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Wang D, Yang D, Yang L, Diao L, Zhang Y, Li Y, Wang H, Ren J, Cheng L, Tan Q, Zhang R, Han X, Zhang X, Wang B, Li D, Chen M, Hermjakob H, Li Y, LaBaer J, Zhou Z, Yu X. Human Autoantigen Atlas: Searching for the Hallmarks of Autoantigens. J Proteome Res 2023. [PMID: 37183442 DOI: 10.1021/acs.jproteome.2c00799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Understanding autoimmunity to endogenous proteins is crucial in diagnosing and treating autoimmune diseases. In this work, we developed a user-friendly AAgAtlas portal (http://biokb.ncpsb.org.cn/aagatlas_portal/index.php#), which can be used to search for 8045 non-redundant autoantigens (AAgs) and 47 post-translationally modified AAgs against 1073 human diseases that are prioritized by a credential score developed by multisource evidence. Using AAgAtlas, the immunogenic properties of human AAgs was systematically elucidated according to their genetic, biophysical, cytological, expression profile, and evolutionary characteristics. The results indicated that human AAgs are evolutionally conserved in protein sequence and enriched in three hydrophilic and polar amino acid residues (K, D, and E) that are located at the protein surface. AAgs are enriched in proteins that are involved in nucleic acid binding, transferase, and the cytoskeleton. Genome, transcriptome, and proteome analyses further indicated that AAb production is associated with gene variance and abnormal protein expression related to the pathological activities of different tumors. Collectively, our data outlines the hallmarks of human AAgs that facilitate the understanding of humoral autoimmunity and the identification of biomarkers of human diseases.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Liuhui Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lihong Diao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuqi Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Ren
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Linlin Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qiaoyun Tan
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ran Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiaohan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bingwei Wang
- College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Meng Chen
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Zhou Zhou
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases and Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
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Jin J, Choi SH, Lee JE, Joo JD, Han JH, Park SY, Kim CY. Antitumor activity of 7-O-succinyl macrolactin A tromethamine salt in the mouse glioma model. Oncol Lett 2017; 13:3767-3773. [PMID: 28529591 DOI: 10.3892/ol.2017.5918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/17/2017] [Indexed: 11/05/2022] Open
Abstract
Chemoradiotherapy with temozolomide is the current standard treatment option for patients with glioblastoma. However, the majority of patients with glioblastoma survive for <2 years. Therefore, it is necessary to develop more effective therapeutic strategies for the treatment of glioblastoma. 7-O-succinyl macrolactin A tromethamine salt (SMA salt), a macrolactin compound, is known to possess an antiangiogenic activity. The present study investigated the antitumor effects of SMA salt in the treatment of glioblastoma by evaluating in vitro and in vivo antitumor effects of SMA salt in an experimental glioblastoma model. The antitumor effects of the drug on human glioblastoma U87MG, U251MG and LN229 cell lines were assessed using in vitro cell viability, migration and invasion assays. Nude mice with established U87MG glioblastoma were assigned to either the control or SMA salt treatment group. The volume of tumors and the duration of survival were also measured. SMA salt affected cell viability and caused a concentration-dependent inhibition effect on the migration and invasion of glioblastoma cell lines. Animals in the SMA salt treatment group demonstrated a significant reduction in tumor volume and an increase in survival (P<0.05). Treatment with SMA salt presented more cytotoxic effects as well as anti-migration and anti-invasion activity compared with the control group in vitro and in vivo. These results suggest that SMA salt has significant antitumor effects on glioblastoma.
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Affiliation(s)
- Jun Jin
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Suh Hee Choi
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Jung Eun Lee
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Jin-Deok Joo
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jung Ho Han
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Su-Young Park
- Research and Development Center, Daewoo Pharmaceutical Ind. Co., Ltd., Busan 49393, Republic of Korea
| | - Chae-Yong Kim
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do 13620, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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Bacolod MD, Das SK, Sokhi UK, Bradley S, Fenstermacher DA, Pellecchia M, Emdad L, Sarkar D, Fisher PB. Examination of Epigenetic and other Molecular Factors Associated with mda-9/Syntenin Dysregulation in Cancer Through Integrated Analyses of Public Genomic Datasets. Adv Cancer Res 2015; 127:49-121. [PMID: 26093898 DOI: 10.1016/bs.acr.2015.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mda-9/Syntenin (melanoma differentiation-associated gene 9) is a PDZ domain containing, cancer invasion-related protein. In this study, we employed multiple integrated bioinformatic approaches to identify the probable epigenetic factors, molecular pathways, and functionalities associated with mda-9 dysregulation during cancer progression. Analyses of publicly available genomic data (e.g., expression, copy number, methylation) from TCGA, GEO, ENCODE, and Human Protein Atlas projects led to the following observations: (a) mda-9 expression correlates with both copy number and methylation level of an intronic CpG site (cg1719774) located downstream of the CpG island, (b) cg1719774 methylation is a likely prognostic marker in glioma, (c) among 22 cancer types, melanoma exhibits the highest mda-9 level, and lowest level of methylation at cg1719774, (d) cg1719774 hypomethylation is also associated with histone modifications (at the mda-9 locus) indicative of more active transcription, (e) using Gene Set Enrichment Analysis (GSEA), and the Virtual Gene Overexpression or Repression (VIGOR) analytical scheme, we were able to predict mda-9's association with extracellular matrix organization (e.g., MMPs, collagen, integrins), IGFBP2 and NF-κB signaling pathways, phospholipid metabolism, cytokines (e.g., interleukins), CTLA-4, and components of complement cascade pathways. Indeed, previous publications have shown that many of the aforementioned genes and pathways are associated with mda-9's functionality.
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Affiliation(s)
- Manny D Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Upneet K Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Steven Bradley
- VCU Bioinformatics Program, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - David A Fenstermacher
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA.
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Abstract
Patients with glioblastoma typically present when tumors are at an advanced stage. Surgical resection, radiotherapy and adjuvant chemotherapy are currently the standard of care for glioblastoma. However, due to the infiltrative and dispersive nature of the tumor, recurrence rate remains high and typically results in very poor prognosis. Efforts to treat the primary tumor are, therefore, palliative rather than curative. From a practical perspective, controlling growth and dispersal of the recurrence may have a greater impact on disease-free survival. In order for cells to disperse, they must first detach from the mass. Preventing detachment may keep tumors that recur more localized and perhaps more amenable to therapy. Here we introduce a new perspective in which a quantifiable mechanical property, namely tissue surface tension, can provide novel information on tumor behavior. The overall theme of the discussion will attempt to integrate how adhesion molecules can alter a tumor's mechanical properties and how, in turn, these properties can be modified to prevent tumor cell detachment and dispersal.
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Affiliation(s)
- Ramsey A Foty
- Department of Surgery, University of Medicine & Dentistry, New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA.
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Onishi M, Ichikawa T, Kurozumi K, Fujii K, Yoshida K, Inoue S, Michiue H, Chiocca EA, Kaur B, Date I. Bimodal anti-glioma mechanisms of cilengitide demonstrated by novel invasive glioma models. Neuropathology 2012; 33:162-74. [PMID: 22989076 DOI: 10.1111/j.1440-1789.2012.01344.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 12/12/2022]
Abstract
Integrins are expressed in tumor cells and tumor endothelial cells, and likely play important roles in glioma angiogenesis and invasion. We investigated the anti-glioma mechanisms of cilengitide (EMD121974), an αvβ3 integrin inhibitor, utilizing the novel invasive glioma models, J3T-1 and J3T-2. Immunohistochemical staining of cells in culture and brain tumors in rats revealed positive αvβ3 integrin expression in J3T-2 cells and tumor endothelial cells, but not in J3T-1 cells. Established J3T-1 and J3T-2 orthotopic gliomas in athymic rats were treated with cilengitide or solvent. J3T-1 gliomas showed perivascular tumor cluster formation and angiogenesis, while J3T-2 gliomas showed diffuse single-cell infiltration without obvious angiogenesis. Cilengitide treatment resulted in a significantly decreased diameter of the J3T-1 tumor vessel clusters and its core vessels when compared with controls, while an anti-invasive effect was shown in the J3T-2 glioma with a significant reduction of diffuse cell infiltration around the tumor center. The survival of cilengitide-treated mice harboring J3T-1 tumors was significantly longer than that of control animals (median survival: 57.5 days and 31.8 days, respectively, P < 0.005), while cilengitide had no effect on the survival of mice with J3T-2 tumors (median survival: 48.9 days and 48.5, P = 0.69). Our results indicate that cilengitide exerts a phenotypic anti-tumor effect by inhibiting angiogenesis and glioma cell invasion. These two mechanisms are clearly shown by the experimental treatment of two different animal invasive glioma models.
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Affiliation(s)
- Manabu Onishi
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Wang L, Liu Z, Balivada S, Shrestha T, Bossmann S, Pyle M, Pappan L, Shi J, Troyer D. Interleukin-1β and transforming growth factor-β cooperate to induce neurosphere formation and increase tumorigenicity of adherent LN-229 glioma cells. Stem Cell Res Ther 2012; 3:5. [PMID: 22330721 PMCID: PMC3340549 DOI: 10.1186/scrt96] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 12/27/2011] [Accepted: 02/10/2012] [Indexed: 01/26/2023] Open
Abstract
INTRODUCTION Glioma stem cells (GSCs) have the property of self-renewal and appear to be a driving force for the initiation and recurrence of gliomas. We recently found that the human tumorigenic LN-229 glioma cell line failed to form neurospheres in serum-free conditions and generated mostly small tumors in vivo, suggesting that either LN-229 GSCs are not active in these conditions or GSCs are absent in the LN-229 cell line. METHODS Using self-renewal assay, soft-agar colony assay, cell proliferation assay, invasion assay, real time PCR analysis, ELISA and in vivo tumorigenic assay, we investigated the effects of interleukin (IL)-1β and transforming growth factor (TGF)-β on the development of GSCs from LN-229 cells. RESULTS Here, we demonstrate that the combination of IL-1β and TGF-β can induce LN-229 cells to form neurospheres in serum-free medium. IL-1β/TGF-β-induced neurospheres display up-regulated expression of stemness factor genes (nestin, Bmi-1, Notch-2 and LIF), and increased invasiveness, drug resistance and tumor growth in vivo: hallmarks of GSCs. These results indicate that IL-1β and TGF-β cooperate to induce a GSC phenotype in the LN-229 cell line. Induction of nestin, LIF and Notch-2 by IL-1β/TGF-β can be reverted after cytokine withdrawal. Remarkably, however, up-regulated Bmi-1 levels remained unchanged after cytokine withdrawal; and the cytokine-withdrawn cells maintained strong clonogenicity, suggesting that Bmi-1 may play a crucial role in tumorigenesis. CONCLUSIONS Our finding indicates that glioma cells without self-renewal capability in standard conditions could also contribute to glioma malignancy when cytokines, such as IL-1β and TGF-β, are present in the tumor environment. Targeting GSC-promoting cytokines that are highly expressed in glioblastomas may contribute to the development of more effective glioma therapies.
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Affiliation(s)
- Lei Wang
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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Sabari J, Lax D, Connors D, Brotman I, Mindrebo E, Butler C, Entersz I, Jia D, Foty RA. Fibronectin matrix assembly suppresses dispersal of glioblastoma cells. PLoS One 2011; 6:e24810. [PMID: 21980357 PMCID: PMC3184095 DOI: 10.1371/journal.pone.0024810] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 08/19/2011] [Indexed: 11/18/2022] Open
Abstract
Glioblastoma (GBM), the most aggressive and most common form of primary brain tumor, has a median survival of 12–15 months. Surgical excision, radiation and chemotherapy are rarely curative since tumor cells broadly disperse within the brain. Preventing dispersal could be of therapeutic benefit. Previous studies have reported that increased cell-cell cohesion can markedly reduce invasion by discouraging cell detachment from the tumor mass. We have previously reported that α5β1 integrin-fibronectin interaction is a powerful mediator of indirect cell-cell cohesion and that the process of fibronectin matrix assembly (FNMA) is crucial to establishing strong bonds between cells in 3D tumor-like spheroids. Here, we explore a potential role for FNMA in preventing dispersal of GBM cells from a tumor-like mass. Using a series of GBM-derived cell lines we developed an in vitro assay to measure the dispersal velocity of aggregates on a solid substrate. Despite their similar pathologic grade, aggregates from these lines spread at markedly different rates. Spreading velocity is inversely proportional to capacity for FNMA and restoring FNMA in GBM cells markedly reduces spreading velocity by keeping cells more connected. Blocking FNMA using the 70 KDa fibronectin fragment in FNMA-restored cells rescues spreading velocity, establishing a functional role for FNMA in mediating dispersal. Collectively, the data support a functional causation between restoration of FNMA and decreased dispersal velocity. This is a first demonstration that FNMA can play a suppressive role in GBM dispersal.
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Affiliation(s)
- Joshua Sabari
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Daniel Lax
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Daniel Connors
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Ian Brotman
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Eric Mindrebo
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Christine Butler
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Ildiko Entersz
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Dongxuan Jia
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Ramsey A. Foty
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- * E-mail:
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