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Xin R, Shen B, Jiang YJ, Liu JB, Li S, Hou LK, Wu W, Jia CY, Wu CY, Fu D, Ma YS, Jiang GX. Comprehensive analysis to identify a novel PTEN-associated ceRNA regulatory network as a prognostic biomarker for lung adenocarcinoma. Front Oncol 2022; 12:923026. [PMID: 36091160 PMCID: PMC9449356 DOI: 10.3389/fonc.2022.923026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most prevalent forms of lung cancer. Competitive endogenous RNA (ceRNA) plays an important role in the pathogenesis of lung cancer. Phosphatase and tensin homolog (PTEN) is one of the most frequently deleted tumour suppressor genes in LUAD. The present study aimed to identify a novel PTEN-associated-ceRNA regulatory network and identify potential prognostic markers associated with LUAD. Transcriptome sequencing profiles of 533 patients with LUAD were obtained from TCGA database, and differentially expressed genes (DEGs) were screened in LUAD samples with PTEN high- (PTENhigh) and low- (PTENlow) expression. Eventually, an important PTEN-related marker was identified, namely, the LINC00460/miR-150-3p axis. Furthermore, the predicted target genes (EME1/HNRNPAB/PLAUR/SEMA3A) were closely related to overall survival and prognosis. The LINC00460/miR-150-3p axis was identified as a clinical prognostic factor through Cox regression analysis. Methylation analyses suggested that abnormal regulation of the predicted target genes might be caused by hypomethylation. Furthermore, immune infiltration analysis showed that the LINC00460/miR-150-3p axis could alter the levels of immune infiltration in the tumour immune microenvironment, and promote the clinical progression of LUAD. To specifically induce PTEN deletion in the lungs, we constructed an STP mouse model (SFTPC-rtTA/tetO-cre/Ptenflox/+). Quantitative PCR (qPCR) and immunohistochemical (IHC) analysis were used to detect predicted target genes. Therefore, we revealed that the PTEN-related LINC00460/miR-150-3p axis based on ceRNA mechanism plays an important role in the development of LUAD and provides a new direction and theoretical basis for its targeted therapy.
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Affiliation(s)
- Rui Xin
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Biao Shen
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Ying-Jie Jiang
- Department of Pathology, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Sha Li
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Wu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Da Fu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
| | - Geng-Xi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
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Construction of a Novel MYC-Associated ceRNA Regulatory Network to Identify Prognostic Biomarkers in Colon Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3216285. [PMID: 35847359 PMCID: PMC9277212 DOI: 10.1155/2022/3216285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Colorectal cancer (CRC) includes colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ). Competitive endogenous RNA (ceRNA) is crucial for cancer pathogenesis. Abnormal expression of MYC is generally associated with a poor colon adenocarcinoma prognosis. The present study aimed to identify a novel MYC-associated ceRNA regulatory network and identify potential prognostic markers associated with COAD. We obtained the transcriptome sequencing profiles of 462 COAD cases from the TCGA database and analyzed differentially expressed genes (DEGs) in MYC high expression (MYChigh) and MYC low expression (Myclow) tumors. We identified an important lncRNA, LINC00114, which effectively predicts overall survival and plays a protective role in COAD. Moreover, the LINC00114/miR-216a-5p axis was identified as a clinical prognostic model. The predicted target genes of the LINC00114/miR-216a-5p axis include uromodulin Like 1 (UMODL1) and oncoprotein induced transcript 3 (OIT3), which are closely related to the survival and prognosis of COAD patients. In summary, we constructed a novel ceRNA regulatory network and identified potential biomarkers for the targeted therapy and prognosis of COAD.
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Domankevich V, Efrati M, Schmidt M, Glikson E, Mansour F, Shai A, Cohen A, Zilberstein Y, Flaisher E, Galalae R, Kelson I, Keisari Y. RIG-1-Like Receptor Activation Synergizes With Intratumoral Alpha Radiation to Induce Pancreatic Tumor Rejection, Triple-Negative Breast Metastases Clearance, and Antitumor Immune Memory in Mice. Front Oncol 2020; 10:990. [PMID: 32766128 PMCID: PMC7379859 DOI: 10.3389/fonc.2020.00990] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Diffusing alpha-emitting radiation therapy (DaRT) employs intratumoral Ra-224-coated seeds that efficiently destroy solid tumors by slowly releasing alpha-emitting atoms inside the tumor. In immunogenic tumor models, DaRT was shown to activate systemic antitumor immunity. Agonists of the membrane-bound toll-like receptors (TLRs) enhanced these effects and led to tumor rejection. Here, we examined the combination of DaRT with agents that activate a different type of pattern recognition receptors, the cytoplasmatic RIG1-like receptors (RLRs). In response to cytoplasmatic viral dsRNA, RLRs activate an antiviral immune response that includes the elevation of antigen presentation. Thus, it was postulated that in low-immunogenic tumor models, RLR activation in tumor cells prior to the induction of their death by DaRT will be superior compared to TLR activation. Intratumoral cytoplasmatic delivery of the dsRNA mimic polyIC by polyethylenimine (PEI), was used to activate RLR, while polyIC without PEI was used to activate TLR. PolyIC(PEI) prior to DaRT synergistically retarded 4T1 triple-negative breast tumors and metastasis development more efficiently than polyIC and rejected panc02 pancreatic tumors in some of the treated mice. Splenocytes from treated mice, adoptively transferred to naive mice in combination with 4T1 tumor cells, delayed tumor development compared to naïve splenocytes. Low-dose cyclophosphamide, known to reduce T regulatory cell number, enhanced the effect of DaRT and polyIC(PEI) and led to high long-term survival rates under neoadjuvant settings, which confirmed metastasis clearance. The epigenetic drug decitabine, known to activate RLR in low doses, was given intraperitoneally prior to DaRT and caused tumor growth retardation, similar to local polyIC(PEI). The systemic and/or local administration of RLR activators was also tested in the squamous cell carcinoma (SCC) tumor model SQ2, in which a delay in tumor re-challenge development was demonstrated. We conclude that RIG-I-like activation prior to intratumoral alpha radiation may serve as a potent combination technique to reduce both tumor growth and the spread of distant metastases in low-immunogenic and metastatic tumor models.
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Affiliation(s)
- Vered Domankevich
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Margalit Efrati
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Michael Schmidt
- Alpha Tau Medical, Tel Aviv-Yafo, Israel.,Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eran Glikson
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Department of Otolaryngology, Head and Neck Surgery, Sheba Medical Center, Tel HaShomer, Israel
| | - Fairuz Mansour
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Amit Shai
- Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Adi Cohen
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yael Zilberstein
- Sackler Cellular and Molecular Imaging Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | | | - Razvan Galalae
- MedAustron, Wiener Neustadt, Austria.,Medical Faculty, Christian-Albrechts University, Kiel, Germany
| | - Itzhak Kelson
- Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yona Keisari
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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Cai X, Qin JJ, Hao SY, Li H, Zeng C, Sun SJ, Yu LB, Gao ZX, Xie J. Clinical characteristics associated with the intracranial dissemination of gliomas. Clin Neurol Neurosurg 2018; 166:141-146. [DOI: 10.1016/j.clineuro.2018.01.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 02/03/2023]
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The Feulgen reaction: A brief review and new perspectives. Acta Histochem 2017; 119:603-609. [PMID: 28739089 DOI: 10.1016/j.acthis.2017.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 11/21/2022]
Abstract
The Feulgen reaction has been proposed by Robert Feulgen and Heinrich Rossenbeck for the identification of DNA nearly a hundred years ago. Since then, many other applications of this cytochemical/topochemical procedure at qualitative and quantitative level have been proposed in relation to DNA and its role in chromatin in human, animal and plant cells. In this article, we briefly review some fundamental aspects of the Feulgen reaction and current applications of such a method in studies of altered chromatin texture, including its association with or preceding changes in transcriptional activities and effect on epigenetic marks. Further perspectives on the use of the Feulgen reaction will depend of the proposal of innovative biological questions in which its reveals appropriate.
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Hentati-Kallel M, Le Jan S, Bernard P, Antonicelli F, Trussardi-Régnier A. Histone deacetylases meet microRNA-associated MMP-9 expression regulation in glucocorticoid-sensitive and -resistant cell lines. Int J Oncol 2016; 50:717-726. [DOI: 10.3892/ijo.2016.3830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 11/05/2022] Open
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Guay SP, Brisson D, Mathieu P, Bossé Y, Gaudet D, Bouchard L. A study in familial hypercholesterolemia suggests reduced methylomic plasticity in men with coronary artery disease. Epigenomics 2015; 7:17-34. [DOI: 10.2217/epi.14.64] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: To assess whether DNA methylation is associated with coronary artery disease (CAD). Materials & methods: An epigenome-wide analysis has been performed on leucocytes from familial hypercholesterolemic (FH) men with (n = 6) or without CAD (n = 6). The results were replicated in an extended sample of FH men (n = 61) and in non-FH men (n = 100) for two of the top differentially methylated loci. Results: FH men with CAD had significantly more hypomethylated and hypermethylated loci and showed less DNA methylation level variability compared with men without CAD (p < 0.001). Moreover, COL14A1 and MMP9 DNA methylation levels were associated with CAD, age of onset of CAD or CAD risk factors. Conclusion: These results suggest that epigenome-wide changes are associated with CAD occurrence in men.
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Affiliation(s)
- Simon-Pierre Guay
- Department of Biochemistry, Université de Sherbrooke, University-Affiliated Chicoutimi Hospital, 305 rue St-Vallier, Saguenay, Québec G7H 5H6, Canada
- ECOGENE-21 & Lipid Clinic, Chicoutimi Hospital, Saguenay, Québec, Canada
| | - Diane Brisson
- ECOGENE-21 & Lipid Clinic, Chicoutimi Hospital, Saguenay, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Patrick Mathieu
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Canada
| | - Yohan Bossé
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Canada
- Department of Molecular Medicine, Université Laval, Québec, Canada
| | - Daniel Gaudet
- ECOGENE-21 & Lipid Clinic, Chicoutimi Hospital, Saguenay, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, University-Affiliated Chicoutimi Hospital, 305 rue St-Vallier, Saguenay, Québec G7H 5H6, Canada
- ECOGENE-21 & Lipid Clinic, Chicoutimi Hospital, Saguenay, Québec, Canada
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Abstract
DNA methylation and histone modification are epigenetic mechanisms that result in altered gene expression and cellular phenotype. The exact role of methylation in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remains unclear. However, aberrations (e.g. loss-/gain-of-function or up-/down-regulation) in components of epigenetic transcriptional regulation in general, and of the methylation machinery in particular, have been implicated in the pathogenesis of these diseases. In addition, many of these components have been identified as therapeutic targets for patients with MDS/AML, and are also being assessed as potential biomarkers of response or resistance to hypomethylating agents (HMAs). The HMAs 5-azacitidine (AZA) and 2'-deoxy-5-azacitidine (decitabine, DAC) inhibit DNA methylation and have shown significant clinical benefits in patients with myeloid malignancies. Despite being viewed as mechanistically similar drugs, AZA and DAC have differing mechanisms of action. DAC is incorporated 100% into DNA, whereas AZA is incorporated into RNA (80-90%) as well as DNA (10-20%). As such, both drugs inhibit DNA methyltransferases (DNMTs; dependently or independently of DNA replication) resulting in the re-expression of tumor-suppressor genes; however, AZA also has an impact on mRNA and protein metabolism via its inhibition of ribonucleotide reductase, resulting in apoptosis. Herein, we first give an overview of transcriptional regulation, including DNA methylation, post-translational histone-tail modifications, the role of micro-RNA and long-range epigenetic gene silencing. We place special emphasis on epigenetic transcriptional regulation and discuss the implication of various components in the pathogenesis of MDS/AML, their potential as therapeutic targets, and their therapeutic modulation by HMAs and other substances (if known). The main focus of this review is laid on dissecting the rapidly evolving knowledge of AZA and DAC with a special focus on their differing mechanisms of action, and the effect of HMAs on transcriptional regulation.
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Affiliation(s)
- Lisa Pleyer
- 3rd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Laboratory for Immunological and Molecular Cancer Research, Oncologic Center, Paracelsus Medical University Hospital Salzburg, Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute , Salzburg , Austria
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Poplineau M, Schnekenburger M, Dufer J, Kosciarz A, Brassart-Pasco S, Antonicelli F, Diederich M, Trussardi-Régnier A. The DNA hypomethylating agent, 5-aza-2'-deoxycytidine, enhances tumor cell invasion through a transcription-dependent modulation of MMP-1 expression in human fibrosarcoma cells. Mol Carcinog 2015; 54:24-34. [PMID: 24038389 DOI: 10.1002/mc.22071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/14/2013] [Accepted: 07/01/2013] [Indexed: 12/13/2022]
Abstract
In diseases such as cancer, cells need to degrade the extracellular matrix (ECM) and therefore require high protease levels. Thus, aberrant tissue degradation is associated to matrix metalloproteinases (MMPs) overexpression resulting from different mechanisms including epigenetic events. One of the most characterized epigenetic mechanisms is DNA methylation causing changes in chromatin conformation, thereby decreasing the accessibility to the transcriptional machinery and resulting in a robust gene silencing. Modulation of DNA methylation by DNA hypomethylating agents such as 5-aza-2'-deoxycytidine (5-azadC) is widely used in epigenetic anticancer treatments. Here, we focus on the effects of this drug on the expression level of MMP-1, -2, and -9 in human HT1080 fibrosarcoma cells. We demonstrate that 5-azadC increases MMP expression at both mRNA and protein levels, and promotes invasion potential of HT1080 cells. Using broad-spectrum and specific MMP inhibitors, we establish that MMP-1, but not MMP-2 and -9, plays a key role in 5-azadC-enhanced cell invasion. We show that 5-azadC induces MMP-1 expression through a transcriptional mechanism without affecting MMP-1 promoter methylation status. Finally, we demonstrate that 5-azadC treatment increases the nuclear levels of Sp1 and Sp3 transcription factors, and modulates their recruitment to the MMP-1 promoter, resulting in chromatin remodeling associated to 5-azadC-induced MMP-1 expression. All together, our data indicate that the hypomethylating agent 5-azadC modulates, mainly via Sp1 recruitment, MMP-1 expression resulting in an increased invasive potential of HT1080 cells.
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Affiliation(s)
- Mathilde Poplineau
- Unité MEDyC, URCA-CNRS FRE 3481, SFR Cap Santé, Faculté de Pharmacie, Université de Reims Champagne-Ardenne, 1 avenue du Maréchal Juin, 51096, Reims, France
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Trask OJ, Moore A, LeCluyse EL. A Micropatterned Hepatocyte Coculture Model for Assessment of Liver Toxicity Using High-Content Imaging Analysis. Assay Drug Dev Technol 2014; 12:16-27. [DOI: 10.1089/adt.2013.525] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- O. Joseph Trask
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | | | - Edward L. LeCluyse
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
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Donnelly KS, Giuliano EA, Sharma A, Mohan RR. Suberoylanilide hydroxamic acid (vorinostat): its role on equine corneal fibrosis and matrix metalloproteinase activity. Vet Ophthalmol 2013; 17 Suppl 1:61-8. [DOI: 10.1111/vop.12129] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kevin S. Donnelly
- Harry S. Truman Veterans Memorial Hospital; 800 Hospital Drive Columbia MO USA
- Department of Veterinary Medicine and Surgery; College of Veterinary Medicine; University of Missouri; 900 East Campus Drive Columbia MO USA
| | - Elizabeth A. Giuliano
- Department of Veterinary Medicine and Surgery; College of Veterinary Medicine; University of Missouri; 900 East Campus Drive Columbia MO USA
| | - Ajay Sharma
- Harry S. Truman Veterans Memorial Hospital; 800 Hospital Drive Columbia MO USA
- Mason Eye Institute; University of Missouri; 1 Hospital Drive Columbia MO USA
| | - Rajiv R. Mohan
- Harry S. Truman Veterans Memorial Hospital; 800 Hospital Drive Columbia MO USA
- Department of Veterinary Medicine and Surgery; College of Veterinary Medicine; University of Missouri; 900 East Campus Drive Columbia MO USA
- Mason Eye Institute; University of Missouri; 1 Hospital Drive Columbia MO USA
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