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Castro-García FP, Corral-Jara KF, Escobedo-Melendez G, Sandoval-Hernandez MA, Rosenstein Y, Roman S, Panduro A, Fierro NA. Conjugated bilirubin affects cytokine profiles in hepatitis A virus infection by modulating function of signal transducer and activator of transcription factors. Immunology 2015; 143:578-87. [PMID: 24943111 DOI: 10.1111/imm.12336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 12/24/2022] Open
Abstract
Hepatitis A virus (HAV) infection is the major cause of acute liver failure in paediatric patients. The clinical spectrum of infection is variable, and liver injury is determined by altered hepatic enzyme function and bilirubin concentration. We recently reported differences in cytokine profiles between distinct HAV-induced clinical courses, and bilirubin has been recognized as a potential immune-modulator. However, how bilirubin may affect cytokine profiles underlying the variability in the course of infection has not been determined. Herein, we used a transcription factor (TF) binding site identification approach to retrospectively analyse cytokine expression in HAV-infected children and to predict the entire set of TFs associated with the expression of specific cytokine profiles. The results suggested that modulation of the activity of signal transducers and activators of transcription proteins (STATs) may play a central role during HAV infection. This led us to compare the degree of STAT phosphorylation in peripheral blood lymphoid cells (PBLCs) from paediatric patients with distinct levels of conjugated bilirubin (CB). Low CB levels in sera were associated with increased STAT-1 and STAT-5 phosphorylation. A positive correlation was observed between the serum interleukin-6 (IL-6) content and CB values, whereas higher levels of CB correlated with reduced serum IL-8 values and with a reduction in the proportion of PBLCs positive for STAT-5 phosphorylation. When CB was used to stimulate patients' PBLCs in vitro, the levels of IL-6 and tumour necrosis factor-α were increased. The data showed that bilirubin plays a role in STAT function and affects cytokine profile expression during HAV infection.
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Affiliation(s)
- Flor P Castro-García
- Unidad de Inmunovirología, Hospital Civil de Guadalajara Fray Antonio Alcalde, Guadalajara, Mexico; Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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Li MD, Wang J, Niu T, Ma JZ, Seneviratne C, Ait-Daoud N, Saadvandi J, Morris R, Weiss D, Campbell J, Haning W, Mawhinney DJ, Weis D, McCann M, Stock C, Kahn R, Iturriaga E, Yu E, Elkashef A, Johnson BA. Transcriptome profiling and pathway analysis of genes expressed differentially in participants with or without a positive response to topiramate treatment for methamphetamine addiction. BMC Med Genomics 2014; 7:65. [PMID: 25495887 PMCID: PMC4279796 DOI: 10.1186/s12920-014-0065-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/19/2014] [Indexed: 01/25/2023] Open
Abstract
Background Developing efficacious medications to treat methamphetamine dependence is a global challenge in public health. Topiramate (TPM) is undergoing evaluation for this indication. The molecular mechanisms underlying its effects are largely unknown. Examining the effects of TPM on genome-wide gene expression in methamphetamine addicts is a clinically and scientifically important component of understanding its therapeutic profile. Methods In this double-blind, placebo-controlled clinical trial, 140 individuals who met the DSM-IV criteria for methamphetamine dependence were randomized to receive either TPM or placebo, of whom 99 consented to participate in our genome-wide expression study. The RNA samples were collected from whole blood for 50 TPM- and 49 placebo-treated participants at three time points: baseline and the ends of weeks 8 and 12. Genome-wide expression profiles and pathways of the two groups were compared for the responders and non-responders at Weeks 8 and 12. To minimize individual variations, expression of all examined genes at Weeks 8 and 12 were normalized to the values at baseline prior to identification of differentially expressed genes and pathways. Results At the single-gene level, we identified 1054, 502, 204, and 404 genes at nominal P values < 0.01 in the responders vs. non-responders at Weeks 8 and 12 for the TPM and placebo groups, respectively. Among them, expression of 159, 38, 2, and 21 genes was still significantly different after Bonferroni corrections for multiple testing. Many of these genes, such as GRINA, PRKACA, PRKCI, SNAP23, and TRAK2, which are involved in glutamate receptor and GABA receptor signaling, are direct targets for TPM. In contrast, no TPM drug targets were identified in the 38 significant genes for the Week 8 placebo group. Pathway analyses based on nominally significant genes revealed 27 enriched pathways shared by the Weeks 8 and 12 TPM groups. These pathways are involved in relevant physiological functions such as neuronal function/synaptic plasticity, signal transduction, cardiovascular function, and inflammation/immune function. Conclusion Topiramate treatment of methamphetamine addicts significantly modulates the expression of genes involved in multiple biological processes underlying addiction behavior and other physiological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0065-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Ju Wang
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Tianhua Niu
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Jennie Z Ma
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | | | - Nassima Ait-Daoud
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | | | - Rana Morris
- Information Management Consultants, Reston, USA.
| | - David Weiss
- Department of Veterans Affairs Cooperative Studies Program Coordination Center, Perry Point, USA.
| | - Jan Campbell
- Department of Psychiatry, University of Missouri, Kansas City, USA.
| | | | | | - Denis Weis
- Lutheran Hospital Office of Research, Des Moines, USA.
| | | | - Christopher Stock
- Department of Veterans Affairs, Salt Lake City Health Care System, Salt Lake City, USA.
| | - Roberta Kahn
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
| | - Erin Iturriaga
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
| | - Elmer Yu
- Veterans Administration Medical Center, Philadelphia, USA.
| | - Ahmed Elkashef
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
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Xie S, Moya C, Bilgin B, Jayaraman A, Walton SP. Emerging affinity-based techniques in proteomics. Expert Rev Proteomics 2010; 6:573-83. [PMID: 19811078 DOI: 10.1586/epr.09.74] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteomes of interest, such as the human proteome, have such complexity that no single technique is adequate for the complete analysis of the constituents. Depending on the goal (e.g., identification of a novel protein vs measurement of the level of a known protein), the tools required can vary significantly. While existing methods provide valuable information, their limitations drive the development of complementary, innovative methods to achieve greater breadth of coverage, dynamic range or specificity of analysis. We will discuss affinity-based methods and their applications, focusing on their unique advantages. In addition, we will describe emerging methods with potential value to proteomics, as well as the challenges that remain for proteomic studies.
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Affiliation(s)
- Shengnan Xie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
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Wren JD, Gusev Y, Isokpehi RD, Berleant D, Braga-Neto U, Wilkins D, Bridges S. Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 2009; 10 Suppl 11:S1. [PMID: 19811674 PMCID: PMC3313274 DOI: 10.1186/1471-2105-10-s11-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hurst RE. Does the biomarker search paradigm need re-booting? BMC Urol 2009; 9:1. [PMID: 19250539 PMCID: PMC2654904 DOI: 10.1186/1471-2490-9-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 02/27/2009] [Indexed: 11/30/2022] Open
Abstract
The clinical problem of bladder cancer is its high recurrence and progression, and that the most sensitive and specific means of monitoring is cystoscopy, which is invasive and has poor patient compliance. Biomarkers for recurrence and progression could make a great contribution, but in spite of decades of research, no biomarkers are commercially available with the requisite sensitivity and specificity. In the post-genomic age, the means to search the entire genome for biomarkers has become available, but the conventional approaches to biomarker discovery are entirely inadequate to yield results with the new technology. Finding clinically useful biomarker panels with sensitivity and specificity equal to that of cystoscopy is a problem of systems biology.
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Wren JD, Wilkins D, Fuscoe JC, Bridges S, Winters-Hilt S, Gusev Y. Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 2008; 9 Suppl 9:S1. [PMID: 18793454 PMCID: PMC2537572 DOI: 10.1186/1471-2105-9-s9-s1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Jonathan D Wren
- Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation; 825 N.E. 13th Street, Oklahoma City, OK 73104-5005, USA.
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