | - Yanyu Qi
- Department of Oncology, The third people's hospital of Chengdu, Chengdu, 610031, China
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14
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Nygaard M, Terkelsen T, Vidas Olsen A, Sora V, Salamanca Viloria J, Rizza F, Bergstrand-Poulsen S, Di Marco M, Vistesen M, Tiberti M, Lambrughi M, Jäättelä M, Kallunki T, Papaleo E. The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer. Front Mol Biosci 2016; 3:78. [PMID: 28018905 PMCID: PMC5156680 DOI: 10.3389/fmolb.2016.00078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/17/2016] [Indexed: 11/24/2022] Open
Abstract
SCAN domains in zinc-finger transcription factors are crucial mediators of protein-protein interactions. Up to 240 SCAN-domain encoding genes have been identified throughout the human genome. These include cancer-related genes, such as the myeloid zinc finger 1 (MZF1), an oncogenic transcription factor involved in the progression of many solid cancers. The mechanisms by which SCAN homo- and heterodimers assemble and how they alter the transcriptional activity of zinc-finger transcription factors in cancer and other diseases remain to be investigated. Here, we provide the first description of the conformational ensemble of the MZF1 SCAN domain cross-validated against NMR experimental data, which are probes of structure and dynamics on different timescales. We investigated the protein-protein interaction network of MZF1 and how it is perturbed in different cancer types by the analyses of high-throughput proteomics and RNASeq data. Collectively, we integrated many computational approaches, ranging from simple empirical energy functions to all-atom microsecond molecular dynamics simulations and network analyses to unravel the effects of cancer-related substitutions in relation to MZF1 structure and interactions.
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Affiliation(s)
- Mads Nygaard
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - André Vidas Olsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Juan Salamanca Viloria
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Fabio Rizza
- Department of Biomedical Sciences, University of Padua Padua, Italy
| | - Sanne Bergstrand-Poulsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Miriam Di Marco
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Mette Vistesen
- Cell Stress and Survival Unit and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Matteo Tiberti
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Matteo Lambrughi
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Marja Jäättelä
- Unit of Cell Death and Metabolism and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Tuula Kallunki
- Unit of Cell Death and Metabolism and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
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15
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Maxfield KE, Taus PJ, Corcoran K, Wooten J, Macion J, Zhou Y, Borromeo M, Kollipara RK, Yan J, Xie Y, Xie XJ, Whitehurst AW. Comprehensive functional characterization of cancer-testis antigens defines obligate participation in multiple hallmarks of cancer. Nat Commun 2015; 6:8840. [PMID: 26567849 PMCID: PMC4660212 DOI: 10.1038/ncomms9840] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/08/2015] [Indexed: 01/18/2023] Open
Abstract
Tumours frequently activate genes whose expression is otherwise biased to the testis,
collectively known as cancer–testis antigens (CTAs). The extent to which
CTA expression represents epiphenomena or confers tumorigenic traits is unknown. In
this study, to address this, we implemented a multidimensional functional genomics
approach that incorporates 7 different phenotypic assays in 11 distinct disease
settings. We identify 26 CTAs that are essential for tumor cell viability and/or are
pathological drivers of HIF, WNT or TGFβ signalling. In particular, we
discover that Foetal and Adult Testis Expressed 1 (FATE1) is a key survival factor
in multiple oncogenic backgrounds. FATE1 prevents the accumulation of the
stress-sensing BH3-only protein, BCL-2-Interacting Killer (BIK), thereby permitting
viability in the presence of toxic stimuli. Furthermore, ZNF165 promotes
TGFβ signalling by directly suppressing the expression of negative feedback
regulatory pathways. This action is essential for the survival of triple negative
breast cancer cells in vitro and in vivo. Thus, CTAs make significant
direct contributions to tumour biology. Proteins usually expressed solely in the testes are often found
over-expressed in cancer and are termed cancer testis antigens. Here, the authors use a
comprehensive screening strategy to identify 26 cancer-testis antigens that promote
tumorigenic behaviour.
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Affiliation(s)
- Kimberly E Maxfield
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Patrick J Taus
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kathleen Corcoran
- Department of Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joshua Wooten
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jennifer Macion
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yunyun Zhou
- Department of Clinical Science, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mark Borromeo
- Department of Neuroscience, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jingsheng Yan
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yang Xie
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Clinical Science, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Xian-Jin Xie
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Clinical Science, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Angelique W Whitehurst
- Simmons Comprehensive Cancer Center, UT-Southwestern Medical Center, Dallas, Texas 75390, USA
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Tsai MH, Wang HC, Lee GW, Lin YC, Chiu SH. A Decision Tree Based Classifier to Analyze Human Ovarian Cancer cDNA Microarray Datasets. J Med Syst 2015; 40:21. [PMID: 26531754 DOI: 10.1007/s10916-015-0361-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022]
Abstract
Ovarian cancer is the deadliest gynaecological disease because of the high mortality rate and there is no any symptom in cancer early stage. It was often the terminal cancer period when patients were diagnosed with ovarian cancer and thus delays a good opportunity of treatment. The current common method for detecting ovarian cancer is blood testing for analyzing the tumor marker CA-125 of serum. However, specificity and sensitivity of CA-125 are insufficient for early detection. Therefore, it has become an urgent issue to look for an efficient method which precisely detects the tumor markers for ovarian cancer. This study aims to find the target genes of ovarian cancer by different algorithms of information science. Feature selection and decision tree were applied to analyze 9600 ovarian cancer-related genes. After screening the target genes, candidate genes will be analyzed by Ingenuity Pathway Analysis (IPA) software to create a genetic pathway model and to understand the interactive relationship in the different pathological stages of ovarian cancer. Finally, this research found 9 oncogenes associated with ovarian cancer and some genes had not been discovered in previous studies. This system will assist medical staffs in diagnosis and treatment at cancer early stage and improve the patient's survival.
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Affiliation(s)
- Meng-Hsiun Tsai
- Department of Management Information System, National Chung Hsing University, No.250, Kuo Kuang Rd., Taichung City, 402, Taiwan. .,Institute of Genomics and Bioinformatics, National Chung Hsing University, No.250, Kuo Kuang Rd., Taichung City, 402, Taiwan.
| | - Hsin-Chieh Wang
- Department of Management Information System, National Chung Hsing University, No.250, Kuo Kuang Rd., Taichung City, 402, Taiwan.
| | - Guan-Wei Lee
- Department of Management Information System, National Chung Hsing University, No.250, Kuo Kuang Rd., Taichung City, 402, Taiwan.
| | - Yi-Chen Lin
- Department of Management Information System, National Chung Hsing University, No.250, Kuo Kuang Rd., Taichung City, 402, Taiwan.
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17
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Liu Y, Wang M, Jiang S, Lu Y, Tao D, Yang Y, Ma Y, Zhang S. Demethylation of CpG islands in the 5' upstream regions mediates the expression of the human testis-specific gene MAGEB16 and its mouse homolog Mageb16. BMB Rep 2014; 47:86-91. [PMID: 24219866 PMCID: PMC4163901 DOI: 10.5483/bmbrep.2014.47.2.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/23/2013] [Accepted: 06/04/2013] [Indexed: 02/05/2023] Open
Abstract
Tissue-specific gene expression is regulated by epigenetic modification involving trans-acting factors. Here, we identified that the human MAGEB16 gene and its mouse homolog, Mageb16, are only expressed in the testis. To investigate the mechanism governing their expression, the promoter methylation status of these genes was examined in different samples. Two CpG islands (CGIs) in the 5' upstream region of MAGEB16 were highly demethylated in human testes, whereas they were methylated in cells without MAGEB16 expression. Similarly, the CGI in Mageb16 was hypomethylated in mouse testes but hypermethylated in other tissues and cells without Mageb16 expression. Additionally, the expression of these genes could be activated by treatment with the demethylation agent 5'-aza-2'-deoxycytidine (5'-aza-CdR). Luciferase assays revealed that both gene promoter activities were inhibited by methylation of the CGI regions. Therefore, we propose that the testis-specific expression of MAGEB16 and Mageb16 is regulated by the methylation status of their promoter regions. [BMB Reports 2014; 47(2): 86-91]
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Affiliation(s)
- Yunqiang Liu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Meiling Wang
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Siyuan Jiang
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yongjie Lu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Dachang Tao
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yuan Yang
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yongxin Ma
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Sizhong Zhang
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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18
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Frequent expression of zinc-finger protein ZNF165 in human urinary bladder transitional cell carcinoma. Immunobiology 2014; 220:68-73. [PMID: 25214475 DOI: 10.1016/j.imbio.2014.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/20/2022]
Abstract
The aim of the study is to evaluate mRNA/protein expression of zinc finger protein 165 (ZNF165) in transitional cell carcinomas (TCCs) of urinary bladder and correlate its expression with the clinicopathological characteristics of patients. In this study, the methods of quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) were utilized to evaluate mRNA/protein expression of ZNF165 in TCC. Independent Student's t test, ANOVA and Chi-square (χ(2)) were used to analyze the data statistically. We observed overexpression of ZNF165 mRNA in testis and majority (59.2%) of TCC patients. ZNF165 mRNA expression was also detected in adjacent noncancerous tissues (ANCTs) and some other normal tissues. Relative mean fold expression of ZNF165 mRNA was found to be significantly (p<0.01) higher in muscle-invasive bladder cancer (MIBC) as compared to non-muscle-invasive bladder cancer (NMIBC) patients. (12.11±9.57 vs. 5.72±2.61, p=0.009). ZNF165 protein expression was demonstrated on archival formalin-fixed, paraffin-embedded (FFPE) bladder tissues using IHC and nuclear staining pattern was detected. No significant difference was observed in protein expression of ZNF165 between the two groups (NMIBC and MIBC patients) (61.1% vs. 55.2%, p=0.629). No significant protein expression of ZNF165 was observed among ANCTs and benign prostatic hyperplasia (BPH) used as control. Our study results suggest that ZNF165 mRNA/protein expression was observed in TCC of human urinary bladder and might be used as a novel diagnostic biomarker and as well a vaccine target in development of urinary bladder cancer specific immunotherapy.
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Association of polymorphisms at HORMAD2 and prognosis in advanced non-small-cell lung cancer patients. Cancer Epidemiol 2014; 38:414-8. [PMID: 24797335 DOI: 10.1016/j.canep.2014.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/15/2014] [Accepted: 03/23/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cancer-testis (CT) genes are predominantly expressed in the testis and are ectopically activated in a wide range of cancers. The expression of CT antigens has been shown to significantly affect the survival of patients with non-small-cell lung cancer (NSCLC). Recently, a genome-wide association study (GWAS) and expression analysis have identified a novel CT gene (HORMAD2) associated with lung cancer risk in Han Chinese people. Thus, the aim of this study is to evaluate the potential prognostic value of HORMAD2 polymorphisms in Han Chinese patients with advanced NSCLC and undergoing first-line platinum-based chemotherapy. MATERIALS AND METHODS We selected eight single-nucleotide polymorphisms (SNPs) of HORMAD2 with the potential function of affecting the binding of transcription factors, and we genotyped these SNPs in 303 patients with advanced NSCLC using the MassARRAY platform. All patients were treated with first-line platinum-based chemotherapy but without surgery. Log-rank test and Cox proportional hazard models were used for the survival analyses. RESULTS Four SNPs at HORMAD2 (rs9620953, rs8135823, rs5753025 and rs9625921) were significantly associated with the survival of advanced NSCLC patients. Among these, patients with the rs9620953 T allele had a significantly reduced risk of death compared to those with the C allele (additive model: HR, 0.53, 95%CI, 0.32-0.89, P=0.016; dominant model: HR, 0.50, 95%CI, 0.29-0.84, P=0.010). Similarly, the G allele at rs8135823 could decrease the death risk of NSCLC patients compared to the T allele (additive model: HR, 0.63, 95%CI, 0.41-0.95, P=0.028; dominant model: HR, 0.60, 95%CI, 0.39-0.93, P=0.022). Furthermore, both the rs5753025 C allele and the rs9625921 G allele also decreased the death risk in NSCLC in different genetic models (additive model for rs5753025: HR, 0.80, 95%CI, 0.65-0.98, P=0.032; heterozygote model for rs9625921: HR, 0.71, 95%CI, 0.51-0.99, P=0.040). In the joint effect analyses, we found that patients with one, two, and three to eight favorable alleles had a better survival compared with patients carrying no alleles. CONCLUSIONS These findings indicate that polymorphisms at the CT gene HORMAD2 might be involved in the prognosis of advanced NSCLC in Han Chinese. Further larger and functional studies are needed to confirm the results.
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Wirth TC. Spontaneous and therapeutic immune responses in hepatocellular carcinoma: implications for current and future immunotherapies. Expert Rev Gastroenterol Hepatol 2014; 8:101-10. [PMID: 24410473 DOI: 10.1586/17474124.2014.862497] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) represents a major health problem in the world, ranking fifth in incidence and third in cancer-related deaths. Due to the unique immunosuppressive microenvironment of the liver, HCC develops in an immunotolerant niche posing an important obstacle to immunotherapy. A number of studies, however, have shown immunogenic properties of HCC by demonstrating spontaneous adaptive immune responses during tumor formation and progression. Furthermore, studies examining immune responses during HCC therapy have revealed that conventional treatments such as surgical resection, locoregional therapy and systemic therapy with antibodies, small molecules or chemotherapy induce adaptive immune responses that contribute to therapeutic effects. These observations have provided a basis for clinical trials involving adoptive transfers of T cells or natural killer cells, peptide and dendritic cell vaccinations or, more recently, virotherapy and inhibition of co-inhibitory molecules. Here, spontaneous and therapeutic immune responses in HCC and their implication for current and future immunotherapies are discussed.
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Affiliation(s)
- Thomas C Wirth
- Department of Gastroenterology, Hepatology and Endocrinology, Medical School Hannover, 30625 Hannover, Germany
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21
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Tan Z, Zhang S, Li M, Wu X, Weng H, Ding Q, Cao Y, Bao R, Shu Y, Mu J, Ding Q, Wu W, Yang J, Zhang L, Liu Y. Regulation of cell proliferation and migration in gallbladder cancer by zinc finger X-chromosomal protein. Gene 2013; 528:261-6. [DOI: 10.1016/j.gene.2013.06.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 06/23/2013] [Accepted: 06/27/2013] [Indexed: 11/28/2022]
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Liang Y, Huimei Hong F, Ganesan P, Jiang S, Jauch R, Stanton LW, Kolatkar PR. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206. Nucleic Acids Res 2012; 40:8721-32. [PMID: 22735705 PMCID: PMC3458555 DOI: 10.1093/nar/gks611] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 Å crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.
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Affiliation(s)
- Yu Liang
- Laboratory for Structural Biochemistry, Stem Cell and Developmental Biology, Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore
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Zhou SF, Mo FR, Bin YH, Hou GQ, Xie XX, Luo GR. Serum immunoreactivity of SMP30 and its tissues expression in hepatocellular carcinoma. Clin Biochem 2010; 44:331-6. [PMID: 21047503 DOI: 10.1016/j.clinbiochem.2010.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 09/29/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To detect serum antibody against SMP30 in HCC patients and to evaluate its potential associations with HCC patient's clinical parameter and expression levels in HCC tissues. DESIGN AND METHODS Serum antibody to SMP30 was tested by ELISA method; SMP30 mRNA and protein expression in HCC patients were analyzed using the methods of in situ nucleic acid hybridization and immunohistochemistry, respectively. RESULTS The highest relevance of SMP30 antibody was associated with HCC (32.4%). The positive rate of SMP30 antibody was not related to the age of patients, tumor size, metastasis and infections of HBV, but the positive rate for SMP30 antibody in the HCC sera with alpha-fetoprotein (AFP) negative was higher (43.6%) compared with that AFP positive (26.2%). Both SMP30 mRNA and protein expression levels were downregulated in HCC and upregulated in adjacent tissues. CONCLUSIONS SMP30 may be useful for HCC serologic screening, especially for the patients with AFP negative.
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Affiliation(s)
- Su-Fang Zhou
- The School of Pre-clinical Sciences, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China.
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Bai G, Liu Y, Zhang H, Su D, Tao D, Yang Y, Ma Y, Zhang S. Promoter demethylation mediates the expression of ZNF645, a novel cancer/testis gene. BMB Rep 2010; 43:400-6. [PMID: 20587329 DOI: 10.5483/bmbrep.2010.43.6.400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cancer/testis (CT) antigens exhibit highly tissue-restricted expression and are considered promising targets for cancer vaccines. Here we identified a novel CT gene ZNF645 which restrictively expresses in normal human testes and lung cancer patients (68.3%). To investigate the promoter methylation status of ZNF645, we carried out bisulfite genomic sequencing and found that the CpG island in its promoter was heavily methylated in normal lung tissues without the expression of ZNF645, whereas there was high demethylation in normal human testes and lung carcinoma tissues with its expression. Also ZNF645 could be remarkably activated in A549 and HEK293T cells treated by DNA demethylation agent 5'-aza-2'-deoxycytidine. And the dual luciferase assay revealed that the promoter activity of the ZNF645 was inhibited by methylation of the CpG island region. Therefore, we proposed that ZNF645 is a CT gene and activated in human testis and lung cancers by demethylation of its promoter region.
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Affiliation(s)
- Gang Bai
- Division of Human Morbid Genomics, State Key Lab of Biotherapy, P R China
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Hartmann TB, Mattern E, Wiedemann N, van Doorn R, Willemze R, Niikura T, Hildenbrand R, Schadendorf D, Eichmüller SB. Identification of selectively expressed genes and antigens in CTCL. Exp Dermatol 2007; 17:324-34. [PMID: 17979976 DOI: 10.1111/j.1600-0625.2007.00637.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The knowledge of tumor-associated antigens is required for most types of immunotherapy and can substantially facilitate diagnosis. To identify potential tumor-associated genes expressed in cutaneous T-cell lymphoma (CTCL), we used three complementary strategies: antigens which elicit a humoral immune response in CTCL patients were detected by serological analysis of a recombinant cDNA expression library. cDNAs differentially expressed in CTCL but not peripheral blood monocytes were identified by comparative cDNA hybridization and suppression subtractive hybridization. We identified 43 genes selectively expressed by CTCL cells, that have not yet been described in the context of CTCL development, but most of which had been reported to be associated with cancer. Expression analysis by database mining and subsequently RT-PCR on selected clones confirmed their selective expression in CTCL tissues. Serological tests showed that 15 clones were recognized by sera of CTCL patients but not of healthy donors. Analysis of serological tests for 11 clones using serum antibody detection array (SADA) and 100 sera of controls and CTCL patients each revealed up to 5% reactive sera in the tumor group. The expression pattern of the detected clones and their immunogenicity demonstrates that they might be relevant for the understanding of CTCL and suggests particularly three clones, HD-CL-41 (DRAK2), HD-CL-49 (nudC) and HD-CL-12 (ZNF195) for further analysis with respect to their prognostic and therapeutic value for CTCL.
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Affiliation(s)
- Tanja B Hartmann
- German Cancer Research Center, Skin Cancer Unit, Heidelberg, Germany
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Dihal AA, Tilburgs C, van Erk MJ, Rietjens IMCM, Woutersen RA, Stierum RH. Pathway and single gene analyses of inhibited Caco-2 differentiation by ascorbate-stabilized quercetin suggest enhancement of cellular processes associated with development of colon cancer. Mol Nutr Food Res 2007; 51:1031-45. [PMID: 17639512 DOI: 10.1002/mnfr.200600261] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim was to investigate mechanisms contributing to quercetin's previously described effects on cell-proliferation and -differentiation, which contradicted its proposed anticarcinogenic potency. In a 10-day experiment, 40 microM quercetin stabilized by 1 mM ascorbate reduced Caco-2 differentiation up to 50% (p < 0.001). Caco-2 RNA from days 5 and 10, hybridized on HG-U133A2.0 Affymetrix GeneChips(R), showed 1,743 affected genes on both days (p < 0.01). All 14 Caco-2 differentiation-associated genes showed decreased expression (p < 0.01), including intestinal alkaline phosphatase, that was confirmed technically (qRT-PCR) and functionally (enzyme-activity). The 1,743 genes contributed to 27 pathways (p < 0.05) categorized under six gene ontology (GO) processes, including apoptosis and cell-cycle. Genes within these GO-processes showed fold changes that suggest increased cell-survival and -proliferation. Furthermore, quercetin down-regulated expression of genes involved in tumor-suppression and phase II metabolism, and up-regulated oncogenes. Gene expression changes mediated by ascorbate-stabilized quercetin were concordant with those occurring in human colorectal carcinogenesis ( approximately 80-90%), but were opposite to those previously described for Caco-2 cells exposed to quercetin without ascorbate ( approximately 75-90%). In conclusion, gene expression among Caco-2 cells exposed to ascorbate-stabilized quercetin showed mechanisms contrary to what is expected for a cancer-preventive agent. Whether this unexpected in vitro effect is relevant in vivo, remains to be elucidated.
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Affiliation(s)
- Ashwin A Dihal
- TNO Quality of Life, Business Unit Biosciences, Zeist, The Netherlands
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Xu Q, Chen W. Developing effective tumor vaccines: basis, challenges and perspectives. FRONTIERS OF MEDICINE IN CHINA 2007; 1:11-19. [PMID: 24557610 DOI: 10.1007/s11684-007-0003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Accepted: 10/20/2006] [Indexed: 06/03/2023]
Abstract
A remarkable advance in tumor immunology during the last decade is the elucidation of the antigenic basis of tumor recognition and destruction. A variety of tumor antigens have been identified using several strategies including conventional experiments and newly developed bioinformatics. Among these antigens, cancer/testis antigen (CT antigen) is considered to be the most promising target for immunotherapy by vaccination. Successful immunotherapy of tumors requires understanding of the natural relationship between the immune system and tumor in the status of differentiation, invasion and maturation. Continued progress in development of effective cancer vaccines depends on the identification of appropriate target antigens, the establishment of optimal immunization strategies without harmful autoimmune responses and the ability of manipulating tumor microenvironment to circumvent immune suppression and to augment the anti-tumor immune response.
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Affiliation(s)
- Qingwen Xu
- Department of Immunology, Peking University Health Science Center, Beijing, 100083, China
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