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Kundu S, Jaiswal M, Babu Mullapudi V, Guo J, Kamat M, Basso KB, Guo Z. Investigation of Glycosylphosphatidylinositol (GPI)-Plasma Membrane Interaction in Live Cells and the Influence of GPI Glycan Structure on the Interaction. Chemistry 2024; 30:e202303047. [PMID: 37966101 PMCID: PMC10922586 DOI: 10.1002/chem.202303047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/16/2023]
Abstract
Glycosylphosphatidylinositols (GPIs) need to interact with other components in the cell membrane to transduce transmembrane signals. A bifunctional GPI probe was employed for photoaffinity-based proximity labelling and identification of GPI-interacting proteins in the cell membrane. This probe contained the entire core structure of GPIs and was functionalized with photoreactive diazirine and clickable alkyne to facilitate its crosslinking with proteins and attachment of an affinity tag. It was disclosed that this probe was more selective than our previously reported probe containing only a part structure of the GPI core for cell membrane incorporation and an improved probe for studying GPI-cell membrane interaction. Eighty-eight unique membrane proteins, many of which are related to GPIs/GPI-anchored proteins, were identified utilizing this probe. The proteomics dataset is a valuable resource for further analyses and data mining to find new GPI-related proteins and signalling pathways. A comparison of these results with those of our previous probe provided direct evidence for the profound impact of GPI glycan structure on its interaction with the cell membrane.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Mohit Jaiswal
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | - Jiatong Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- UF Health Cancer Centre, University of Florida, Gainesville, FL 32611, USA
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2
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Sun W, Ma S, Jin X, Ma Y. Combined analysis of mRNA-miRNA from testis tissue in Tibetan sheep with different FecB genotypes. Open Life Sci 2023; 18:20220605. [PMID: 37250847 PMCID: PMC10224625 DOI: 10.1515/biol-2022-0605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 05/31/2023] Open
Abstract
Testis size is important for identifying breeding animals with adequate sperm production. The aim of this study was to survey the expression profile of mRNA and miRNA in testis tissue from rams carrying different FecB genotypes, including the wild-type and heterozygous genotypes in Tibetan sheep. Comparative transcriptome profiles for ovine testes were established for wild-type and heterozygote Tibetan sheep by next-generation sequencing. RNA-seq results identified 3,910 (2,034 up- and 1,876 downregulated) differentially expressed (DE) genes and 243 (158 up- and 85 downregulated) DE microRNAs (miRNAs) in wild-type vs heterozygote sheep, respectively. Combined analysis of mRNA-seq and miRNA-seq revealed that 20 miRNAs interacted with 48 true DE target genes in wild-type testes compared to heterozygous genotype testes. These results provide evidence for a functional series of genes operating in Tibetan sheep testis. In addition, quantitative real-time PCR analysis showed that the expression trends of randomly selected DE genes in testis tissues from different genotypes were consistent with high-throughput sequencing results.
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Affiliation(s)
- Wu Sun
- Department of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, 810016, China
- Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, 810016, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, 810016, China
| | - Shike Ma
- Department of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, 810016, China
- Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, 810016, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, 810016, China
| | - Xiayang Jin
- Department of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, 810016, China
- Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, 810016, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, 810016, China
| | - Yuhong Ma
- Department of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, 810016, China
- Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, 810016, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, 810016, China
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3
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Kundu S, Lin C, Jaiswal M, Mullapudi VB, Craig KC, Chen S, Guo Z. Profiling Glycosylphosphatidylinositol (GPI)-Interacting Proteins in the Cell Membrane Using a Bifunctional GPI Analogue as the Probe. J Proteome Res 2023; 22:919-930. [PMID: 36700487 PMCID: PMC9992086 DOI: 10.1021/acs.jproteome.2c00728] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glycosylphosphatidylinositol (GPI) anchorage of cell surface proteins to the membrane is biologically important and ubiquitous in eukaryotes. However, GPIs do not contain long enough lipids to span the entire membrane bilayer. To transduce binding signals, GPIs must interact with other membrane components, but such interactions are difficult to define. Here, a new method was developed to explore GPI-interacting membrane proteins in live cell with a bifunctional analogue of the glucosaminylphosphatidylinositol motif conserved in all GPIs as a probe. This probe contained a diazirine functionality in the lipid and an alkynyl group on the glucosamine residue to respectively facilitate the cross-linkage of GPI-binding membrane proteins with the probe upon photoactivation and then the installation of biotin to the cross-linked proteins via a click reaction for affinity-based protein isolation and analysis. Profiling the proteins pulled down from the Hela cells revealed 94 unique and 18 overrepresented proteins compared to the control, and most of them are membrane proteins and many are GPI-related. The results have proved not only the concept of using the new bifunctional GPI probe to investigate GPI-binding membrane proteins but also the important role of inositol in the biological functions of GPI anchors and GPI-anchored proteins.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - Chuwei Lin
- Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida32611, United States
| | - Mohit Jaiswal
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | | | - Kendall C Craig
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida32611, United States
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
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4
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Multiple Genetic Loci Associated with Pug Dog Thoracolumbar Myelopathy. Genes (Basel) 2023; 14:genes14020385. [PMID: 36833311 PMCID: PMC9957375 DOI: 10.3390/genes14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Pug dogs with thoracolumbar myelopathy (PDM) present with a specific clinical phenotype that includes progressive pelvic limb ataxia and paresis, commonly accompanied by incontinence. Vertebral column malformations and lesions, excessive scar tissue of the meninges, and central nervous system inflammation have been described. PDM has a late onset and affects more male than female dogs. The breed-specific presentation of the disorder suggests that genetic risk factors are involved in the disease development. To perform a genome-wide search for PDM-associated loci, we applied a Bayesian model adapted for mapping complex traits (BayesR) and a cross-population extended haplotype homozygosity test (XP-EHH) in 51 affected and 38 control pugs. Nineteen associated loci (harboring 67 genes in total, including 34 potential candidate genes) and three candidate regions under selection (with four genes within or next to the signal) were identified. The multiple candidate genes identified have implicated functions in bone homeostasis, fibrotic scar tissue, inflammatory responses, or the formation, regulation, and differentiation of cartilage, suggesting the potential relevance of these processes to the pathogenesis of PDM.
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Kouri N, Murray ME, Reddy JS, Serie DJ, Soto-Beasley A, Allen M, Carrasquillo MM, Wang X, Castanedes MC, Baker MC, Rademakers R, Uitti RJ, Graff-Radford NR, Wszolek ZK, Schellenberg GD, Crook JE, Ertekin-Taner N, Ross OA, Dickson DW. Latent trait modeling of tau neuropathology in progressive supranuclear palsy. Acta Neuropathol 2021; 141:667-680. [PMID: 33635380 PMCID: PMC8043857 DOI: 10.1007/s00401-021-02289-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/01/2022]
Abstract
Progressive supranuclear palsy (PSP) is the second most common neurodegenerative Parkinsonian disorder after Parkinson's disease, and is characterized as a primary tauopathy. Leveraging the considerable clinical and neuropathologic heterogeneity associated with PSP, we measured tau neuropathology as quantitative traits to perform a genome-wide association study (GWAS) within PSP to identify genes and biological pathways that underlie the PSP disease process. In 882 PSP cases, semi-quantitative scores for phosphorylated tau-immunoreactive coiled bodies (CBs), neurofibrillary tangles (NFTs), tufted astrocytes (TAs), and tau threads were documented from 18 brain regions, and converted to latent trait (LT) variables using the R ltm package. LT analysis utilizes a multivariate regression model that links categorical responses to unobserved covariates allowing for a reduction of dimensionality, generating a single, continuous variable to account for the multiple lesions and brain regions assessed. We first tested for association with PSP LTs and the top PSP GWAS susceptibility loci. Significant SNP/LT associations were identified at rs242557 (MAPT H1c sub-haplotype) with hindbrain CBs and rs1768208 (MOBP) with forebrain tau threads. Digital microscopy was employed to quantify phosphorylated tau burden in midbrain tectum and red nucleus in 795 PSP cases and tau burdens were used as quantitative phenotypes in GWAS. Top associations were identified at rs1768208 with midbrain tectum and red nucleus tau burden. Additionally, we performed a PSP LT GWAS on an initial cohort, a follow-up SNP panel (37 SNPs, P < 10-5) in an extended cohort, and a combined analysis. Top SNP/LT associations were identified at SNPs in or near SPTBN5/EHD4, SEC13/ATP2B2, EPHB1/PPP2R3A, TBC1D8, IFNGR1/OLIG3, ST6GAL1, HK1, CALB1, and SGCZ. Finally, testing for SNP/transcript associations using whole transcriptome and whole genome data identified significant expression quantitative trait loci at rs3088159/SPTBN5/EHD4 and rs154239/GHRL. Modeling tau neuropathology heterogeneity using LTs as quantitative phenotypes in a GWAS may provide substantial insight into biological pathways involved in PSP by affecting regional tau burden.
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Affiliation(s)
- Naomi Kouri
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Daniel J Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Alexandra Soto-Beasley
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Minerva M Carrasquillo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- VIB-UAntwerp Center for Molecular Neurology, Antwerp, Belgium
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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Jones T, Naslavsky N, Caplan S. Eps15 Homology Domain Protein 4 (EHD4) is required for Eps15 Homology Domain Protein 1 (EHD1)-mediated endosomal recruitment and fission. PLoS One 2020; 15:e0239657. [PMID: 32966336 PMCID: PMC7511005 DOI: 10.1371/journal.pone.0239657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/10/2020] [Indexed: 11/19/2022] Open
Abstract
Upon internalization, receptors are trafficked to sorting endosomes (SE) where they undergo sorting and are then packaged into budding vesicles that undergo fission and transport within the cell. Eps15 Homology Domain Protein 1 (EHD1), the best-characterized member of the Eps15 Homology Domain Protein (EHD) family, has been implicated in catalyzing the fission process that releases endosome-derived vesicles for recycling to the plasma membrane. Indeed, recent studies suggest that upon receptor-mediated internalization, EHD1 is recruited from the cytoplasm to endosomal membranes where it catalyzes vesicular fission. However, the mechanism by which this recruitment occurs remains unknown. Herein, we demonstrate that the EHD1 paralog, EHD4, is required for the recruitment of EHD1 to SE. We show that EHD4 preferentially dimerizes with EHD1, and knock-down of EHD4 expression by siRNA, shRNA or by CRISPR/Cas9 gene-editing leads to impaired EHD1 SE-recruitment and enlarged SE. Moreover, we demonstrate that at least 3 different asparagine-proline-phenylalanine (NPF) motif-containing EHD binding partners, Rabenosyn-5, Syndapin2 and MICAL-L1, are required for the recruitment of EHD1 to SE. Indeed, knock-down of any of these SE-localized EHD interaction partners leads to enlarged SE, presumably due to impaired endosomal fission. Overall, we identify a novel mechanistic role for EHD4 in recruitment of EHD1 to SE, thus positioning EHD4 as an essential component of the EHD1-fission machinery at SE.
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Affiliation(s)
- Tyler Jones
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States of America
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States of America
- * E-mail:
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7
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Budi EH, Hoffman S, Gao S, Zhang YE, Derynck R. Integration of TGF-β-induced Smad signaling in the insulin-induced transcriptional response in endothelial cells. Sci Rep 2019; 9:16992. [PMID: 31740700 PMCID: PMC6861289 DOI: 10.1038/s41598-019-53490-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023] Open
Abstract
Insulin signaling governs many processes including glucose homeostasis and metabolism, and is therapeutically used to treat hyperglycemia in diabetes. We demonstrated that insulin-induced Akt activation enhances the sensitivity to TGF-β by directing an increase in cell surface TGF-β receptors from a pool of intracellular TGF-β receptors. Consequently, increased autocrine TGF-β signaling in response to insulin participates in insulin-induced angiogenic responses of endothelial cells. With TGF-β signaling controlling many cell responses, including differentiation and extracellular matrix deposition, and pathologically promoting fibrosis and cancer cell dissemination, we addressed to which extent autocrine TGF-β signaling participates in insulin-induced gene responses of human endothelial cells. Transcriptome analyses of the insulin response, in the absence or presence of a TGF-β receptor kinase inhibitor, revealed substantial positive and negative contributions of autocrine TGF-β signaling in insulin-responsive gene responses. Furthermore, insulin-induced responses of many genes depended on or resulted from autocrine TGF-β signaling. Our analyses also highlight extensive contributions of autocrine TGF-β signaling to basal gene expression in the absence of insulin, and identified many novel TGF-β-responsive genes. This data resource may aid in the appreciation of the roles of autocrine TGF-β signaling in normal physiological responses to insulin, and implications of therapeutic insulin usage.
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Affiliation(s)
- Erine H Budi
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, 94143-0669, USA
| | - Steven Hoffman
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, 94143-0669, USA
| | - Shaojian Gao
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-1906, USA
| | - Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Rik Derynck
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, 94143-0669, USA.
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Silvers CR, Miyamoto H, Messing EM, Netto GJ, Lee YF. Characterization of urinary extracellular vesicle proteins in muscle-invasive bladder cancer. Oncotarget 2017; 8:91199-91208. [PMID: 29207636 PMCID: PMC5710916 DOI: 10.18632/oncotarget.20043] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022] Open
Abstract
The mechanisms of bladder cancer progression are unknown, and new treatments and biomarkers are needed. Patient urinary extracellular vesicles (EVs) derive in part from bladder cancer cells and contain a specific protein cargo which may provide information about the disease. We conducted a proteomics study comparing EVs from the muscle-invasive bladder cancer (MIBC) cell line TCCSUP to EVs from normal urothelial line SVHUC. GO term analysis showed that TCCSUP EVs are enriched in proteins associated with the cell membrane, extracellular matrix, and inflammation and angiogenesis signaling pathways. Proteins characteristic of cancer EVs were further screened at the mRNA level in bladder cancer cell lines. In Western blots, three of six proteins examined showed greater than fifteenfold enrichment in patient urinary EVs compared to healthy volunteers (n = 6). Finally, we performed immunohistochemical staining of bladder tissue microarrays for three proteins of interest. One of them, transaldolase (TALDO1), is a nearly ubiquitous enzyme and normally thought to reside in the cytoplasm. To our surprise, nuclei were stained for transaldolase in 94% of MIBC tissue samples (n = 51). While cytoplasmic transaldolase was found in 89–90% of both normal urothelium (n = 79) and non-muscle-invasive samples (n = 71), the rate falls to 39% in MIBC samples (P < 0.001), and negative cytoplasmic staining was correlated with worse cancer-specific survival in MIBC patients (P = 0.008). The differential EV proteomics strategy reported here successfully identified a number of proteins associated with bladder cancer and points the way to future investigation.
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Affiliation(s)
| | - Hiroshi Miyamoto
- Department of Urology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA.,Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Edward M Messing
- Department of Urology, University of Rochester Medical Center, Rochester, NY, USA
| | - George J Netto
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yi-Fen Lee
- Department of Urology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
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9
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Non-immune immunoglobulins shield Schistosoma japonicum from host immunorecognition. Sci Rep 2015; 5:13434. [PMID: 26299686 PMCID: PMC4547136 DOI: 10.1038/srep13434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/27/2015] [Indexed: 11/18/2022] Open
Abstract
Schistosomiasis is a major human parasitic disease with a global impact. Schistosoma japonicum, the most difficult to control, can survive within host veins for decades. Mechanisms of immune evasion by the parasite, including antigenic variation and surface masking, have been implicated but not well defined. In this study, we defined the immunoglobulin-binding proteomes of S. japonicum using human IgG, IgM, and IgE as the molecular bait for affinity purification, followed by protein identification by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Several proteins situated at the tegument of S. japonicum were able to nonselectively bind to the Fc domain of host immunoglobulins, indicating a mechanism for the avoidance of host immune attachment and recognition. The profile of the immunoglobulin-binding proteomes provides further clues for immune evasion mechanisms adopted by S. japonicum.
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10
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EHD proteins: key conductors of endocytic transport. Trends Cell Biol 2010; 21:122-31. [PMID: 21067929 DOI: 10.1016/j.tcb.2010.10.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/07/2010] [Accepted: 10/07/2010] [Indexed: 12/12/2022]
Abstract
Regulation of endocytic transport is controlled by an elaborate network of proteins. Rab GTP-binding proteins and their effectors have well-defined roles in mediating specific endocytic transport steps, but until recently less was known about the four mammalian dynamin-like C-terminal Eps15 homology domain (EHD) proteins that also regulate endocytic events. In recent years, however, great strides have been made in understanding the structure and function of these unique proteins. Indeed, a growing body of literature addresses EHD protein structure, interactions with binding partners, functions in mammalian cells, and the generation of various new model systems. Accordingly, this is now an opportune time to pause and review the function and mechanisms of action of EHD proteins, and to highlight some of the challenges and future directions for the field.
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11
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George M, Rainey MA, Naramura M, Ying G, Harms DW, Vitaterna MH, Doglio L, Crawford SE, Hess RA, Band V, Band H. Ehd4 is required to attain normal prepubertal testis size but dispensable for fertility in male mice. Genesis 2010; 48:328-42. [PMID: 20213691 DOI: 10.1002/dvg.20620] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The four highly homologous members of the C-terminal EH domain-containing (EHD) protein family (EHD1-4) regulate endocytic recycling. To delineate the role of EHD4 in normal physiology and development, mice with a conditional knockout of the Ehd4 gene were generated. PCR of genomic DNA and Western blotting of organ lysates from Ehd4(-/-) mice confirmed EHD4 deletion. Ehd4(-/-) mice were viable and born at expected Mendelian ratios; however, males showed a 50% reduction in testis weight, obvious from postnatal day 31. An early (Day 10) increase in germ cell proliferation and apoptosis and a later increase in apoptosis (Day 31) were seen in the Ehd4(-/-) testis. Other defects included a progressive reduction in seminiferous tubule diameter, dysregulation of seminiferous epithelium, and head abnormalities in elongated spermatids. As a consequence, lower sperm counts and reduced fertility were observed in Ehd4(-/-) males. Interestingly, EHD protein expression was seen to be temporally regulated in the testis and EHD4 levels peaked between days 10 and 15. In the adult testis, EHD4 was highly expressed in primary spermatocytes and EHD4 deletion altered the levels of other EHD proteins in an age-dependent manner. We conclude that high levels of EHD1 in the adult Ehd4(-/-) testis functionally compensate for lack of EHD4 and prevents the development of severe fertility defects. Our results suggest a role for EHD4 in the proper development of postmitotic and postmeiotic germ cells and implicate EHD protein-mediated endocytic recycling as an important process in germ cell development and testis function.
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Affiliation(s)
- Manju George
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC-Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
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12
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Austin P, Heller M, Williams DE, McIntosh LP, Vogl AW, Foster LJ, Andersen RJ, Roberge M, Roskelley CD. Release of membrane-bound vesicles and inhibition of tumor cell adhesion by the peptide Neopetrosiamide A. PLoS One 2010; 5:e10836. [PMID: 20520768 PMCID: PMC2877099 DOI: 10.1371/journal.pone.0010836] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 05/04/2010] [Indexed: 11/25/2022] Open
Abstract
Background Neopetrosiamide A (NeoA) is a 28-amino acid tricyclic peptide originally isolated from a marine sponge as a tumor cell invasion inhibitor whose mechanism of action is unknown. Methodology/Principal Findings We show that NeoA reversibly inhibits tumor cell adhesion, disassembles focal adhesions in pre-attached cells, and decreases the level of β1 integrin subunits on the cell surface. NeoA also induces the formation of dynamic, membrane-bound protrusions on the surface of treated cells and the release of membrane-bound vesicles into the culture medium. Proteomic analysis indicates that the vesicles contain EGF and transferrin receptors as well as a number of proteins involved in adhesion and migration including: β1 integrin and numerous α integrin subunits; actin and actin-binding proteins such as cofilin, moesin and myosin 1C; and membrane modulating eps15 homology domain (EHD) proteins. Surface labeling, trafficking inhibition, and real-time imaging experiments all suggest that β1 integrin-containing vesicles are released directly from NeoA-induced cell surface protrusions rather than from vesicles generated intracellularly. The biological activity of NeoA is dependent on its disulfide bond pattern and NMR spectroscopy indicates that the peptide is globular with a continuous ridge of hydrophobic groups flanked by charged amino acid residues that could facilitate a simultaneous interaction with lipids and proteins in the membrane. Conclusions/Significance NeoA is an anti-adhesive peptide that decreases cell surface integrin levels through a novel, yet to be elucidated, mechanism that involves the release of adhesion molecule-containing vesicles from the cell surface.
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Affiliation(s)
- Pamela Austin
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Markus Heller
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David E. Williams
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth and Ocean Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lawrence P. McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - A. Wayne Vogl
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond J. Andersen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth and Ocean Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin D. Roskelley
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- The Program in Breast Cancer Metastasis, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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13
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Rao N, Jhamb D, Milner DJ, Li B, Song F, Wang M, Voss SR, Palakal M, King MW, Saranjami B, Nye HLD, Cameron JA, Stocum DL. Proteomic analysis of blastema formation in regenerating axolotl limbs. BMC Biol 2009; 7:83. [PMID: 19948009 PMCID: PMC2794268 DOI: 10.1186/1741-7007-7-83] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 11/30/2009] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Following amputation, urodele salamander limbs reprogram somatic cells to form a blastema that self-organizes into the missing limb parts to restore the structure and function of the limb. To help understand the molecular basis of blastema formation, we used quantitative label-free liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS)-based methods to analyze changes in the proteome that occurred 1, 4 and 7 days post amputation (dpa) through the mid-tibia/fibula of axolotl hind limbs. RESULTS We identified 309 unique proteins with significant fold change relative to controls (0 dpa), representing 10 biological process categories: (1) signaling, (2) Ca2+ binding and translocation, (3) transcription, (4) translation, (5) cytoskeleton, (6) extracellular matrix (ECM), (7) metabolism, (8) cell protection, (9) degradation, and (10) cell cycle. In all, 43 proteins exhibited exceptionally high fold changes. Of these, the ecotropic viral integrative factor 5 (EVI5), a cell cycle-related oncoprotein that prevents cells from entering the mitotic phase of the cell cycle prematurely, was of special interest because its fold change was exceptionally high throughout blastema formation. CONCLUSION Our data were consistent with previous studies indicating the importance of inositol triphosphate and Ca2+ signaling in initiating the ECM and cytoskeletal remodeling characteristic of histolysis and cell dedifferentiation. In addition, the data suggested that blastema formation requires several mechanisms to avoid apoptosis, including reduced metabolism, differential regulation of proapoptotic and antiapoptotic proteins, and initiation of an unfolded protein response (UPR). Since there is virtually no mitosis during blastema formation, we propose that high levels of EVI5 function to arrest dedifferentiated cells somewhere in the G1/S/G2 phases of the cell cycle until they have accumulated under the wound epidermis and enter mitosis in response to neural and epidermal factors. Our findings indicate the general value of quantitative proteomic analysis in understanding the regeneration of complex structures.
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Affiliation(s)
- Nandini Rao
- Department of Biology and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Deepali Jhamb
- School of Informatics and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Derek J Milner
- Department of Cell and Developmental Biology, and Regeneration Biology and Tissue Engineering Theme, Institute for Genomic Biology, University of Illinois-Urbana Champaign, Urbana, IL, USA
| | - Bingbing Li
- Department of Biology and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fengyu Song
- Department of Oral Biology, School of Dentistry and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Mu Wang
- Department of Biochemistry, School of Medicine and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - S Randal Voss
- Department of Biology and Spinal Cord and Brain Injury Center, University of Kentucky at Lexington, Lexington, KY, USA
| | - Mathew Palakal
- School of Informatics and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Michael W King
- Department of Biochemistry, School of Medicine and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Behnaz Saranjami
- Department of Biology and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Holly LD Nye
- Department of Cell and Developmental Biology, and Regeneration Biology and Tissue Engineering Theme, Institute for Genomic Biology, University of Illinois-Urbana Champaign, Urbana, IL, USA
| | - Jo Ann Cameron
- Department of Cell and Developmental Biology, and Regeneration Biology and Tissue Engineering Theme, Institute for Genomic Biology, University of Illinois-Urbana Champaign, Urbana, IL, USA
| | - David L Stocum
- Department of Biology and Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
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14
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Sengupta S, George M, Miller KK, Naik K, Chou J, Cheatham MA, Dallos P, Naramura M, Band H, Zheng J. EHD4 and CDH23 are interacting partners in cochlear hair cells. J Biol Chem 2009; 284:20121-9. [PMID: 19487694 DOI: 10.1074/jbc.m109.025668] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cadherin 23 (CDH23), a transmembrane protein localized near the tips of hair cell stereocilia in the mammalian inner ear, is important for delivering mechanical signals to the mechano-electric transducer channels. To identify CDH23-interacting proteins, a membrane-based yeast two-hybrid screen of an outer hair cell (OHC) cDNA library was performed. EHD4, a member of the C-terminal EH domain containing a protein family involved in endocytic recycling, was identified as a potential interactor. To confirm the interaction, we first demonstrated the EHD4 mRNA expression in hair cells using in situ hybridization. Next, we showed that EHD4 co-localizes and co-immunoprecipitates with CDH23 in mammalian cells. Interestingly, the co-immunoprecipitation was found to be calcium-sensitive. To investigate the role of EHD4 in hearing, compound action potentials were measured in EHD4 knock-out (KO) mice. Although EHD4 KO mice have normal hearing sensitivity, analysis of mouse cochlear lysates revealed a 2-fold increase in EHD1, but no increase in EHD2 or EHD3, in EHD4 KO cochleae compared with wild type, suggesting that a compensatory increase in EHD1 levels may account for the absence of a hearing defect in EHD4 KO mice. Taken together, these data indicate that EHD4 is a novel CDH23-interacting protein that could regulate CDH23 trafficking/localization in a calcium-sensitive manner.
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Affiliation(s)
- Soma Sengupta
- Department of Communication Sciences and Disorders, Hugh Knowles Center, Northwestern University, Evanston, Illinois 60208, USA
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15
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Abstract
The evolutionarily conserved Eps15 homology domain (EHD)/receptor-mediated endocytosis (RME)-1 family of C-terminal EH domain proteins has recently come under intense scrutiny because of its importance in intracellular membrane transport, especially with regard to the recycling of receptors from endosomes to the plasma membrane. Recent studies have shed new light on the mode by which these adenosine triphosphatases function on endosomal membranes in mammals and Caenorhabditis elegans. This review highlights our current understanding of the physiological roles of these proteins in vivo, discussing conserved features as well as emerging functional differences between individual mammalian paralogs. In addition, these findings are discussed in light of the identification of novel EHD/RME-1 protein and lipid interactions and new structural data for proteins in this family, indicating intriguing similarities to the Dynamin superfamily of large guanosine triphosphatases.
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Affiliation(s)
- Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.
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16
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Abstract
All four of the C-terminal Eps15 homology domain (EHD) proteins have been implicated in the regulation of endocytic trafficking. However, the high level of amino acid sequence identity among these proteins has made it challenging to elucidate the precise function of individual EHD proteins. We demonstrate here with specific peptide antibodies that endogenous EHD4 localizes to Rab5-, early embryonic antigen 1 (EEA1)- and Arf6-containing endosomes and colocalizes with internalized transferrin in the cell periphery. Knock-down of EHD4 expression by both small interfering RNA and short hairpin RNA leads to the generation of enlarged early endosomal structures that contain Rab5 and EEA1 as well as internalized transferrin or major histocompatibility complex class I molecules. In addition, cargo destined for degradation, such as internalized low-density lipoprotein, also accumulates in the enlarged early endosomes in EHD4-depleted cells. Moreover, we have demonstrated that these enlarged early endosomes are enriched in levels of the activated GTP-bound Rab5. Finally, we show that endogenous EHD4 and EHD1 interact in cells, suggesting coordinated involvement in the regulation of receptor transport along the early endosome to endocytic recycling compartment axis. The results presented herein provide evidence that EHD4 is involved in the control of trafficking at the early endosome and regulates exit of cargo toward both the recycling compartment and the late endocytic pathway.
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Affiliation(s)
- Mahak Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
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17
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Yu F, Kang B, Li Y, Li Y. Functional analysis of schistosomes EF-hand domain-containing tegument proteins. CHINESE SCIENCE BULLETIN-CHINESE 2007. [DOI: 10.1007/s11434-007-0312-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Blume JJ, Halbach A, Behrendt D, Paulsson M, Plomann M. EHD proteins are associated with tubular and vesicular compartments and interact with specific phospholipids. Exp Cell Res 2006; 313:219-31. [PMID: 17097635 DOI: 10.1016/j.yexcr.2006.10.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 09/22/2006] [Accepted: 10/05/2006] [Indexed: 10/23/2022]
Abstract
The four Eps15 homology (EH) domain-containing proteins, EHD1-EHD4, have recently been ascribed roles in the regulation of the recycling of distinct receptor molecules and are often found associated with tubular structures. Here, we report the analysis of all four EHD proteins with regard to tissue distribution, intracellular localization and lipid binding properties. Specific antibodies reveal distinct expression profiles for the individual proteins in tissues and at intracellular locations, where they potentially interact with specific phospholipids. Moreover, EHD proteins colocalize with vesicular and tubular structures, implying roles in transport processes and cytoskeletal dynamics. Protein variants carrying mutations in the N-terminal nucleotide-binding P-loop region are no longer associated with phospholipids or membrane compartments, while deletion of the C-terminal EH domain affects targeting to tubular structures. All EHD proteins are able to bind to phospholipids, but localizations differ for each protein.
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Affiliation(s)
- Jessica J Blume
- Center for Biochemistry and Center for Molecular Medicine, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str 52, D-50931 Cologne, Germany
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19
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Rapaport D, Auerbach W, Naslavsky N, Pasmanik-Chor M, Galperin E, Fein A, Caplan S, Joyner AL, Horowitz M. Recycling to the plasma membrane is delayed in EHD1 knockout mice. Traffic 2006; 7:52-60. [PMID: 16445686 DOI: 10.1111/j.1600-0854.2005.00359.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
EHD1 is a member of the EHD family that contains four mammalian homologs. Among the invertebrate orthologs are a single Drosophila and Caenorhabditis elegans proteins and two plant members. They all contain three modules, a N-terminal domain that contains nucleotide-binding motifs, a central coiled-coil domain involved in oligomerization and a C-terminal region that harbors the EH domain. Studies in C. elegans and EHD1 depletion by RNA interference in human cells have demonstrated that it regulates recycling of membrane proteins. We addressed the physiological role of EHD1 through its inactivation in the mouse. Ehd1 knockout mice were indistinguishable from normal mice, had a normal life span and showed no histological abnormalities. Analysis of transferrin uptake in Ehd1(-/-) embryonic fibroblasts demonstrated delayed recycling to the plasma membrane with accumulation of transferrin in the endocytic recycling compartment. Our results corroborate the established role of EHD1 in the exit of membrane proteins from recycling endosomes in vivo in a mouse model.
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Affiliation(s)
- Debora Rapaport
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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20
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Abstract
Exogenously and endogenously originated signals are propagated within the cell by functional and physical networks of proteins, leading to numerous biological outcomes. Many protein-protein interactions take place between binding domains and short peptide motifs. Frequently, these interactions are inducible by upstream signaling events, in which case one of the two binding surfaces may be created by a posttranslational modification. Here, we discuss two protein networks. One, the EH-network, is based on the Eps15 homology (EH) domain, which binds to peptides containing the sequence Asp-Pro-Phe (NPF). The other, which we define as the monoubiquitin (mUb) network, relies on monoubiquitination, which is emerging as an important posttranslational modification that regulates protein function. Both networks were initially implicated in the control of plasma membrane receptor endocytosis and in the regulation of intracellular trafficking routes. The ramifications of these two networks, however, appear to extend into many other aspects of cell physiology as well, such as transcriptional regulation, actin cytoskeleton remodeling, and DNA repair. The focus of this review is to integrate available knowledge of the EH- and mUb networks with predictions of genetic and physical interactions stemming from functional genomics approaches.
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Affiliation(s)
- Simona Polo
- Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
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21
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Shao Y, Akmentin W, Toledo-Aral JJ, Rosenbaum J, Valdez G, Cabot JB, Hilbush BS, Halegoua S. Pincher, a pinocytic chaperone for nerve growth factor/TrkA signaling endosomes. J Cell Biol 2002; 157:679-91. [PMID: 12011113 PMCID: PMC2173850 DOI: 10.1083/jcb.200201063] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A central tenet of nerve growth factor (NGF) action that is poorly understood is its ability to mediate cytoplasmic signaling, through its receptor TrkA, that is initiated at the nerve terminal and conveyed to the soma. We identified an NGF-induced protein that we termed Pincher (pinocytic chaperone) that mediates endocytosis and trafficking of NGF and its receptor TrkA. In PC12 cells, overexpression of Pincher dramatically stimulated NGF-induced endocytosis of TrkA, unexpectedly at sites of clathrin-independent macropinocytosis within cell surface ruffles. Subsequently, a system of Pincher-containing tubules mediated the delivery of NGF/TrkA-containing vesicles to cytoplasmic accumulations. These vesicles selectively and persistently mediated TrkA-erk5 mitogen-activated protein kinase signaling. A dominant inhibitory mutant form of Pincher inhibited the NGF-induced endocytosis of TrkA, and selectively blocked TrkA-mediated cytoplasmic signaling of erk5, but not erk1/2, kinases. Our results indicate that Pincher mediates pinocytic endocytosis of functionally specialized NGF/TrkA endosomes with persistent signaling potential.
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Affiliation(s)
- Yufang Shao
- Department of Neurobiology and Behavior, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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