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Carmy-Bennun T, Myer C, Bhattacharya SK, Hackam AS. Quantitative proteomic analysis after neuroprotective MyD88 inhibition in the retinal degeneration 10 mouse. J Cell Mol Med 2021; 25:9533-9542. [PMID: 34562309 PMCID: PMC8505828 DOI: 10.1111/jcmm.16893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/18/2022] Open
Abstract
Progressive photoreceptor death occurs in blinding diseases such as retinitis pigmentosa. Myeloid differentiation primary response protein 88 (MyD88) is a central adaptor protein for innate immune system Toll-like receptors (TLR) and induces cytokine secretion during retinal disease. We recently demonstrated that inhibiting MyD88 in mouse models of retinal degeneration led to increased photoreceptor survival, which was associated with altered cytokines and increased neuroprotective microglia. However, the identity of additional molecular changes associated with MyD88 inhibitor-induced neuroprotection is not known. In this study, we used isobaric tags for relative and absolute quantification (iTRAQ) labelling followed by LC-MS/MS for quantitative proteomic analysis on the rd10 mouse model of retinal degeneration to identify protein pathways changed by MyD88 inhibition. Quantitative proteomics using iTRAQ LC-MS/MS is a high-throughput method ideal for providing insight into molecular pathways during disease and experimental treatments. Forty-two proteins were differentially expressed in retinas from mice treated with MyD88 inhibitor compared with control. Notably, increased expression of multiple crystallins and chaperones that respond to cellular stress and have anti-apoptotic properties was identified in the MyD88-inhibited mice. These data suggest that inhibiting MyD88 enhances chaperone-mediated retinal protection pathways. Therefore, this study provides insight into molecular events contributing to photoreceptor protection from modulating inflammation.
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Affiliation(s)
- Tal Carmy-Bennun
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ciara Myer
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.,Miami Integrative Metabolomics Research Center, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.,Miami Integrative Metabolomics Research Center, Miami, FL, USA
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.,Miami Integrative Metabolomics Research Center, Miami, FL, USA
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2
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Myer C, Abdelrahman L, Banerjee S, Khattri RB, Merritt ME, Junk AK, Lee RK, Bhattacharya SK. Aqueous humor metabolite profile of pseudoexfoliation glaucoma is distinctive. Mol Omics 2021; 16:425-435. [PMID: 32149291 DOI: 10.1039/c9mo00192a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pseudoexfoliation (PEX) is a known cause of secondary open angle glaucoma. PEX glaucoma is associated with structural and metabolic changes in the eye. Despite similarities, PEX and primary open angle glaucoma (POAG) may have differences in the composition of metabolites. We analyzed the metabolites of the aqueous humor (AH) of PEX subjects sequentially first using nuclear magnetic resonance (1H NMR: HSQC and TOCSY), and subsequently with liquid chromatography tandem mass spectrometry (LC-MS/MS) implementing isotopic ratio outlier analysis (IROA) quantification. The findings were compared with previous results for POAG and control subjects analyzed using identical sequential steps. We found significant differences in metabolites between the three conditions. Principle component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) indicated clear grouping based on the metabolomes of the three conditions. We used machine learning algorithms and a percentage set of the data to train, and utilized a different or larger dataset to test whether a trained model can correctly classify the test dataset as PEX, POAG or control. Three different algorithms: linear support vector machines (SVM), deep learning, and a neural network were used for prediction. They all accurately classified the test datasets based on the AH metabolome of the sample. We next compared the AH metabolome with known AH and TM proteomes and genomes in order to understand metabolic pathways that may contribute to alterations in the AH metabolome in PEX. We found potential protein/gene pathways associated with observed significant metabolite changes in PEX.
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Affiliation(s)
- Ciara Myer
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA
| | - Leila Abdelrahman
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA
| | - Santanu Banerjee
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA and Department of Surgery, University of Miami, Miami, Florida, USA
| | | | | | - Anna K Junk
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA and Miami Veterans Affairs Healthcare System, Miami, Florida, USA
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA. and Miami Integrative Metabolomics Research Center, University of Miami, Miami, Florida, USA
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3
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Gupta VK, Sharma NS, Durden B, Garrido VT, Kesh K, Edwards D, Wang D, Myer C, Mateo-Victoriano B, Kollala SS, Ban Y, Gao Z, Bhattacharya SK, Saluja A, Singh PK, Banerjee S. Hypoxia-Driven Oncometabolite L-2HG Maintains Stemness-Differentiation Balance and Facilitates Immune Evasion in Pancreatic Cancer. Cancer Res 2021; 81:4001-4013. [PMID: 33990397 DOI: 10.1158/0008-5472.can-20-2562] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/09/2020] [Accepted: 05/12/2021] [Indexed: 12/16/2022]
Abstract
In pancreatic cancer, the robust fibroinflammatory stroma contributes to immune suppression and renders tumors hypoxic, altering intratumoral metabolic pathways and leading to poor survival. One metabolic enzyme activated during hypoxia is lactate dehydrogenase A (LDHA). As a result of its promiscuous activity under hypoxia, LDHA produces L-2 hydroxyglutarate (L-2HG), an epigenetic modifier, that regulates the tumor transcriptome. However, the role of L-2HG in remodeling the pancreatic tumor microenvironment is not known. Here we used mass spectrometry to detect L-2HG in serum samples from patients with pancreatic cancer, comprising tumor cells as well as stromal cells. Both hypoxic pancreatic tumors as well as serum from patients with pancreatic cancer accumulated L-2HG as a result of promiscuous activity of LDHA. This abnormally accumulated L-2HG led to H3 hypermethylation and altered gene expression, which regulated a critical balance between stemness and differentiation in pancreatic tumors. Secreted L-2HG inhibited T-cell proliferation and migration, suppressing antitumor immunity. In a syngeneic orthotopic model of pancreatic cancer, inhibition of LDH with GSK2837808A decreased L-2HG, induced tumor regression, and sensitized tumors to anti-PD1 therapy. In conclusion, hypoxia-mediated promiscuous activity of LDH produces L-2HG in pancreatic tumor cells, regulating the stemness-differentiation balance and contributing to immune evasion. Targeting LDH can be developed as a potential therapy to sensitize pancreatic tumors to checkpoint inhibitor therapy. SIGNIFICANCE: This study shows that promiscuous LDH activity produces L-2HG in pancreatic tumor and stromal cells, modulating tumor stemness and immune cell function and infiltration in the tumor microenvironment.
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Affiliation(s)
- Vineet K Gupta
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Nikita S Sharma
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Brittany Durden
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Vanessa T Garrido
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Kousik Kesh
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Dujon Edwards
- Department of Surgery, University of Miami, Miami, Florida
| | - Dezhen Wang
- University of Nebraska Medical School, Omaha, Nebraska
| | - Ciara Myer
- Department of Ophthalmology, University of Miami, Miami, Florida.,Miami Integrative Metabolomic Research Center, University of Miami, Miami, Florida
| | | | | | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Zhen Gao
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | - Sanjoy K Bhattacharya
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida.,Department of Ophthalmology, University of Miami, Miami, Florida.,Miami Integrative Metabolomic Research Center, University of Miami, Miami, Florida
| | - Ashok Saluja
- Department of Surgery, University of Miami, Miami, Florida.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida
| | | | - Sulagna Banerjee
- Department of Surgery, University of Miami, Miami, Florida. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, Florida.,Miami Integrative Metabolomic Research Center, University of Miami, Miami, Florida
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4
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Musada GR, Dvoriantchikova G, Myer C, Ivanov D, Bhattacharya SK, Hackam AS. The effect of extrinsic Wnt/β-catenin signaling in Muller glia on retinal ganglion cell neurite growth. Dev Neurobiol 2020; 80:98-110. [PMID: 32267608 DOI: 10.1002/dneu.22741] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/04/2020] [Accepted: 03/31/2020] [Indexed: 12/23/2022]
Abstract
Muller glia are the predominant glial cell type in the retina, and they structurally and metabolically support retinal neurons. Wnt/β-catenin signaling pathways play essential roles in the central nervous system, including glial and neuronal differentiation, axonal growth, and neuronal regeneration. We previously demonstrated that Wnt signaling activation in retinal ganglion cells (RGC) induces axonal regeneration after injury. However, whether Wnt signaling within the adjacent Muller glia plays an axongenic role is not known. In this study, we characterized the effect of Wnt signaling in Muller glia on RGC neurite growth. Primary Muller glia and RGC cells were grown in transwell co-cultures and adenoviral constructs driving Wnt regulatory genes were used to activate and inhibit Wnt signaling specifically in primary Muller glia. Our results demonstrated that activation of Wnt signaling in Muller glia significantly increased RGC average neurite length and branch site number. In addition, the secretome of Muller glia after induction or inhibition of Wnt signaling was characterized using protein profiling of conditioned media by Q Exactive mass spectrometry. The Muller glia secretome after activation of Wnt signaling had distinct and more numerous proteins involved in regulation of axon extension, axon projection and cell adhesion. Furthermore, we showed highly redundant expression of Wnt signaling ligands in Muller glia and Frizzled receptors in RGCs and Muller glia. Therefore, this study provides new information about potential neurite growth promoting molecules in the Muller glia secretome, and identified Wnt-dependent target proteins that may mediate the axonal growth.
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Affiliation(s)
- Ganeswara Rao Musada
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Galina Dvoriantchikova
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ciara Myer
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dmitry Ivanov
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
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5
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Myer C, Perez J, Abdelrahman L, Mendez R, Khattri RB, Junk AK, Bhattacharya SK. Differentiation of soluble aqueous humor metabolites in primary open angle glaucoma and controls. Exp Eye Res 2020; 194:108024. [PMID: 32246983 DOI: 10.1016/j.exer.2020.108024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 01/06/2023]
Abstract
We report an analysis of the aqueous humor (AH) metabolome of primary open angle glaucoma (POAG) in comparison to normal controls. The AH samples were obtained from human donors [control (n = 35), POAG (n = 23)]. The AH samples were subjected to one-dimensional 1H nuclear magnetic resonance (NMR) analyses on a Bruker Avance 600 MHz instrument with a 1.7 mM NMR probe. The same samples were then subjected to isotopic ratio outlier analysis (IROA) using a Q Exactive orbitrap mass spectrometer after chromatography on an Accela 600 HPLC. Clusterfinder Build 3.1.10 was used for identification and quantification based on long-term metabolite matrix standards. In total, 278 metabolites were identified in control samples and 273 in POAG AH. The metabolites identified were fed into previously reported proteome and genome information and the OmicsNet interaction network generator to construct a protein-metabolite interactions network with an embedded protein-protein network. Significant differences in metabolite composition in POAG compared to controls were identified indicating potential protein/gene pathways associated with these metabolites. These results will expand our previous understanding of the impeded AH metabolite composition, provide new insight into the regulation of AH outflow, and likely aid in future AH and trabecular meshwork multi-omics network analyses.
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Affiliation(s)
- Ciara Myer
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Jordan Perez
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA; Case Western Reserve University, Cleveland, OH, USA
| | - Leila Abdelrahman
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Roberto Mendez
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA; Department of Surgery, University of Miami, Miami, FL, USA
| | - Ram B Khattri
- Department of Biochemistry and Molecular Biochemistry, University of Florida, Gainesville, FL, USA
| | - Anna K Junk
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA; Miami Veterans Affairs Health Care System, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA.
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6
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Abstract
"Omics" revolution during the last few decades has vastly increased the understanding of the biological processes that remained obscure in part due to the lack of quality data. Genomics, transcriptomics, epigenomics, proteomics, lipidomics, metabolomics, and microbiomics form an invaluable array of fields that contribute holistically to a global understanding of the intertwined roles of the basic constituents of life and how they comprehensively paint a picture of disease. Metabolomics, in particular, is the study of metabolites, which are the products of cellular metabolic processes (small molecules, i.e., fatty acids, amino acids, or carbohydrates, are part of metabolomics). In this chapter, it is explained how to achieve a metabolomics profiling of aqueous humor using a special isotopic carbon labeling, a novel technique that combines a tremendous effectiveness with simplicity. The very nature of this technique guarantees the exclusion of false positives, since the algorithms are based on the recognition of unique isotopic patterns.
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Affiliation(s)
| | - Ciara Myer
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anna Junk
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Miami Veterans Affairs Healthcare System, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
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7
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Sherman JM, Davis S, Albamonte-Petrick S, Chatburn RL, Fitton C, Green C, Johnston J, Lyrene RK, Myer C, Othersen HB, Wood R, Zach M, Zander J, Zinman R. Care of the child with a chronic tracheostomy. This official statement of the American Thoracic Society was adopted by the ATS Board of Directors, July 1999. Am J Respir Crit Care Med 2000; 161:297-308. [PMID: 10619835 DOI: 10.1164/ajrccm.161.1.ats1-00] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Koch BL, Myer C, Egelhoff JC. Congenital epulis. AJNR Am J Neuroradiol 1997; 18:739-41. [PMID: 9127041 PMCID: PMC8338476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Congenital epulis of the newborn is a rare gingival tumor that occurs along the alveolar ridge. We report the prenatal sonographic and postnatal MR imaging findings in an infant with maxillary and mandibular congenital epulides.
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Affiliation(s)
- B L Koch
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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9
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Myers WC, Myer C. The multiple personality debate. J Am Acad Child Adolesc Psychiatry 1996; 35:261-2. [PMID: 8714312 DOI: 10.1097/00004583-199603000-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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10
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Li Y, Witte D, Myer C, Gluckman J, Pavelic Z, Pavelic L, Stambrook P. Involvement of episomal hpv31 in a laryngeal carcinoma - persistent episomal maintenance of hpv DNA after passage through nude-mice. Int J Oncol 1994; 4:1377-82. [PMID: 21567065 DOI: 10.3892/ijo.4.6.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We describe the involvement of HPV31 in a laryngeal carcinoma, a highly unusual anatomic site for this HPV subtype. In situ hybridization with a type-specific HPV probe identified infected tumor cells. Diagnostic Southern blot analysis confirmed that the HPV was type 31, and also revealed that the HPV DNA was episomal. The tumor was passaged in nude mice, and analysis of HPV DNA in the passaged tumor revealed that the viral DNA had persisted and that it had remained episomal. The status of p53 in the tumor was examined by Southern blots and by PCR analysis of a closely linked, highly polymorphic dinucleotide repeat region. There was no apparent allele loss or loss of heterozygosity at p53 or at the locus of another putative tumor suppressor gene at 17p distal to p53. To assess the integrity of the p53 gene in more detail, exons 4 through 11 were amplified by PCR, and the amplified DNA was directly sequenced. No mutations in p53 were observed, suggesting that other mechanisms such as sequestration of p53 by the E6 or E7 products may have contributed to the malignancy.
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Affiliation(s)
- Y Li
- UNIV CINCINNATI,COLL MED,DEPT ANAT & CELL BIOL,231 BETHESDA AVE,CINCINNATI,OH 45267. UNIV CINCINNATI,COLL MED,DEPT OTOLARYNGOL HEAD & NECK SURG,CINCINNATI,OH 45267. CHILDRENS HOSP MED CTR,CINCINNATI,OH 45229
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11
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Abstract
We present a case of congenital midline cervical cleft (CMCC), a sporadic lesion with a predilection for white females. It characteristically occurs in the midline ventral neck and consists of a cephalad skin tag, a mucosal surface, and a caudal sinus. There is an associated submucosal fibrous cord and interwoven bundles of skeletal muscle. This is occasionally tethered to the mandible and/or sternum causing neck contractures. CMCC is usually isolated, but rare cases have been associated with midline clefts of the tongue, lower lip, mandible, and sternum. The embryogenesis is unclear but arguments are given here that CMCC represents ectopic first branchial arch derivatives, including the lower lip and/or tongue.
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Affiliation(s)
- M A Bergevin
- Department of Pathology, Children's Hospital Medical Center, University of Cincinnati College of Medicine, Ohio 45229
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13
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Abstract
This is the second of a two-part review of salivary gland disease in children. Part 1, on acquired non-neoplastic disease appeared on pages 314 through 322 in the June issue of this volume.
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14
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Abstract
The early recognition of salivary gland disease depends upon a high index of suspicion by the clinician. A systematic approach to salivary gland disease in children is presented by a group of algorithms, which is supplemented by a discussion of the historical, physical, and diagnostic test findings characteristic of salivary gland pathology. Therapeutic alternatives are discussed for both neoplastic and non-neoplastic disorders.
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