1
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Le MK, Oishi N, Mochizuki K, Kondo T. Immunohistochemical detection of cancer genetic abnormalities. Pathol Res Pract 2024; 255:155109. [PMID: 38340581 DOI: 10.1016/j.prp.2024.155109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/07/2024] [Indexed: 02/12/2024]
Abstract
New applications of immunohistochemistry (IHC) expand rapidly due to the development of molecular analyses and an increased understanding of molecular biology. IHC becomes much more important as a screening or even a confirmatory test for molecular changes in cancer. The past decades have witnessed the release of many immunohistochemical markers of the new generation. The novel markers have extensively high specificity and sensitivity for the detection of genetic abnormalities. In addition to diagnostic utility, IHC has been validated to be a practical tool in terms of treatments, especially molecular targeted therapy. In this review, we first describe the common alterations of protein IHC staining in human cancer: overexpression, underexpression, or loss of expression and altered staining pattern. Next, we examine the relationship between staining patterns and genetic aberrations regarding both conventional and novel IHC markers. We also mention current mutant-specific and fusion-specific antibodies and their concordance with molecular techniques. We then describe the basic molecular mechanisms from genetic events to corresponding protein expression patterns (membranous, cytoplasmic, or nuclear patterns). Finally, we shortly discuss the applications of immunohistochemistry in molecular targeted therapy. IHC markers can serve as a complementary or companion diagnostic test to provide valuable information for targeted therapy. Moreover, immunohistochemistry is also crucial as a companion diagnostic test in immunotherapy. The increased number of IHC novel antibodies is broadening its application in anti-cancer therapies.
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Affiliation(s)
- Minh-Khang Le
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Naoki Oishi
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan.
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2
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Lee S, Kim G, Lee J, Lee AC, Kwon S. Mapping cancer biology in space: applications and perspectives on spatial omics for oncology. Mol Cancer 2024; 23:26. [PMID: 38291400 PMCID: PMC10826015 DOI: 10.1186/s12943-024-01941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.
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Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea
| | - Gyeongjun Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario, ON, M5S 3H6, Canada
| | - Amos C Lee
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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3
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Zhang Y, Zhang Y, Feng Y, Zhang N, Chen S, Gu C, Hu L, Sheng J, Xu B, Feng N. Construction of circRNA-based ceRNA network and its prognosis-associated subnet of clear cell renal cell carcinoma. Cancer Med 2021; 10:8210-8221. [PMID: 34569727 PMCID: PMC8607260 DOI: 10.1002/cam4.4311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are novel biomarkers of various cancers. CircRNAs can sponge miRNAs and regulate target mRNAs, which was called competing endogenous RNAs (ceRNA). This study was designed to identify circRNAs related to patients with clear cell renal cell carcinoma (ccRCC) and the first to select three independent Gene Expression Omnibus microarrays covering circRNAs, miRNAs, and mRNAs for multiple analyses. The data of clinical cases applied in our study were obtained from The Cancer Genome Atlas. We successfully conducted a circRNA/miRNA/mRNA ceRNA network related to ccRCC patients via R software and Cytoscape including 8 circRNAs, 6 miRNAs, and 49 mRNAs. The prognosis‐associated subnet covered 8 circRNAs, 6 miRNAs, and 22 mRNAs. Quantitative real‐time PCR was applied to measure our prediction in three renal cell lines and 23 pairs of tissues. Small interfering RNA targeting the back‐splice region of hsa_circ_0001167 was further implied to confirm the regulation. Ultimately, hsa_circ_0001167/hsa‐miR‐595/CCDC8 regulatory axis was identified in this study, which may serve as prognostic indicators. Lower levels of hsa_circ_0001167 and CCDC8 were potentially correlated with worse patient survival.
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Affiliation(s)
- Yuwei Zhang
- Department of Urology, Affiliated Wuxi No. 2 Hospital of Nanjing Medical University, Wuxi, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yangkun Feng
- Medical College of Nantong University, Nantong, China
| | - Nan Zhang
- Department of Urology, Affiliated Wuxi No. 2 Hospital of Nanjing Medical University, Wuxi, China
| | - Saisai Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Chaoqun Gu
- Medical College of Nantong University, Nantong, China
| | - Lei Hu
- Department of Urology, Affiliated Wuxi No. 2 Hospital of Nanjing Medical University, Wuxi, China
| | - Jiayi Sheng
- Department of Urology, Affiliated Wuxi No. 2 Hospital of Nanjing Medical University, Wuxi, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Southeast University, Nanjing, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No. 2 Hospital of Nanjing Medical University, Wuxi, China.,Medical College of Nantong University, Nantong, China
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4
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Zhang Z, Luo J, Shang J, Li M, Wu FX, Pan Y, Wang J. Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1070-1081. [PMID: 31403441 DOI: 10.1109/tcbb.2019.2934407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Homozygous and heterozygous deletions commonly exist in the human genome. For current structural variation detection tools, it is significant to determine whether a deletion is homozygous or heterozygous. However, the problems of sequencing errors, micro-homologies, and micro-insertions prohibit common alignment tools from identifying accurate breakpoint locations, and often result in detecting false structural variations. In this study, we present a novel deletion detection tool called Sprites2. Comparing with Sprites, Sprites2 makes the following modifications: (1) The distribution of insert size is used in Sprites2, which can identify the type of deletions and improve the accuracy of deletion calls. (2) A precise alignment method based on AGE (one algorithm simultaneously aligning 5' and 3' ends between two sequences) is adopted in Sprites2 to identify breakpoints, which is helpful to resolve the problems introduced by sequencing errors, micro-homologies, and micro-insertions. In order to test and verify the performance of Sprites2, some simulated and real datasets are adopted in our experiments, and Sprites2 is compared with five popular tools. The experimental results show that Sprites2 can improve the performance of deletion detection. Sprites2 can be downloaded from https://github.com/zhangzhen/sprites2.
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5
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Fu P, Bu C, Cui B, Li N, Wu J. Screening of differentially expressed genes and identification of AMACR as a prognostic marker in prostate cancer. Andrologia 2021; 53:e14067. [PMID: 33861880 DOI: 10.1111/and.14067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
Prostate cancer, the second most common cancer found in male over the world, was estimated to have 191,930 new cases and 33,330 deaths in 2020 in the United States. Prostate cancer is very common in male, about 12.1% of men will acquire this cancer in their lifetime, and a higher risk was reported in older men and African American men. Gene deregulations have been found to be extensively associated with cancer development. To gain further insight into how gene deregulation affects prostate cancer, we analysed three gene profiling datasets of prostate cancer from Gene Expression Omnibus (GEO) applying bioinformatic tools in our study. Firstly, we identified common differently expressed genes (DEGs) shared by the three gene profiling datasets, constructed protein-protein interaction network and determined top 10 hub genes. Further DEGs validation in TCGA and Human Protein Atlas Database identified AMACR as the core gene. We then analysed the role of AMACR in prostate cancer cell lines and found that AMACR-knockdown resulted in the decreased cell proliferation and increased apoptosis. These results suggest an oncogenic role of AMACR in prostate cancer, and it could be a potential biomarker for the diagnosis of prostate cancer.
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Affiliation(s)
- Ping Fu
- Department of Oncology, People's Hospital of Zhangqiu District, Jinan City, China
| | - Chunying Bu
- Department of Internal Medicine, People's Hospital of Zhangqiu District, Jinan City, China
| | - Bin Cui
- Department of Oncology, People's Hospital of Zhangqiu District, Jinan City, China
| | - Na Li
- Department of Internal Medicine Nursing, People's Hospital of Zhangqiu District, Jinan City, China
| | - Jifeng Wu
- Department of Oncology, People's Hospital of Zhangqiu District, Jinan City, China
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6
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Kong G, Lee H, Tran Q, Kim C, Park J, Kwon SH, Kim SH, Park J. Current Knowledge on the Function of α-Methyl Acyl-CoA Racemase in Human Diseases. Front Mol Biosci 2020; 7:153. [PMID: 32760737 PMCID: PMC7372137 DOI: 10.3389/fmolb.2020.00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
Branched chain fatty acids perform very important functions in human diet and drug metabolism. they cannot be metabolized in mitochondria and are instead processed and degraded in peroxisomes due to the presence of methyl groups on the carbon chains. Oxidative degradation pathways for lipids include α- and β-oxidation and several pathways. In all metabolic pathways, α-methyl acyl-CoA racemase (AMACR) plays an essential role by regulating the metabolism of lipids and drugs. AMACR regulates β-oxidation of branched chain lipids in peroxisomes and mitochondria and promotes chiral reversal of 2-methyl acids. AMACR defects cause sensory-motor neuronal and liver abnormalities in humans. These phenotypes are inherited and are caused by mutations in AMACR. In addition, AMACR has been found to be overexpressed in prostate cancer. In addition, the protein levels of AMACR have increased significantly in many types of cancer. Therefore, AMACR may be an important marker in tumors. In this review, a comprehensive overview of AMACR studies in human disease will be described.
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Affiliation(s)
- Gyeyeong Kong
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyunji Lee
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Quangdon Tran
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Chaeyeong Kim
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jisoo Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Life Science, Hyehwa Liberal Arts College, LINC Plus Project Group, Daejeon University, Daejeon, South Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Seon-Hwan Kim
- Department of Neurosurgery, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jongsun Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
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7
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Xie H, Nie L, Zhang M, Su Z, Chen X, Xu M, Gong J, Chen N, Zhou Q. Suppression of α-methylacyl-coenzyme A racemase by miR200c inhibits prostate adenocarcinoma cell proliferation and migration. Exp Ther Med 2019; 19:1806-1816. [PMID: 32104236 PMCID: PMC7027128 DOI: 10.3892/etm.2019.8406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/02/2019] [Indexed: 02/05/2023] Open
Abstract
Overexpression of α-methylacyl-coenzyme A racemase (AMACR/P504S) is a major abnormality that has been observed in prostate cancer, whereas microRNA (miRNA/miR) 200c, is downregulated. The aim of the present study was to explore whether miR200c was able to exert any regulatory effects on AMACR. To meet this aim, bioinformatics analysis was performed to identify potential binding sites for miR200c in the 3′-untranslated region (3′-UTR) of AMACR. Recombinant adenoviral and dual reporter gene assays were designed to examine the binding of miR200c to the potential seed sequences in the AMACR 3′-UTR. Conventional reverse transcription (RT)-PCR, RT-quantitative (q)PCR and western blotting were also used to examine the regulatory effects of miR200c on AMACR at the mRNA and protein levels. Furthermore, Cell Counting Kit-8, wound healing and Transwell assays were performed to investigate the biological effects of miR200c-AMACR deregulation on prostate cancer cell proliferation, migration and invasion. It was revealed that miR200c post-transcriptionally suppressed AMACR expression by interacting with the 90–97 nucleotide sequence of the AMACR mRNA 3′-UTR. Artificial overexpression of miR200c significantly downregulated the mRNA and protein levels of AMACR in DU145 and PC-3 prostate cancer cells. Knockdown of AMACR by RNA interference, or overexpression of miR200c by recombinant adenoviral Ad-miR200c, inhibited prostate cancer cell proliferation, migration and invasiveness. Taken together, the results of the present study revealed that miR200c may suppress the AMACR expression level post-transcriptionally. The results also indicate that perturbation of the miR200c-AMACR regulatory mechanism may be involved in prostate carcinogenesis and that this may be exploited in future therapeutic approaches to prostate cancer.
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Affiliation(s)
- Hanbing Xie
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ling Nie
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Mengni Zhang
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhengzheng Su
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xueqin Chen
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Miao Xu
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jing Gong
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ni Chen
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qiao Zhou
- Pathology Department and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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8
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Langevin SM, Kuhnell D, Niu L, Biesiada J, Leung YK, Deka R, Chen A, Medvedovic M, Kelsey KT, Kasper S, Zhang X. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics 2019; 11:987-1002. [PMID: 31215230 DOI: 10.2217/epi-2018-0172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: The goal of this study was to comprehensively interrogate and map DNA methylation across 16 CpG-dense regions previously associated with oral and pharyngeal squamous cell carcinoma (OPSCC). Materials & methods: Targeted multiplex bisulfite amplicon sequencing was performed on four OPSCC cell lines and primary non-neoplastic oral epithelial cells. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed for a subset of associated genes. Results: There was clear differential methylation between one or more OPSCC cell lines and control cells for the majority of CpG-dense regions. Conclusion: Targeted multiplex bisulfite amplicon sequencing allowed us to efficiently map methylation across the entire region of interest with a high degree of sensitivity and helps shed light on novel differentially methylated regions that may have value as biomarkers of OPSCC.
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Affiliation(s)
- Scott M Langevin
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Cincinnati Cancer Center, Cincinnati, OH 45267, USA
| | - Damaris Kuhnell
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Liang Niu
- Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jacek Biesiada
- Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yuet-Kin Leung
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ranjan Deka
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Aimin Chen
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mario Medvedovic
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Pathology & Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Susan Kasper
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiang Zhang
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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9
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Exploiting the transcriptional specificity of the alpha-methylacyl-CoA racemase AMACR promoter for the molecular imaging of prostate cancer. Oncotarget 2018; 9:36693-36704. [PMID: 30613352 PMCID: PMC6291171 DOI: 10.18632/oncotarget.26401] [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] [Received: 10/17/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
The metabolic protein alpha-methylacyl-CoA racemase (AMACR) is significantly overexpressed in prostate cancer compared to the normal prostate and other non-malignant tissue. Though an attractive target, there are no reports in the literature on leveraging the expression of AMACR for the molecular imaging of prostate cancer. Here, we used a molecular-genetic imaging strategy to exploit the transcriptional specificity of the AMACR promoter for the in vivo detection of prostate cancer using the reporter gene luciferase. We performed a stepwise truncation of the promoter and identified a 565 base pair minimal promoter for AMACR that retained both high activity and specificity. Following identification of the minimal promoter for AMACR, we used an advanced two-step transcriptional amplification system to maximize the promoter output. We showed that our optimized AMACR promoter can drive expression of luciferase for molecular imaging in subcutaneous xenograft models of androgen receptor-positive and androgen receptor-negative prostate cancer using a non-replicative adenovirus for gene delivery. Our results provide evidence that the AMACR promoter can be exploited to drive the cancer-specific expression of reporter genes and potentially even be incorporated into conditionally replicative adenoviruses for oncolytic therapy and other applications.
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10
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Huang W, Feng Y, Liang J, Yu H, Wang C, Wang B, Wang M, Jiang L, Meng W, Cai W, Medvedovic M, Chen J, Paul C, Davidson WS, Sadayappan S, Stambrook PJ, Yu XY, Wang Y. Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration. Nat Commun 2018; 9:700. [PMID: 29453456 PMCID: PMC5816015 DOI: 10.1038/s41467-018-03019-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 01/12/2018] [Indexed: 12/20/2022] Open
Abstract
The goal of replenishing the cardiomyocyte (CM) population using regenerative therapies following myocardial infarction (MI) is hampered by the limited regeneration capacity of adult CMs, partially due to their withdrawal from the cell cycle. Here, we show that microRNA-128 (miR-128) is upregulated in CMs during the postnatal switch from proliferation to terminal differentiation. In neonatal mice, cardiac-specific overexpression of miR-128 impairs CM proliferation and cardiac function, while miR-128 deletion extends proliferation of postnatal CMs by enhancing expression of the chromatin modifier SUZ12, which suppresses p27 (cyclin-dependent kinase inhibitor) expression and activates the positive cell cycle regulators Cyclin E and CDK2. Furthermore, deletion of miR-128 promotes cell cycle re-entry of adult CMs, thereby reducing the levels of fibrosis, and attenuating cardiac dysfunction in response to MI. These results suggest that miR-128 serves as a critical regulator of endogenous CM proliferation, and might be a novel therapeutic target for heart repair.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Yuliang Feng
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Jialiang Liang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Hao Yu
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Cheng Wang
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences and Faculty of Science, Radboud University, Nijmegen, 6525, Gelderland, The Netherlands
| | - Boyu Wang
- Samaritan Medical Center, 830 Washington Street, Watertown, NY, 13601, USA
| | - Mingyang Wang
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Lin Jiang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Wei Meng
- Division of Liver Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China
| | - Wenfeng Cai
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Jenny Chen
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Sakthivel Sadayappan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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11
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Ma R, Liang J, Huang W, Guo L, Cai W, Wang L, Paul C, Yang HT, Kim HW, Wang Y. Electrical Stimulation Enhances Cardiac Differentiation of Human Induced Pluripotent Stem Cells for Myocardial Infarction Therapy. Antioxid Redox Signal 2018; 28:371-384. [PMID: 27903111 PMCID: PMC5770128 DOI: 10.1089/ars.2016.6766] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIMS Electrical stimulation (EleS) can promote cardiac differentiation, but the underlying mechanism is not well known. This study investigated the effect of EleS on cardiomyocyte (CM) differentiation of human induced pluripotent stem cells (hiPSCs) and evaluated the therapeutic effects for the treatment of myocardial infarction (MI). RESULTS Cardiac differentiation of hiPSCs was induced with EleS after embryoid body formation. Spontaneously beating hiPSCs were observed as early at 2 days when treated with EleS compared with control treatment. The cardiac differentiation efficiency of hiPSCs was significantly enhanced by EleS. In addition, the functional maturation of hiPSC-CMs under EleS was confirmed by calcium indicators, intracellular Ca2+ levels, and expression of structural genes. Mechanistically, EleS mediated cardiac differentiation of hiPSCs through activation of Ca2+/PKC/ERK pathways, as revealed by RNA sequencing, quantitative polymerase chain reaction, and Western blotting. After transplantation in immunodeficient MI mice, EleS-preconditioned hiPSC-derived cells significantly improved cardiac function and attenuated expansion of infarct size. The preconditioned hiPSC-derived CMs were functionally integrated with the host heart. INNOVATION We show EleS as an efficacious time-saving approach for CM generation. The global RNA profiling shows that EleS can accelerate cardiac differentiation of hiPSCs through activation of multiple pathways. The cardiac-mimetic electrical signals will provide a novel approach to generate functional CMs and facilitate cardiac tissue engineering for successful heart regeneration. CONCLUSION EleS can enhance efficiency of cardiac differentiation in hiPSCs and promote CM maturation. The EleS-preconditioned CMs emerge as a promising approach for clinical application in MI treatment. Antioxid. Redox Signal. 28, 371-384.
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Affiliation(s)
- Ruilian Ma
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Jialiang Liang
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Wei Huang
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Linlin Guo
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Wenfeng Cai
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Lei Wang
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Christian Paul
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Huang-Tian Yang
- 2 Key Laboratory of Stem Cell Biology and Laboratory of Molecular Cardiology, Institute of Health Sciences, Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) and Shanghai Jiao Tong University School of Medicine (SJTUSM) , Shanghai, China
| | - Ha Won Kim
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Yigang Wang
- 1 Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati , Cincinnati, Ohio
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Induction of alpha-methylacyl-CoA racemase by miR-138 via up-regulation of β-catenin in prostate cancer cells. J Cancer Res Clin Oncol 2017; 143:2201-2210. [PMID: 28741117 DOI: 10.1007/s00432-017-2484-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
PURPOSE Alpha-methylacyl-CoA racemase (AMACR) is highly overexpressed in prostate cancer (PCa) and its transcriptional regulators include various transcription factors and CTNNB1/β-catenin. Our previous findings suggested a post-transcriptional regulation by the tumor-suppressive microRNA miR-138 in PCa. Thus, the aim of this study was to demonstrate the direct interaction of miR-138 with the 3'-UTR of AMACR. Furthermore, the influence of miR-138 on the expression of AMACR and selected AMACR regulators was investigated in PCa cells. METHODS Using DU-145, PC-3, and LNCaP PCa cells, the effect of exogenous miR-138 on AMACR and selected AMACR regulators was determined by quantitative PCR and Western blot. Luciferase reporter assays were used to verify target and promoter interaction. RESULTS Using a luciferase reporter assay a direct interaction of miR-138 with the AMACR-3'-UTR was confirmed. Surprisingly, AMACR expression was up-regulated by up to 125% by exogenous miR-138 in PCa cells. The lack of any miR-138 binding sites within the AMACR promoter suggested an indirect mechanism of up-regulation. Therefore, the effect of miR-138 on selected AMACR regulators including CTNNB1/β-catenin, RELA, SMAD4, SP1, and TCF4 was evaluated. MiR-138 solely evoked an up-regulation of CTNNB1 mRNA expression and β-catenin protein levels by up to 75%. Further in silico analysis revealed a binding site for miR-138 within the CTNNB1 promoter. MiR-138 could enhance the activity of the CTNNB1 promoter, which in turn could contribute to the observed AMACR up-regulation. CONCLUSIONS The present findings suggest that miR-138 can indirectly up-regulate AMACR via transcriptional induction of CTNNB1, at least in vitro in PCa cells.
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Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 2016; 8:442-57. [PMID: 26992833 PMCID: PMC5126213 DOI: 10.15252/emmm.201506055] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor‐specific mutations not only in protein‐coding sequences but also in non‐coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this “dark matter” of the genome. Malignancy‐driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5′‐UTR and 3′‐UTR. Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non‐coding RNA, such as microRNA, lncRNA, and lincRNA. A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR‐21 as well as tumor suppressor genes such as TP53/p53,APC,BRCA1, or RB1 can be affected by these alterations. In summary, coding‐independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non‐coding or allegedly silent mutations in tumorigenesis.
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Affiliation(s)
- Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany
| | - Lorenz Bartsch
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Julia C Berkmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Karin Fröse
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jana Heitmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Caroline Hoppe
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Deetje Iggena
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Danny Jazmati
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Philipp Karschnia
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Miriam Linsenmeier
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Thomas Maulhardt
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Lino Möhrmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Johannes Morstein
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Stella V Paffenholz
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Paula Röpenack
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Timo Rückert
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ludger Sandig
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maximilian Schell
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Anna Steinmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Gjendine Voss
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jacqueline Wasmuth
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maria E Weinberger
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ramona Wullenkord
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
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AMACR amplification and overexpression in primary imatinib-naïve gastrointestinal stromal tumors: a driver of cell proliferation indicating adverse prognosis. Oncotarget 2015; 5:11588-603. [PMID: 25473890 PMCID: PMC4294386 DOI: 10.18632/oncotarget.2597] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/18/2014] [Indexed: 12/12/2022] Open
Abstract
Non-random gains of chromosome 5p have been observed in clinically aggressive gastrointestinal stromal tumors, whereas the driving oncogenes on 5p remain to be characterized. We used an integrative genomic and functional approach to identify amplified oncogenes on 5p and to evaluate the relevance of AMACR amplification at 5p13.3 and its overexpression in gastrointestinal stromal tumors. Thirty-seven tumor samples, imatinib-sensitive GIST882 cell line, and imatinib-resistant GIST48 cell line were analyzed for DNA imbalances using array-based genomic profiling. Forty-one fresh tumor samples of various risk categories were enriched for pure tumor cells by laser capture microdissection and quantified for AMACR mRNA expression. AMACR-specific fluorescence in situ hybridization and immunohistochemistry were both informative in tissue microarray sections of 350 independent primary gastrointestinal stromal tumors, including 213 cases with confirmed KIT /PDGFRA genotypes. To assess the oncogenic functions of AMACR, GIST882 and GIST48 cell lines were stably silenced against their endogenous AMACR expression. In 59% of cases featuring 5p gains, two major amplicons encompassed discontinuous chromosomal regions that were differentially overrepresented in high-risk cases, including the one harboring the mRNA-upregulated AMACR gene. Gene amplification was detected in 19.7% of cases (69/350) and strongly related to protein overexpression (p<0.001), although 52% of AMACR-overexpressing cases exhibited no amplification. Both gene amplification and protein overexpression were significantly associated with epithelioid histology, larger size, increased mitoses, higher risk levels, and unfavorable genotypes (all p≤0.03). They were also independently predictive of decreased disease-free survival (overexpression, p<0.001; amplification, p=0.020) in the multivariate analysis. Concomitant with downregulated cyclin D1, cyclin E, and CDK4, AMACR knockdown suppressed cell proliferation and induced G1-phase arrest, but did not affect apoptosis in both GIST882 and GIST48 cells. In conclusion, AMACR amplification is a mechanism driving increased mRNA and protein expression and conferring aggressiveness through heightened cell proliferation in gastrointestinal stromal tumors.
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Moir-Meyer GL, Pearson JF, Lose F, Scott RJ, McEvoy M, Attia J, Holliday EG, Pharoah PD, Dunning AM, Thompson DJ, Easton DF, Spurdle AB, Walker LC. Rare germline copy number deletions of likely functional importance are implicated in endometrial cancer predisposition. Hum Genet 2015; 134:269-78. [PMID: 25381466 DOI: 10.1007/s00439-014-1507-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/29/2014] [Indexed: 01/15/2023]
Abstract
Endometrial cancer is the most common invasive gynaecological cancer in women, and relatively little is known about inherited risk factors for this disease. This is the first genome-wide study to explore the role of common and rare germline copy number variants (CNVs) in predisposition to endometrial cancer. CNVs were called from germline DNA of 1,209 endometrioid endometrial cancer cases and 528 cancer-unaffected female controls. Overall CNV load of deletions or DNA gains did not differ significantly between cases and controls (P > 0.05), but cases presented with an excess of rare germline deletions overlapping likely functional genomic regions including genes (P = 8 × 10(-10)), CpG islands (P = 1 × 10(-7)) and sno/miRNAs regions (P = 3 × 10(-9)). On average, at least one additional gene and two additional CpG islands were disrupted by rare deletions in cases compared to controls. The most pronounced difference was that over 30 sno/miRNAs were disrupted by rare deletions in cases for every single disruption event in controls. A total of 13 DNA repair genes were disrupted by rare deletions in 19/1,209 cases (1.6%) compared to one gene in 1/528 controls (0.2%; P = 0.007), and this increased DNA repair gene loss in cases persisted after excluding five individuals carrying CNVs disrupting mismatch repair genes MLH1, MSH2 and MSH6 (P = 0.03). There were 34 miRNA regions deleted in at least one case but not in controls, the most frequent of which encompassed hsa-mir-661 and hsa-mir-203. Our study implicates rare germline deletions of functional and regulatory regions as possible mechanisms conferring endometrial cancer risk, and has identified specific regulatory elements as candidates for further investigation.
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Affiliation(s)
- Gemma L Moir-Meyer
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand,
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Li CF, Fang FM, Lan J, Wang JW, Kung HJ, Chen LT, Chen TJ, Li SH, Wang YH, Tai HC, Yu SC, Huang HY. AMACR amplification in myxofibrosarcomas: a mechanism of overexpression that promotes cell proliferation with therapeutic relevance. Clin Cancer Res 2014; 20:6141-52. [PMID: 25384383 DOI: 10.1158/1078-0432.ccr-14-1182] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Myxofibrosarcomas frequently display arm-level gains on 5p. We characterized the pathogenetic and therapeutic relevance of the α-methylacyl coenzyme A racemase (AMACR) at 5p13.3. EXPERIMENTAL DESIGN AMACR mRNA expression in myxofibrosarcomas was analyzed using the public transcriptome and laser-microdissected sarcoma cells. We performed florescence in situ hybridization (FISH) and immunohistochemistry in independent samples for clinical correlates. In AMACR-overexpressing myxofibrosarcoma cells and xenografts, we elucidated the biologic function of AMACR using RNA interference and explored the therapeutic effect and mechanism of an AMACR inhibitor, ebselen oxide. RESULTS AMACR protein overexpression and gene amplification were significantly associated with each other (P < 0.001), with higher tumor grades (both P ≤ 0.002), and univariately with worse metastasis-free survival (MFS; both P < 0.0001) and disease-specific survival (DSS; P = 0.0002 for overexpression; P = 0.0062 for amplification). AMACR protein overexpression also independently portended adverse outcome (DSS, P = 0.007; MFS, P = 0.001). However, 39% of AMACR-overexpression cases did not show gene amplification, implying alternative regulatory mechanisms. In myxofibrosarcoma cell lines, stable AMACR knockdown suppressed cell proliferation, anchorage-independent growth, and expression of cyclin D1 and cyclin T2. These growth-promoting attributes of AMACR were corroborated in the AMACR-silenced xenograft model and AMACR-underexpressed myxofibrosarcomas, showing decreased labeling for cyclin D1, cyclin T2, and Ki-67. Compared with fibroblasts, AMACR-expressing myxofibrosarcoma cells were more susceptible to ebselen oxide, which not only decreased viable cells, promoted proteasome-mediated degradation of AMACR protein, and induced cellular apoptosis in vitro, but also dose-dependently suppressed xenografted tumor growth in vivo. CONCLUSIONS Overexpressed AMACR in myxofibrosarcomas can be amplification-driven, associated with tumor aggressiveness, and may be relevant as a druggable target.
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Affiliation(s)
- Chien-Feng Li
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan. Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan. Department of Biotechnology, Southern Taiwan University, Tainan, Taiwan
| | - Fu-Min Fang
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jui Lan
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jun-Wen Wang
- Department of Orthopedic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Tainan, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Tzu-Ju Chen
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
| | - Shau-Hsuan Li
- Division of Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yu-Hui Wang
- Institute of Biosignal Transduction, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Chun Tai
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
| | - Shih-Chen Yu
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hsuan-Ying Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
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Lee YE, He HL, Lee SW, Chen TJ, Chang KY, Hsing CH, Li CF. AMACR overexpression as a poor prognostic factor in patients with nasopharyngeal carcinoma. Tumour Biol 2014; 35:7983-91. [PMID: 24833092 DOI: 10.1007/s13277-014-2065-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 05/06/2014] [Indexed: 11/30/2022] Open
Abstract
The molecular prognostic adjunct in patients with nasopharyngeal carcinomas (NPCs) still remains obscured. Through data mining from published transcriptomic database, alpha-methylacyl-CoA racemase (AMACR) was first identified as a differentially upregulated gene in NPC tissues, which is a key enzyme for isometric conversion of fatty acids entering the β-oxidation. Given the roles of AMACR in prognostication and frontline therapeutic regimen of common carcinomas, such as prostate cancer, we explored AMACR immunoexpression status and its clinical significance in NPC patients. AMACR immunohistochemistry was retrospectively performed and analyzed using H-score for biopsy specimens from 124 NPC patients who received standard treatment without distant metastasis at initial diagnosis. Those cases with H-score larger than the median value were construed as featuring AMACR overexpression. The findings were correlated with the clinicopathological variables, disease-specific survival (DSS), distant metastasis-free survival (DMFS), and local recurrence-free survival (LRFS). Endogenous AMACR protein expressions were assessed by real-time reverse-transcription polymerase chain reaction (RT-PCR) and Western blotting in NPC cells and non-neoplastic mucosal cells. AMACR overexpression was significantly associated with increment of primary tumor status (P = 0.009) and univariately predictive of adverse outcomes for DSS, DMFS, and LRFS. In the multivariate comparison, AMACR overexpression still remained prognostically independent to portend worse DSS (P = 0.006, hazard ratio = 2.129), DMFS (P = 0.001, hazard ratio = 2.795), and LRFS (P = 0.041, hazard ratio = 2.009), together with advanced American Joint of Cancer Committee (AJCC) stages III-IV. Compared with non-neoplastic cells, both HONE1 and TW01 NPC cells demonstrated markedly increased AMACR expression. AMACR overexpression was identified as an important prognosticator and a potential therapeutic target in the future.
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Affiliation(s)
- Ying-En Lee
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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Abstract
Recent advances in genetic analysis especially DNA sequencing technology open a new strategy for adult disease prevention by genetic screening. Physicians presently treat disease pathology with less emphasis on disease risk prevention/reduction. Genetic screening has reduced the incidence of untreatable childhood genetic diseases and improved the care of newborns. The opportunity exists to expand screening programs and reduce the incidence of adult onset diseases via genetic risk identification and disease intervention. This article outlines the approach, challenges, and benefits of such screening for adult genetic disease risks.
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Dayi N, Baba HA, Schmid KW, Schmitz KJ. Increased expression of α-methylacyl-coenzyme A racemase (AMACR; p504s) and p16 in distal hyperplastic polyps. Diagn Pathol 2013; 8:178. [PMID: 24152881 PMCID: PMC3818439 DOI: 10.1186/1746-1596-8-178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/15/2013] [Indexed: 01/25/2023] Open
Abstract
Background Hyperplastic polyps (HP) and sessile serrated adenomas (SSA) share morphological similarities. In this immunohistochemical study we chose a panel of potential relevant and promising biomarkers including α-methylacyl-coenzyme A racemase (AMACR; p504s), which is involved in the degradation of branched chained fatty acids derivates, and analysed a cohort of HPs and SSAs in order to identify different immunophenotypes in relation to lesion localisation. Methods 154 specimen were carefully selected and a micro tissue array (TMA) was constructed. Immunohistochemistry of p16Ink4a, Ki67, α-methylacyl-coenzyme A racemase (AMACR; p504s), BRAF, CK 20, MLH1 and β-catenin was performed and and immunoexpression was compared among proximal and distal HPs as well as SSAs. Results None of the markers revealed a differential expression among HPs and SSAs. However, the study demonstrates a significant overexpression of AMACR (p = 0.004) and p16Ink4a (p = 0.028) in distal HPs compared to proximal HPs. In addition AMACR overexpression was associated with increased p16Ink4a immunoexpression (p < 0.001). Conclusions In this study we describe differential AMACR and p16Ink4a in HPs in relation to their localisation. Distal HPs were characterized by AMACR and p16Ink4a overexpression in contrast to proximal HPs, although morphological identically. Thus AMACR overexpression points towards a pathobiological relevance of the protein in distal HPs. In context of recently published data this suggest distal HPs as potential precursor lesions of certain adenoma subtypes. However, at this point of time this finding remains speculative and needs to be confirmed by further studies. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1836116001066768
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Affiliation(s)
| | | | | | - Klaus J Schmitz
- Institute of Pathology and Neuropathology, University of Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany.
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Lloyd MD, Yevglevskis M, Lee GL, Wood PJ, Threadgill MD, Woodman TJ. α-Methylacyl-CoA racemase (AMACR): Metabolic enzyme, drug metabolizer and cancer marker P504S. Prog Lipid Res 2013; 52:220-30. [DOI: 10.1016/j.plipres.2013.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
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Ouyang B, Leung YK, Wang V, Chung E, Levin L, Bracken B, Cheng L, Ho SM. α-Methylacyl-CoA racemase spliced variants and their expression in normal and malignant prostate tissues. Urology 2011; 77:249.e1-7. [PMID: 21195844 DOI: 10.1016/j.urology.2010.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 07/21/2010] [Accepted: 08/02/2010] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To evaluate the possibility of using α-methylacyl-CoA racemase (AMACR) variants to improve the specificity of prostate cancer (CaP) detection. AMACR has been used as a diagnostic biomarker for CaP and is now a standard biomarker for needle biopsy specimens with ambiguous lesions. METHODS We used in silico analysis and molecular cloning to discover new AMACR variants and quantitative reverse transcription-polymerase chain reaction (RT-PCR) to measure the transcript levels of AMACR and its variants in 4 prostate cell lines and in 23 pairs of CaP and adjacent normal tissue. RESULTS We found 4 novel variants, IAs, IBL, IBLd, and IBLi. Transcript levels of most AMACR variants were significantly upregulated in CaP compared with its adjacent normal counterparts. A variants, the functional variants based on bioinformatic analysis, showed levels of transcript expression in CaP in this order: IA≫IAd=IIA≫IIAs>IAs. In contrast, the expression of the B variants, which appear to be nonfunctional due to the absence of exon 3, was lower than that of the A variants. IB was the most abundant form of B variant; and expression of IIB was negligible. More important, the difference between levels of variant IA, IAd, IIA, IIAs, IB, and IBLi in CaP and normal tissue was significantly higher than the difference in levels of total AMACR. CONCLUSIONS Our data suggest that AMACR variants have better power than total AMACR in discriminating between CaP and adjacent normal tissue. These findings may be useful for the development of future diagnostic assays.
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Affiliation(s)
- Bin Ouyang
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio 45267, USA
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Berretta R, Moscato P. Cancer biomarker discovery: the entropic hallmark. PLoS One 2010; 5:e12262. [PMID: 20805891 PMCID: PMC2923618 DOI: 10.1371/journal.pone.0012262] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 06/26/2010] [Indexed: 12/29/2022] Open
Abstract
Background It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.
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Affiliation(s)
- Regina Berretta
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Pablo Moscato
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
- Australian Research Council Centre of Excellence in Bioinformatics, Callaghan, New South Wales, Australia
- * E-mail:
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Zhang X, Wu M, Xiao H, Lee MT, Levin L, Leung YK, Ho SM. Methylation of a single intronic CpG mediates expression silencing of the PMP24 gene in prostate cancer. Prostate 2010; 70:765-76. [PMID: 20054818 PMCID: PMC2857536 DOI: 10.1002/pros.21109] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND We previously demonstrated that a putative anti-tumor gene, peroxisomal membrane protein 4, 24 kDa (PMP24 or PXMP4), is silenced via DNA methylation of a CpG island in its 5' flanking region (5'-CGI) in prostate cancer (PCa) cells. METHODS To identify demethylation hypersensitive site(s) in PMP24 5'-CGI, PC-3 cells with methylated 5'-CGI were treated with a low-dose of 5-aza-2'-deoxycytidine (5-aza-dC) just sufficient to reactivate gene expression, referred as the limited demethylation approach. Gel shift assays and promoter analyzes were performed to demonstrate the role of the hypersensitive site in PMP24 gene regulation. Transfection of a methylated oligonucleotide corresponding to the hypersensitive site was conducted to determine the effect of site-specific methylation on the gene expression. Bisulfite sequencing analysis was performed to reveal the methylation status of PMP24 promoter in cultured cells and microdissected samples. In situ hybridization was applied to determine expression positivity of PMP24 mRNA. RESULTS A 5-aza-dC hypersensitive site encompasses two CpG dinucleotides in intron 1 was identified. Methylation of the first, but not the second, CpG dinucleotide of this site disrupted DNA-protein interactions and suppressed the gene expression. Using archival specimens, we found the first CpG dinucleotide of the hypersensitive site is hypermethylated with a loss of PMP24 mRNA expression in microdissected PCa cells when compared to normal prostatic epithelial cells. CONCLUSIONS These findings support a critical role for a single intronic CpG dinucleotide in PMP24 gene regulation through DNA methylation. The data suggest that methylation-mediated silencing of PMP24 is a molecular event associated with prostate carcinogenesis.
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Affiliation(s)
- Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Cincinnati Cancer Consortium, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | - Hong Xiao
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Ming-Tsung Lee
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Linda Levin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Yuet-Kin Leung
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Cincinnati Cancer Consortium, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Shuk-Mei Ho
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Cincinnati Cancer Consortium, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Correspondence to: Shuk-Mei Ho, Department of Environmental Health, University of Cincinnati, College of Medicine, Kettering Laboratory, Suite 128, 3223 Eden Ave., Cincinnati, OH 45267. Telephone: (513)-558-5701. Fax: (513)-558-0071.
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Waters KM, Tan R, Opresko LK, Quesenberry RD, Bandyopadhyay S, Chrisler WB, Weber TJ. Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis. Mol Carcinog 2009; 48:1059-69. [PMID: 19526458 DOI: 10.1002/mc.20558] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have investigated gene expression patterns underlying reversible and irreversible anchorage-independent growth (AIG) phenotypes to identify more sensitive markers of cell transformation for studies directed at interrogating carcinogenesis responses. In JB6 mouse epidermal cells, basic fibroblast growth factor (bFGF) induces an unusually efficient and reversible AIG response, relative to 12-O-tetradecanoyl phorbol-13-acetate (TPA)-induced AIG which is irreversible. The reversible and irreversible AIG phenotypes are characterized by largely nonoverlapping global gene expression profiles. However, a subset of differentially expressed genes were identified as common to reversible and irreversible AIG phenotypes, including genes regulated in a reciprocal fashion. Hepatic leukemia factor (HLF) and D-site albumin promoter-binding protein (DBP) were increased in both bFGF and TPA soft agar colonies and selected for functional validation. Ectopic expression of human HLF and DBP in JB6 cells resulted in a marked increase in TPA- and bFGF-regulated AIG responses. HLF and DBP expression were increased in soft agar colonies arising from JB6 cells exposed to gamma radiation and in a human basal cell carcinoma tumor tissue, relative to paired nontumor tissue. Subsequent biological network analysis suggests that many of the differentially expressed genes that are common to bFGF- and TPA-dependent AIG are regulated by c-Myc, SP-1, and HNF-4 transcription factors. Collectively, we have identified a potential molecular switch that mediates the transition from reversible to irreversible AIG.
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Affiliation(s)
- Katrina M Waters
- Computational Biology and Bioinformatics Groups, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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