170 results on '"Ryan, James C"'
Search Results
152. Reply
- Author
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Ryan, James C., primary and Kritzman, Mark, additional
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- 1980
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153. Identification of MHC Class Ib Ligands for Stimulatory and Inhibitory Ly49 Receptors and Induction of Potent NK Cell Alloresponses in Rats.
- Author
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Ke-Zheng Dai, Naper, Christian, Vaage, John T., and Ryan, James C.
- Subjects
- *
RATS , *LIGANDS (Biochemistry) , *KILLER cells , *LECTINS , *DNA mutational analysis - Abstract
Early studies indicate that rats may have a repertoire of MHC class Ib-reactive Ly49 stimulatory receptors capable of mounting memory-like NK cell alloresponses. In this article, we provide molecular and functional evidence for this assumption. Pairs of Ly49 receptors with sequence similarities in the lectin-like domains, but with opposing signaling functions, showed specificity for ligands with class Ia-like structural features encoded from the first telomeric MHC class Ib gene cluster, RT1-CE, which is syntenic with the H2-D/H2-L/H2-Q cluster in mice. The activating Ly49s4 receptor and its inhibitory counterparts, Ly49i4 and Ly49i3, reacted with all allelic variants of RT1-U, whereas Ly49s5 and Ly49i5 were specific for RT1-Eu. NK cell cytolytic responses were predictably activated and inhibited, and potent in vivo NK alloresponses were induced by repeated MHC class Ib alloimmunizations. Additional Ly49-class Ib interactions, including RT1-Cl with the Ly49s4/Ly49i4/Ly49i3 group of receptors, were characterized using overexpressed receptor/ligand pairs, in vitro functional assays, and limited mutational analyses. Obvious, as well as subtle, Ly49-class Ib interactions led to ligand-induced receptor calibration and NK subset expansions in vivo. Together, these studies suggest that in vivo NK alloresponses are controlled by pleomorphic Ly49-class Ib interactions, some of which may not be easily detectable in vitro. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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154. Memory T Cell Proliferation before Hepatitis C Virus Therapy Predicts Antiviral Immune Responses and Treatment Success.
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Méndez-Lagares G, Lu D, Chen C, Terrault N, Segal MR, Khalili M, Monto A, Shen H, Manos MM, Lanier LL, Ryan JC, McCune JM, and Hartigan-O'Connor DJ
- Subjects
- Adaptive Immunity immunology, Antibodies, Viral blood, Drug Therapy, Combination, Female, Hepatitis C, Chronic immunology, Humans, Immunity, Innate immunology, Interferon-alpha therapeutic use, Longitudinal Studies, Lymphocyte Activation immunology, Male, Middle Aged, Oligopeptides therapeutic use, Polyethylene Glycols therapeutic use, Proline analogs & derivatives, Proline therapeutic use, Prospective Studies, Recombinant Proteins therapeutic use, Ribavirin therapeutic use, T-Box Domain Proteins biosynthesis, Treatment Outcome, Antiviral Agents therapeutic use, CD4-Positive T-Lymphocytes immunology, Cell Proliferation, Hepacivirus immunology, Hepatitis C, Chronic drug therapy, Immunologic Memory immunology
- Abstract
The contribution of the host immune system to the efficacy of new anti-hepatitis C virus (HCV) drugs is unclear. We undertook a longitudinal prospective study of 33 individuals with chronic HCV treated with combination pegylated IFN-α, ribavirin, and telaprevir/boceprevir. We characterized innate and adaptive immune cells to determine whether kinetics of the host response could predict sustained virologic response (SVR). We show that characteristics of the host immune system present before treatment were correlated with successful therapy. Augmentation of adaptive immune responses during therapy was more impressive among those achieving SVR. Most importantly, active memory T cell proliferation before therapy predicted SVR and was associated with the magnitude of the HCV-specific responses at week 12 after treatment start. After therapy initiation, the most important correlate of success was minimal monocyte activation, as predicted by previous in vitro work. In addition, subjects achieving SVR had increasing expression of the transcription factor T-bet, a driver of Th1 differentiation and cytotoxic effector cell maturation. These results show that host immune features present before treatment initiation predict SVR and eventual development of a higher frequency of functional virus-specific cells in blood. Such host characteristics may also be required for successful vaccine-mediated protection., (Copyright © 2018 by The American Association of Immunologists, Inc.)
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- 2018
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155. NKG2D ligand expression in Crohn's disease and NKG2D-dependent stimulation of CD8 + T cell migration.
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Vadstrup K, Galsgaard ED, Jensen H, Lanier LL, Ryan JC, Chen SY, Nolan GP, Vester-Andersen MK, Pedersen JS, Gerwien J, Jensen T, and Bendtsen F
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- Adult, C-Reactive Protein metabolism, Case-Control Studies, Endothelial Cells cytology, Endothelial Cells metabolism, Female, GPI-Linked Proteins genetics, GPI-Linked Proteins metabolism, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class I metabolism, Humans, Intercellular Signaling Peptides and Proteins genetics, Intercellular Signaling Peptides and Proteins metabolism, Intestinal Mucosa metabolism, Intestines cytology, Ligands, Lymphocyte Activation, Male, Middle Aged, Monocytes metabolism, NK Cell Lectin-Like Receptor Subfamily K genetics, RNA, Messenger genetics, RNA, Messenger metabolism, CD8-Positive T-Lymphocytes cytology, Cell Movement, Crohn Disease genetics, Down-Regulation, NK Cell Lectin-Like Receptor Subfamily K metabolism
- Abstract
Interaction between the activating NKG2D receptor on lymphocytes and its ligands MICA, MICB, and ULBP1-6 modulate T and NK cell activity and may contribute to the pathogenesis of Crohn's disease (CD). NKG2D ligands are generally not expressed on the cell surface of normal, non-stressed cells, but expression of MICA and MICB in CD intestine has been reported. In this exploratory study, we further characterize the expression of NKG2D and its ligands, including the less well-described ULBP4-6, in CD, and test if NKG2D ligand interactions are involved in the migration of activated T cells into the affected mucosal compartments. Intestinal tissue from CD patients and healthy controls were analyzed by flow cytometry, mass cytometry, and immunohistochemistry for expression of NKG2D and ligands, and for cytokine release. Furthermore, NKG2D-dependent chemotaxis of activated CD8
+ T cells across a monolayer of ligand-expressing human intestinal endothelial cells was examined. Activated lymphocytes down-regulated NKG2D expression upon accumulation in inflamed CD intestine. NKG2D expression on CD56+ T and γδ T cells from inflamed tissue seemed inversely correlated with CRP levels and cytokine release. B cells, monocytes, mucosal epithelium, and vascular endothelium expressed NKG2D ligands in inflamed CD intestine. The expression of NKG2D ligands was correlated with cytokine release, but was highly variable between patients. Stimulation of vascular intestinal endothelial cells in vitro induced expression of NKG2D ligands, including MICA/B and ULBP2/6. Blockade of NKG2D on CD8+ T cells inhibited the migration over ligand-expressing endothelial cells. Intestinal induction of NKG2D ligands and ligand-induced down-regulation of NKG2D in CD suggest that the NKG2D-ligand interaction may be involved in both the activation and recruitment of NKG2D+ lymphocytes into the inflamed CD intestine., (Copyright © 2017 Elsevier Inc. All rights reserved.)- Published
- 2017
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156. IL-33 promotes growth and liver metastasis of colorectal cancer in mice by remodeling the tumor microenvironment and inducing angiogenesis.
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Zhang Y, Davis C, Shah S, Hughes D, Ryan JC, Altomare D, and Peña MM
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- Animals, Cell Line, Tumor, Colon immunology, Colorectal Neoplasms genetics, Colorectal Neoplasms immunology, Gene Expression Regulation, Neoplastic, Humans, Interleukin-33 analysis, Interleukin-33 genetics, Liver immunology, Liver Neoplasms genetics, Liver Neoplasms immunology, Liver Neoplasms pathology, Male, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Neovascularization, Pathologic genetics, Neovascularization, Pathologic immunology, Neovascularization, Pathologic pathology, Rectum immunology, Colon pathology, Colorectal Neoplasms pathology, Interleukin-33 immunology, Liver pathology, Liver Neoplasms secondary, Rectum pathology, Tumor Microenvironment
- Abstract
Liver metastasis is the major cause of death from colorectal cancer (CRC). Understanding its mechanisms is necessary for timely diagnosis and development of effective therapies. Interleukin-33 (IL-33) is an IL-1 cytokine family member that uniquely functions as a cytokine and nuclear factor. It is released by necrotic epithelial cells and activated innate immune cells, functioning as an alarmin or an early danger signal. Its role in invoking type 2 immune response has been established; however, it has contrasting roles in tumor development and metastasis. We identified IL-33 as a potently upregulated cytokine in a highly metastatic murine CRC cell line and examined its role in tumor growth and metastasis to the liver. IL-33 was transgenically expressed in murine and human adenocarcinoma and carcinoma cell lines and their growth and spontaneous metastasis to the liver were assessed in orthotopic models of CRC in wild-type C57Bl/6 and Il33 knockout mice. The results showed that increased expression of IL-33 in CRC cells enhanced their tumor take, growth, and liver metastasis. Tumor- rather than host-derived IL-33 induced the enhanced recruitment of CD11b
+ GR1+ and CD11b+ F4/80+ myeloid cells to remodel the tumor microenvironment by increased expression of mobilizing cytokines, and tumor angiogenesis by activating endothelial cells. IL-33 expression was elevated in patient tumor tissues, induced early in adenoma development, and activated by pro-inflammatory cytokines derived from the tumor microenvironment. The data suggest that tumor-derived IL-33 modulates the tumor microenvironment to potently promote colon carcinogenesis and liver metastasis, underscoring its potential as a therapeutic target. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)- Published
- 2017
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157. Improved Survival Among all Interferon-α-Treated Patients in HCV-002, a Veterans Affairs Hepatitis C Cohort of 2211 Patients, Despite Increased Cirrhosis Among Nonresponders.
- Author
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Cozen ML, Ryan JC, Shen H, Cheung R, Kaplan DE, Pocha C, Brau N, Aytaman A, Schmidt WN, Pedrosa M, Anand BS, Chang KM, Morgan T, and Monto A
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- Adult, Cohort Studies, Female, Hepatitis C epidemiology, Humans, Interferon-alpha administration & dosage, Male, Middle Aged, Proportional Hazards Models, Ribavirin administration & dosage, Ribavirin therapeutic use, United States epidemiology, United States Department of Veterans Affairs, Hepatitis C drug therapy, Interferon-alpha therapeutic use, Liver Cirrhosis etiology
- Abstract
Background: As the era of interferon-alpha (IFN)-based therapy for hepatitis C ends, long-term treatment outcomes are now being evaluated., Aim: To more fully understand the natural history of hepatitis C infection by following a multisite cohort of patients., Methods: Patients with chronic HCV were prospectively enrolled in 1999-2000 from 11 VA medical centers and followed through retrospective medical record review., Results: A total of 2211 patients were followed for an average of 8.5 years after enrollment. Thirty-one percent of patients received HCV antiviral therapy, 15 % with standard IFN/ribavirin only, 16 % with pegylated IFN/ribavirin, and 26.7 % of treated patients achieved sustained virologic response (SVR). Cirrhosis developed in 25.8 % of patients. Treatment nonresponders had a greater than twofold increase in the hazard of cirrhosis and hepatocellular carcinoma, compared to untreated patients, whereas SVR patients were only marginally protected from cirrhosis. Nearly 6 % developed hepatocellular carcinoma, and 27.1 % died during the follow-up period. Treated patients, regardless of response, had a significant survival benefit compared to untreated patients (HR 0.58, CI 0.46-0.72). Improved survival was also associated with college education, younger age, lower levels of alcohol consumption, and longer duration of medical service follow-up-factors typically associated with treatment eligibility., Conclusions: As more hepatitis C patients are now being assessed for all-oral combination therapy, these results highlight that patient compliance and limiting harmful behaviors contribute a significant proportion of the survival benefit in treated patients and that the long-term clinical benefits of SVR may be less profound than previously reported., Competing Interests: All authors declare that they have no conflict of interest related to the data or interpretation of this study.
- Published
- 2016
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158. Protective association of colonoscopy against proximal and distal colon cancer and patterns in interval cancer.
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Shergill AK, Conners EE, McQuaid KR, Epstein S, Ryan JC, Shah JN, Inadomi J, and Somsouk M
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- Adenocarcinoma diagnosis, Adenocarcinoma pathology, Adenoma diagnosis, Adenoma pathology, Aged, Aged, 80 and over, Case-Control Studies, Cohort Studies, Colon pathology, Colorectal Neoplasms diagnosis, Colorectal Neoplasms pathology, Female, Humans, Incidence, Male, Middle Aged, Odds Ratio, Protective Factors, Rectum pathology, Retrospective Studies, United States, United States Department of Veterans Affairs, Adenocarcinoma epidemiology, Adenoma epidemiology, Colonoscopy statistics & numerical data, Colorectal Neoplasms epidemiology, Early Detection of Cancer statistics & numerical data
- Abstract
Background: The protective effect of colonoscopy against proximal colorectal cancer is variable and depends on the detection and complete removal of precancerous polyps., Objective: To estimate the efficacy of colonoscopy in a medical center with open-access screening colonoscopy since 1998., Design: Nested case-control study with incidence density sampling., Setting: University-affiliated Veterans Affairs Medical Center., Patients: Colorectal cancer (CRC) cases and control subjects selected from screening age patients matched by age, gender, and date of first primary care visit., Main Outcome Measurement: Colonoscopy preceding the CRC diagnosis date., Results: A total of 20.2% of CRC cases had a colonoscopy in the preceding 10 years compared with 49.0% of control subjects (adjusted odds ratio [aOR], 0.20; 95% confidence interval [CI], 0.11-0.34). Colonoscopy was strongly associated with decreased odds of both distal CRC (aOR, 0.16; 95% CI, 0.07-0.34) and proximal CRC (aOR, 0.26; 95% CI, 0.11-0.58). The fraction of cases attributed to interval cancers was 10.5%. Missed lesions predominantly localized to the cecum and rectum, and recurrent lesions clustered in the hepatic flexure. Cecal intubation rate was 93% (98% in adequately prepped patients), and the adenoma detection rate was 45.2% in the control group., Limitations: Single-center, retrospective case-control design., Conclusion: In an open access colonoscopy program characterized by a high cecal intubation rate and adenoma detection rate, colonoscopy was strongly associated with reduced odds of both distal and proximal CRC. Among interval cancers, missed lesions clustered in the cecum and rectum and recurrent lesions in the hepatic flexure., (Published by Elsevier Inc.)
- Published
- 2015
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159. Microarray applications to understand the impact of exposure to environmental contaminants in wild dolphins (Tursiops truncatus).
- Author
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Mancia A, Abelli L, Kucklick JR, Rowles TK, Wells RS, Balmer BC, Hohn AA, Baatz JE, and Ryan JC
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- Animals, Aroclors, Atlantic Ocean, Female, Geography, Gulf of Mexico, Male, Polychlorinated Biphenyls, Real-Time Polymerase Chain Reaction, Sex Factors, Bottle-Nosed Dolphin metabolism, Environmental Exposure, Environmental Pollutants toxicity, Gene Expression Regulation drug effects, Microarray Analysis methods
- Abstract
It is increasingly common to monitor the marine environment and establish geographic trends of environmental contamination by measuring contaminant levels in animals from higher trophic levels. The health of an ecosystem is largely reflected in the health of its inhabitants. As an apex predator, the common bottlenose dolphin (Tursiops truncatus) can reflect the health of near shore marine ecosystems, and reflect coastal threats that pose risk to human health, such as legacy contaminants or marine toxins, e.g. polychlorinated biphenyls (PCBs) and brevetoxins. Major advances in the understanding of dolphin biology and the unique adaptations of these animals in response to the marine environment are being made as a result of the development of cell-lines for use in in vitro experiments, the production of monoclonal antibodies to recognize dolphin proteins, the development of dolphin DNA microarrays to measure global gene expression and the sequencing of the dolphin genome. These advances may play a central role in understanding the complex and specialized biology of the dolphin with regard to how this species responds to an array of environmental insults. This work presents the creation, characterization and application of a new molecular tool to better understand the complex and unique biology of the common bottlenose dolphin and its response to environmental stress and infection. A dolphin oligo microarray representing 24,418 unigene sequences was developed and used to analyze blood samples collected from 69 dolphins during capture-release health assessments at five geographic locations (Beaufort, NC, Sarasota Bay, FL, Saint Joseph Bay, FL, Sapelo Island, GA and Brunswick, GA). The microarray was validated and tested for its ability to: 1) distinguish male from female dolphins; 2) differentiate dolphins inhabiting different geographic locations (Atlantic coasts vs the Gulf of Mexico); and 3) study in detail dolphins resident in one site, the Georgia coast, known to be heavily contaminated by Aroclor 1268, an uncommon polychlorinated (PCB) mixture. The microarray was able to distinguish dolphins by sex, geographic location, and corroborate previously published health irregularities for the Georgia dolphins. Genes involved in xenobiotic metabolism, development/differentiation and oncogenic pathways were found to be differentially expressed in GA dolphins. The report bridges the advancements in dolphin genome sequencing to the first step towards providing a cost-effective means to screen for indicators of chemical toxin exposure as well as disease status in top level predators., (Copyright © 2014 Elsevier B.V. All rights reserved.)
- Published
- 2015
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160. Machine learning approaches to investigate the impact of PCBs on the transcriptome of the common bottlenose dolphin (Tursiops truncatus).
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Mancia A, Ryan JC, Van Dolah FM, Kucklick JR, Rowles TK, Wells RS, Rosel PE, Hohn AA, and Schwacke LH
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- Animals, Bottle-Nosed Dolphin genetics, Environmental Monitoring, Female, Male, Real-Time Polymerase Chain Reaction, Artificial Intelligence, Bottle-Nosed Dolphin metabolism, Environmental Exposure, Polychlorinated Biphenyls toxicity, Transcriptome drug effects, Water Pollutants, Chemical toxicity
- Abstract
As top-level predators, common bottlenose dolphins (Tursiops truncatus) are particularly sensitive to chemical and biological contaminants that accumulate and biomagnify in the marine food chain. This work investigates the potential use of microarray technology and gene expression profile analysis to screen common bottlenose dolphins for exposure to environmental contaminants through the immunological and/or endocrine perturbations associated with these agents. A dolphin microarray representing 24,418 unigene sequences was used to analyze blood samples collected from 47 dolphins during capture-release health assessments from five different US coastal locations (Beaufort, NC, Sarasota Bay, FL, Saint Joseph Bay, FL, Sapelo Island, GA and Brunswick, GA). Organohalogen contaminants including pesticides, polychlorinated biphenyl congeners (PCBs) and polybrominated diphenyl ether congeners were determined in blubber biopsy samples from the same animals. A subset of samples (n = 10, males; n = 8, females) with the highest and the lowest measured values of PCBs in their blubber was used as strata to determine the differential gene expression of the exposure extremes through machine learning classification algorithms. A set of genes associated primarily with nuclear and DNA stability, cell division and apoptosis regulation, intra- and extra-cellular traffic, and immune response activation was selected by the algorithm for identifying the two exposure extremes. In order to test the hypothesis that these gene expression patterns reflect PCB exposure, we next investigated the blood transcriptomes of the remaining dolphin samples using machine-learning approaches, including K-nn and Support Vector Machines classifiers. Using the derived gene sets, the algorithms worked very well (100% success rate) at classifying dolphins according to the contaminant load accumulated in their blubber. These results suggest that gene expression profile analysis may provide a valuable means to screen for indicators of chemical exposure., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
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161. Expanded use of aggressive therapies improves survival in early and intermediate hepatocellular carcinoma.
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Ho EY, Cozen ML, Shen H, Lerrigo R, Trimble E, Ryan JC, Corvera CU, and Monto A
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- Aged, Antineoplastic Agents adverse effects, Carcinoma, Hepatocellular mortality, Carcinoma, Hepatocellular pathology, Chemotherapy, Adjuvant, Humans, Kaplan-Meier Estimate, Liver Neoplasms mortality, Liver Neoplasms pathology, Male, Middle Aged, Neoplasm Staging, Proportional Hazards Models, Retrospective Studies, Risk Factors, San Francisco, Tertiary Care Centers, Time Factors, Treatment Outcome, Antineoplastic Agents therapeutic use, Carcinoma, Hepatocellular therapy, Catheter Ablation adverse effects, Catheter Ablation mortality, Hepatectomy adverse effects, Hepatectomy mortality, Liver Neoplasms therapy, Liver Transplantation adverse effects, Liver Transplantation mortality
- Abstract
Background: Despite the increasing annual incidence of hepatocellular carcinoma (HCC) in the USA, now estimated at 2.7 cases per 100 000 population, only a small proportion of patients receive treatment and 5-year survival rates range from 9% to 17%., Objectives: The present study examines the effects of multimodal treatment on survival in a mixed-stage HCC cohort, focusing on the impact of radical therapy in patients with Barcelona Clinic Liver Cancer (BCLC) stage B disease., Methods: A retrospective review of the medical records of 254 patients considered for HCC treatment between 2003 and 2011 at a large tertiary referral centre was conducted., Results: A total of 195 (76.8%) patients were treated with a median of two liver-directed interventions. Median survival time was 16 months. In proportional hazards analysis, radiofrequency ablation (RFA) and resection were associated with significantly improved 1- and 5-year survival among patients with BCLC stage 0-A disease. In patients with BCLC stage B disease, RFA conferred a survival benefit at 1 year and resection was associated with significantly improved survival at 5 years., Conclusions: As one of few studies to track the complete course of sequential HCC therapies, the findings of the present study suggest that HCC patients with intermediate-stage (BCLC stage B) disease may benefit from aggressive interventions not currently included in societal guidelines., (© 2014 International Hepato-Pancreato-Biliary Association.)
- Published
- 2014
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162. Monocyte activation by interferon α is associated with failure to achieve a sustained virologic response after treatment for hepatitis C virus infection.
- Author
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Hartigan-O'Connor DJ, Lin D, Ryan JC, Shvachko VA, Cozen ML, Segal MR, Terrault NA, Lanier LL, Manos MM, and McCune JM
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- Adult, Antigen-Presenting Cells, Case-Control Studies, Cohort Studies, Dendritic Cells, Female, Humans, Interferon alpha-2, Interferon-alpha administration & dosage, Male, Middle Aged, Polyethylene Glycols administration & dosage, Recombinant Proteins administration & dosage, Recombinant Proteins therapeutic use, Retrospective Studies, Ribavirin administration & dosage, Antiviral Agents therapeutic use, Hepatitis C drug therapy, Interferon-alpha therapeutic use, Monocytes drug effects, Monocytes physiology, Polyethylene Glycols therapeutic use, Ribavirin therapeutic use
- Abstract
Background: Interferon α (IFN-α) and ribavirin can induce a sustained virologic response (SVR) in some but not all hepatitis C virus (HCV)-infected patients. The mechanism of effective treatment is unclear. One possibility is that IFN-α differentially improves the functional capacity of classic myeloid dendritic cells (mDCs) by altering expression of surface molecules or cytokines. Others have proposed that antigen-presenting cell activation could be paradoxically detrimental during HCV infection because of the production by monocytes of substances inhibitory or toxic to plasmacytoid dendritic cells., Methods: We examined responses to in vitro IFN-α treatment of peripheral blood leukocyte samples from a retrospective treatment cohort of nearly 200 HCV-seropositive patients who had undergone antiviral therapy with ribavirin and pegylated IFN. We analyzed the variable responses of antigen-presenting cell subsets to drug., Results: We found that patients achieving SVR were no more likely to have robust mDC activation in response to IFN-α than those who did not achieve SVR. Rather, patients achieving SVR were distinguished by restrained monocyte activation in the presence of IFN-α, a factor that was second in importance only to IL28B genotype in its association with SVR., Conclusions: These results suggest that interindividual variability in the response of monocytes to IFN-α is an important determinant of treatment success with IFN-α-based regimens.
- Published
- 2014
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163. Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis.
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Johnson JG, Morey JS, Neely MG, Ryan JC, and Van Dolah FM
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- Dinoflagellida growth & development, Gene Expression Regulation, Metabolic Networks and Pathways, Oligonucleotide Array Sequence Analysis, Signal Transduction, Dinoflagellida genetics, Transcriptome
- Abstract
The toxic dinoflagellate, Karenia brevis, forms dense blooms in the Gulf of Mexico that persist for many months in coastal waters, where they can cause extensive marine animal mortalities and human health impacts. The mechanisms that enable cell survival in high density, low growth blooms, and the mechanisms leading to often rapid bloom demise are not well understood. To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate., (Published by Elsevier B.V.)
- Published
- 2012
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164. Binding and uptake of H-ferritin are mediated by human transferrin receptor-1.
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Li L, Fang CJ, Ryan JC, Niemi EC, Lebrón JA, Björkman PJ, Arase H, Torti FM, Torti SV, Nakamura MC, and Seaman WE
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- Antigens, CD genetics, Cell Line, Cloning, Molecular, Endosomes metabolism, Humans, Lysosomes metabolism, Protein Binding, Receptors, Transferrin genetics, Transferrin metabolism, Antigens, CD metabolism, Apoferritins metabolism, B-Lymphocytes metabolism, Receptors, Transferrin metabolism, T-Lymphocytes metabolism
- Abstract
Ferritin is a spherical molecule composed of 24 subunits of two types, ferritin H chain (FHC) and ferritin L chain (FLC). Ferritin stores iron within cells, but it also circulates and binds specifically and saturably to a variety of cell types. For most cell types, this binding can be mediated by ferritin composed only of FHC (HFt) but not by ferritin composed only of FLC (LFt), indicating that binding of ferritin to cells is mediated by FHC but not FLC. By using expression cloning, we identified human transferrin receptor-1 (TfR1) as an important receptor for HFt with little or no binding to LFt. In vitro, HFt can be precipitated by soluble TfR1, showing that this interaction is not dependent on other proteins. Binding of HFt to TfR1 is partially inhibited by diferric transferrin, but it is hindered little, if at all, by HFE. After binding of HFt to TfR1 on the cell surface, HFt enters both endosomes and lysosomes. TfR1 accounts for most, if not all, of the binding of HFt to mitogen-activated T and B cells, circulating reticulocytes, and all cell lines that we have studied. The demonstration that TfR1 can bind HFt as well as Tf raises the possibility that this dual receptor function may coordinate the processing and use of iron by these iron-binding molecules.
- Published
- 2010
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165. Pinch force and forearm-muscle load during routine colonoscopy: a pilot study.
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Shergill AK, Asundi KR, Barr A, Shah JN, Ryan JC, McQuaid KR, and Rempel D
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- Adult, Allied Health Personnel, Analysis of Variance, Biomechanical Phenomena, Electromyography, Female, Forearm physiology, Gastroenterology, Humans, Male, Middle Aged, Musculoskeletal Diseases prevention & control, Occupational Diseases prevention & control, Occupational Health, Pilot Projects, Probability, Stress, Mechanical, Thumb physiology, Colonoscopy methods, Muscle Strength physiology, Pinch Strength
- Abstract
Background and Objective: Overuse injuries of the hand, wrist, forearm, and shoulder are common among endoscopists and may be from repetitive pinching and gripping forces or awkward posturing. In this pilot study, we evaluated distal upper-extremity musculoskeletal load during colonoscopy (1) to confirm the feasibility of performing ergonomic measurements in endoscopists and (2) to identify tasks that may contribute to overuse injuries., Design and Subjects: Three experienced gastroenterologists were evaluated during 3 colonoscopies each., Setting: Veterans Affairs Medical Center, San Francisco, California., Main Outcome Measurement: Right-thumb pinch force using a thumb-force sensor and bilateral forearm-muscle activity using electromyography., Results: The mean duration of the 9 colonoscopies was 19.5 minutes. The highest mean (SD) right-thumb peak pinch forces occurred during left (10.4 [4.1] N) and right (10.1 [4.5] N) colon insertion, which exceeded the injury threshold of 10 N. Mean peak forearm-muscle activity was also greatest during left and right colon insertion. Activity of the left abductor pollicis longus, left extensor carpi radialis, and right extensor carpi radialis exceeded the American Conference of Industrial Hygienists (ACGIH) hand activity level (HAL) action limit. The left extensor carpi radialis was at the ACGIH HAL threshold limit., Limitations: The small sample size, no force measurement for the left thumb, and all the gastroenterologists were men., Conclusion: The pinch forces and forearm-muscle loads applied during routine colonoscopy may pose a risk for overuse injuries at the elbow and wrist.
- Published
- 2009
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166. A prospective study to examine persistent HCV reinfection in injection drug users who have previously cleared the virus.
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Currie SL, Ryan JC, Tracy D, Wright TL, George S, McQuaid R, Kim M, Shen H, and Monto A
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- Alcoholism epidemiology, Demography, Enzyme-Linked Immunosorbent Assay, Female, Follow-Up Studies, Hepacivirus genetics, Hepacivirus isolation & purification, Hepatitis C immunology, Humans, Male, Middle Aged, Prevalence, Prospective Studies, RNA, Viral genetics, Recurrence, Surveys and Questionnaires, Health Status, Hepatitis C epidemiology, Hepatitis C virology, Substance Abuse, Intravenous epidemiology
- Abstract
Background: Many HCV-infected persons with recent or ongoing injection drug use (IDU) do not receive HCV treatment due to the perceived risk of HCV reinfection. There are few prospective studies investigating HCV reinfection among IDUs., Methods: Two hundred and twenty-four persons with past or ongoing IDU were followed from 1997 to 2007. Baseline and every 6-month follow-up data were collected including demographics, IDU, and sexual behaviors. Serum was tested for the presence of HCV antibody and serially for HCV RNA. Resolvers were defined as HCV antibody and RIBA positive and RNA negative at two consecutive time points or as becoming HCV RNA negative after HCV antiviral treatment. Reinfection was defined by the presence of HCV RNA at > or =2 visits., Results: One hundred and eighty-six persons had chronic HCV and 38 had resolved HCV. The resolvers were followed for a total of 214 person-years. Forty-two percent of resolvers reported ongoing IDU, representing 58 person-years of IDU. Only one reinfection occurred in the resolvers, for a reinfection rate of 0.47 cases/100 person-years of follow-up. The single reinfection, which occurred in a person who continued to inject drugs, represents a reinfection rate of 1.75 cases/100 person-years of IDU., Conclusion: These data suggest that despite ongoing IDU, persistent HCV reinfection is lower than previously published. This can be attributed to a more clinically relevant definition of reinfection. This information will better help clinicians make informed decisions regarding HCV treatment options for patients who may continue to inject illicit drugs.
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- 2008
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167. Transcriptional profiling of whole blood and serum protein analysis of mice exposed to the neurotoxin Pacific Ciguatoxin-1.
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Ryan JC, Bottein Dechraoui MY, Morey JS, Rezvani A, Levin ED, Gordon CJ, Ramsdell JS, and Van Dolah FM
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- Animals, Antibody Formation genetics, Ciguatera Poisoning genetics, Ciguatera Poisoning immunology, Ciguatoxins, Cluster Analysis, Disease Models, Animal, Immunoassay, Male, Mice, Mice, Inbred C57BL, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Th2 Cells immunology, Time Factors, Blood Proteins metabolism, Ciguatera Poisoning blood, Gene Expression Profiling methods, Proteomics methods, RNA blood, Transcription, Genetic drug effects
- Abstract
Ciguatoxins (CTX) are a suite of cyclic polyether toxins produced by the marine dinoflagellate Gambierdiscus sp., are potent activators of voltage-gated sodium channels and a leading cause of human poisoning from food fish. This report characterizes the genomic and proteomic response in whole blood of adult male mice exposed i.p. to 264 ng/kg of the Pacific congener of CTX (P-CTX-1) at 1, 4 and 24h. Whole genome microarray expression data were filtered by tightness of fit between replicates, fold change (1.8) and p-value (10(-5)), resulting in 183 annotated genes used for trending analysis, K-means clustering and ontology classification. Genes involved with cytokine signaling, proteasome complex and ribosomal function were dominant. qPCR performed on 19 genes of interest had a correlation of 0.95 to array results by Pearson's correlation coefficient. Serum protein analysis showed small but significant changes in 6 of 60 proteins assayed: Ccl2, Ccl12, CD40, IL-10, leptin and M-CSF. In large part, the gene expression was consistent with a Th2 immune response with interesting similarities to expression seen in asthmatic models.
- Published
- 2007
- Full Text
- View/download PDF
168. Strain-dependent expression of four structurally related rat Ly49 receptors; correlation with NK gene complex haplotype and NK alloreactivity.
- Author
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Kveberg L, Dai KZ, Dissen E, Ryan JC, Rolstad B, Vaage JT, and Naper C
- Subjects
- Amino Acid Sequence, Animals, Antibodies, Monoclonal immunology, Antigens, Ly metabolism, Histocompatibility Antigens Class I metabolism, Lectins, C-Type metabolism, Ligands, Molecular Sequence Data, Polymorphism, Restriction Fragment Length, Rats, Receptors, NK Cell Lectin-Like, Antigens, Ly analysis, Antigens, Ly genetics, Haplotypes, Killer Cells, Natural immunology, Lectins, C-Type analysis, Lectins, C-Type genetics
- Abstract
Natural killer (NK) cells from certain rat strains promptly kill MHC allogeneic lymphocytes in vivo, a rejection phenomenon termed allogeneic lymphocyte cytotoxicity (ALC). ALC can be reproduced in vitro, and is preferentially mediated by a subset of NK cells expressing the Ly49 stimulatory receptor 3 (Ly49s3) in PVG strain rats. Functional studies have suggested that Ly49s3 triggers NK cell alloreactivity, but its importance relative to other Ly49 receptors has not been investigated. In this study, we have characterized three rat Ly49 receptors with close sequence similarity to Ly49s3 in the extracellular region, i.e., Ly49s4, Ly49 inhibitory receptor 3 (Ly49i3), and Ly49i4. Similar to Ly49s3, Ly49s4 mediated cellular activation while Ly49i4 inhibited NK cytolytic function. Ly49s4, -i3, and -i4 all reacted with a previously described anti-Ly49s3 monoclonal antibody (mAb) (DAR13), but not a novel mAb (STOK6), which was shown to be specific for Ly49s3. Expression of these Ly49 receptors varied markedly between inbred strains, in patterns related to their NK gene complex (NKC) haplotype, and ability to mediate ALC. Three major groups of NKC haplotypes could be discerned by restriction fragment length polymorphism analysis. Ly49s3 was present in strains from one of the groups, which corresponded with the "high" ALC responders. Ly49s3 surface expression was also markedly reduced in the presence of its putative MHC class Ib ligand(s) in MHC congenic strains. These data support the notion that Ly49s3 functions as a triggering MHC receptor both in vitro and in vivo. MHC ligands for the other three Ly49 receptors remain to be determined.
- Published
- 2006
- Full Text
- View/download PDF
169. Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray.
- Author
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Lidie KB, Ryan JC, Barbier M, and Van Dolah FM
- Subjects
- Animals, Cluster Analysis, Databases, Nucleic Acid, Dinoflagellida metabolism, Gene Library, Genes, cdc, Genome, Multigene Family, Oligonucleotide Array Sequence Analysis standards, Signal Transduction genetics, Dinoflagellida genetics, Expressed Sequence Tags chemistry, Gene Expression, Oligonucleotide Array Sequence Analysis methods
- Abstract
Karenia brevis (Davis) is the dinoflagellate responsible for nearly annual red tides in the Gulf of Mexico. Although the mechanisms regulating the growth and toxicity of this problematic organism are of considerable interest, little information is available on its molecular biology. We therefore constructed a complementary DNA library from which to gain insight into its expressed genome and to develop tools for studying its gene expression. Large-scale sequencing yielded 7001 high-quality expressed sequence tags (ESTs), which clustered into 5280 unique gene groups. The vast majority of genes expressed fell into a low-abundance class, with the highest expressed gene accounting for only 1% of the total ESTs. Approximately 29% of genes were found to have similarity to known sequences in other organisms after BLAST similarity comparisons to the GenBank public protein database using a cutoff of P < 10e(-4). We identified for the first time in a dinoflagellate a suite of conserved eukaryotic genes involved in cell cycle control, intracellular signaling, and the transcription and translation machinery. At least 40% of gene clusters displayed single nucleotide polymorphisms, suggesting the presence of multiple gene copies. The average GC content of ESTs was 51%, with a slight preference for G or C in the third codon position (53.5%). The ESTs were used to develop an oligonucleotide microarray containing 4629 unique features and 3462 replicate probes. Microarray labeling has been optimized, and the microarray has been validated for probe specificity and reproducibility. This is the first information to be developed on the expressed genome of K. brevis and provides the basis from which to begin functional genomic studies on this harmful algal bloom species.
- Published
- 2005
- Full Text
- View/download PDF
170. Molecular cloning of KLRI1 and KLRI2, a novel pair of lectin-like natural killer-cell receptors with opposing signalling motifs.
- Author
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Saether PC, Westgaard IH, Flornes LM, Hoelsbrekken SE, Ryan JC, Fossum S, and Dissen E
- Subjects
- Amino Acid Motifs, Amino Acid Sequence, Animals, Cloning, Molecular, DNA, Complementary, Killer Cells, Natural immunology, Killer Cells, Natural metabolism, Lectins, C-Type metabolism, Mice, Molecular Sequence Data, Phylogeny, Rats, Receptors, Immunologic immunology, Receptors, Immunologic metabolism, Sequence Analysis, DNA, Signal Transduction genetics, Signal Transduction immunology, Signal Transduction physiology, Lectins, C-Type genetics, Receptors, Immunologic genetics
- Abstract
We here report the molecular cloning of a novel family of killer-cell lectin-like (KLR) receptors in the rat and the mouse, termed KLRI. In both species, there are two members, KLRI1 and KLRI2. While the extracellular lectin-like domains of KLRI1 and KLRI2 are similar [74% (rat) and 83% (mouse) amino acid identity], they differ intracellularly. KLRI1 has two immunoreceptor tyrosine-based inhibition motifs (ITIMs) in the cytoplasmic domain, suggesting an inhibitory function. KLRI2 has no ITIM, but a positively charged lysine residue in the transmembrane region, suggesting association with activating adapter molecules. Klri1 and Klri2 are localized within the natural killer (NK) cell gene complex on rat chromosome 4 and mouse chromosome 6. By RT-PCR and Northern blot analysis KLRI1 and KLRI2 were selectively expressed by NK cells in both rat and mouse. Epitope-tagged expression constructs of rat KLRI1 and rat KLRI2 induced surface expression of a nondisulphide-linked protein of M(r) 36,000/39,000 and M(r) 34,000, respectively.
- Published
- 2005
- Full Text
- View/download PDF
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