1
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Zhao R, Liu JH, Qiu ZL. Value of serum iron and urine neutrophil gelatinase-associated lipocalin in predicting the mortality of critically ill patients with sepsis. CLIN INVEST MED 2024; 47:4-12. [PMID: 38546383 DOI: 10.3138/cim-2024-2672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
INTRODUCTION We aimed to investigate the association of iron metabolism-related parameters with 60-day mortality in critically ill patients with sepsis. METHODS Serum or urine concentrations of iron metabolism-related parameters on intensive care unit admission were measured in a prospective cohort of 133 eligible patients with sepsis according to the Sepsis-3 criteria, and these values were compared between survivors and nonsurvivors, categorized according to their 60-day survival status. Cox regression analyses were performed to examine the association between iron parameters and 60-day mortality. Kaplan-Meier methods were used to illustrate the differences in survival between different iron parameters. RESULTS Of the 133 patients included in the study, 61 (45.8%) had died by day 60. After adjusting for confounding variables, higher concentrations of serum iron (cut-off 9.5 μmol/mL) and higher concentrations of urine neutrophil gelatinase-associated lipocalin (uNGAL; cut-off 169.3 ng/mL) were associated with a significantly greater risk of death in the Cox regression analysis. These two biomarkers combined with Sequential Organ Failure Assessment (SOFA) scores increased the area under the receiver operating characteristic (AUROC) curve to 0.85. DISCUSSION These findings suggest that higher concentrations of serum iron and uNGAL are each associated with higher 60-day mortality, and they add significant accuracy to this prediction in combination with SOFA. Abbreviations: uNGAL: urine neutrophil gelatinase-associated lipocalin; ICU: intensive care unit; SOFA: Sequential Organ Failure Assessment; APACHE II: the Acute Physiology and Chronic Health Evaluation II; ELISA: enzyme-linked immunosorbent assay; HR: hazard ratio; CIs: confidence intervals; WBC: white blood cell; TBIL: total bilirubin.
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Affiliation(s)
- Rui Zhao
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
- These authors contributed equally to this work
| | - Jiang-Hua Liu
- Department of Medical Records and Statistics, Shanghai PuDong Guangming Hospital of Traditional Chinese Medicine, Shanghai, China
- These authors contributed equally to this work
| | - Ze-Liang Qiu
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Emergency, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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2
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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3
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Kapp KL, Ji Choi M, Bai K, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. PATHWAYS ASSOCIATED WITH POSITIVE SEPSIS SURVIVAL OUTCOMES IN AFRICAN AMERICAN/BLACK AND NON-HISPANIC WHITE PATIENTS WITH URINARY TRACT INFECTION. Shock 2023; 60:362-372. [PMID: 37493584 PMCID: PMC10527228 DOI: 10.1097/shk.0000000000002176] [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] [Indexed: 07/27/2023]
Abstract
ABSTRACT Urinary tract infections (UTIs) are a common cause of sepsis worldwide. Annually, more than 60,000 US deaths can be attributed to sepsis secondary to UTIs, and African American/Black adults have higher incidence and case-fatality rates than non-Hispanic White adults. Molecular-level factors that may help partially explain differences in sepsis survival outcomes between African American/Black and Non-Hispanic White adults are not clear. In this study, patient samples (N = 166) from the Protocolized Care for Early Septic Shock cohort were analyzed using discovery-based plasma proteomics. Patients had sepsis secondary to UTIs and were stratified according to self-identified racial background and sepsis survival outcomes. Proteomics results suggest patient heterogeneity across mechanisms driving survival from sepsis secondary to UTIs. Differentially expressed proteins (n = 122, false discovery rate-adjusted P < 0.05) in Non-Hispanic White sepsis survivors were primarily in immune system pathways, while differentially expressed proteins (n = 47, false discovery rate-adjusted P < 0.05) in African American/Black patients were mostly in metabolic pathways. However, in all patients, regardless of racial background, there were 16 differentially expressed proteins in sepsis survivors involved in translation initiation and shutdown pathways. These pathways are potential targets for prognostic intervention. Overall, this study provides information about molecular factors that may help explain disparities in sepsis survival outcomes among African American/Black and Non-Hispanic White patients with primary UTIs.
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Affiliation(s)
- Kathryn L. Kapp
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kun Bai
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A. Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C. Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M. Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
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4
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Kapp KL, Arul AB, Zhang KC, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. Proteomic changes associated with racial background and sepsis survival outcomes. Mol Omics 2022; 18:923-937. [PMID: 36097965 DOI: 10.1039/d2mo00171c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intra-abdominal infection is a common cause of sepsis, and intra-abdominal sepsis leads to ∼156 000 U.S. deaths annually. African American/Black adults have higher incidence and mortality rates from sepsis compared to Non-Hispanic White adults. A limited number of studies have traced survival outcomes to molecular changes; however, these studies primarily only included Non-Hispanic White adults. Our goal is to better understand molecular changes that may contribute to differences in sepsis survival in African American/Black and Non-Hispanic White adults with primary intra-abdominal infection. We employed discovery-based plasma proteomics of patient samples from the Protocolized Care for Early Septic Shock (ProCESS) cohort (N = 107). We identified 49 proteins involved in the acute phase response and complement system whose expression levels are associated with both survival outcome and racial background. Additionally, 82 proteins differentially-expressed in survivors were specific to African American/Black or Non-Hispanic White patients, suggesting molecular-level heterogeneity in sepsis patients in key inflammatory pathways. A smaller, robust set of 19 proteins were in common in African American/Black and Non-Hispanic White survivors and may represent potential universal molecular changes in sepsis. Overall, this study identifies molecular factors that may contribute to differences in survival outcomes in African American/Black patients that are not fully explained by socioeconomic or other non-biological factors.
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Affiliation(s)
- Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA
| | - Kevin C Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.,Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
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5
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He H, Huang T, Guo S, Yu F, Shen H, Shao H, Chen K, Zhang L, Wu Y, Tang X, Yuan X, Liu J, Zhou Y. Identification of a novel sepsis prognosis model and analysis of possible drug application prospects: Based on scRNA-seq and RNA-seq data. Front Immunol 2022; 13:888891. [PMID: 36389695 PMCID: PMC9650379 DOI: 10.3389/fimmu.2022.888891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/11/2022] [Indexed: 08/18/2023] Open
Abstract
Sepsis is a disease with a high morbidity and mortality rate. At present, there is a lack of ideal biomarker prognostic models for sepsis and promising studies using prognostic models to predict and guide the clinical use of medications. In this study, 71 differentially expressed genes (DEGs) were obtained by analyzing single-cell RNA sequencing (scRNA-seq) and transcriptome RNA-seq data, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analyses were performed on these genes. Then, a prognosis model with CCL5, HBD, IFR2BP2, LTB, and WFDC1 as prognostic signatures was successfully constructed after univariate LASSO regression analysis and multivariate Cox regression analysis. Kaplan-Meier (K-M) survival analysis, receiver operating characteristic (ROC) time curve analysis, internal validation, and principal component analysis (PCA) further validated the model for its high stability and predictive power. Furthermore, based on a risk prediction model, gene set enrichment analysis (GSEA) showed that multiple cellular functions and immune function signaling pathways were significantly different between the high- and low-risk groups. In-depth analysis of the distribution of immune cells in healthy individuals and sepsis patients using scRNA-seq data revealed immunosuppression in sepsis patients and differences in the abundance of immune cells between the high- and low-risk groups. Finally, the genetic targets of immunosuppression-related drugs were used to accurately predict the potential use of clinical agents in high-risk patients with sepsis.
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Affiliation(s)
- Haihong He
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Tingting Huang
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Shixing Guo
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Fan Yu
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Hongwei Shen
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Haibin Shao
- Department of General Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Keyan Chen
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Lijun Zhang
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yunfeng Wu
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xi Tang
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xinhua Yuan
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jiao Liu
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yiwen Zhou
- Department of Emergency Laboratory, Clinical Laboratory Medical Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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6
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Li M, Ren R, Yan M, Chen S, Chen C, Yan J. Identification of novel biomarkers for sepsis diagnosis via serum proteomic analysis using iTRAQ-2D-LC-MS/MS. J Clin Lab Anal 2021; 36:e24142. [PMID: 34825737 PMCID: PMC8761403 DOI: 10.1002/jcla.24142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/06/2021] [Accepted: 11/13/2021] [Indexed: 11/09/2022] Open
Abstract
Background Sepsis is a common cause of morbidity and mortality in the ICU patients. Early diagnosis and appropriate patient management is the key to improve the patient survival and to limit disabilities in sepsis patients. This study was aimed to find new diagnostic biomarkers of sepsis. Methods In this study, serum proteomic profiles in sepsis patients by iTRAQ2D‐LC‐MS/MS. Thirty seven differentially expressed proteins were identified in patients with sepsis, and six proteins including ApoC3, SERPINA1, VCAM1, B2M, GPX3, and ApoE were selected for further verification by ELISA and immunoturbidimetry in 53 patients of non‐sepsis, 37 patients of sepsis, and 35 patients of septic shock. Descriptive statistics, functional enrichment analysis, and ROC curve analysis were conducted. Results The level of ApoC3 was gradually decreased among non‐sepsis, sepsis, and septic shock groups (p = 0.049). The levels of VCAM1 (p = 0.010), B2M (p = 0.004), and ApoE (p = 0.039) were showing an increased tread in three groups, with the peak values of B2M and ApoE in the sepsis group. ROC curve analysis for septic diagnosis showed that the areas under ROC curve (AUC) of ApoC3, VCAM1, B2M, and ApoE were 0.625, 0.679, 0.581, and 0.619, respectively, which were lower than that of PCT (AUC 0.717) and CRP (AUC 0.706), but there were no significant differences between each index and PCT or CRP. The combination including four validated indexes and two classical infection indexes for septic diagnosis had the highest AUC‐ROC of 0.772. Conclusion Proteins of ApoC3, VCAM1, B2M, and ApoE provide a supplement to classical biomarkers for septic diagnosis.
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Affiliation(s)
- Meng Li
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Rongrong Ren
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Molei Yan
- Department of Intensive Care, Zhejiang Hospital, Hangzhou, China
| | - Shangzhong Chen
- Department of Intensive Care, Zhejiang Hospital, Hangzhou, China
| | - Chen Chen
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Jing Yan
- Department of Intensive Care, Zhejiang Hospital, Hangzhou, China
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7
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Miao H, Chen S, Ding R. Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics. Front Immunol 2021; 12:733537. [PMID: 34745104 PMCID: PMC8566982 DOI: 10.3389/fimmu.2021.733537] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.
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Affiliation(s)
- He Miao
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, China
| | - Song Chen
- Department of Trauma Intensive Care Unit, The First Affiliated Hospital of Hainan Medical University, Haikou, China.,Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Renyu Ding
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, China
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8
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Singh A, Jha RR, Kamal R, Kesavachandran C, Patel DK. Dispersive liquid–liquid microextraction for the analysis of specific marker compounds in human exposed with Polyaromatic hydrocarbons (PAHs). Microchem J 2021. [DOI: 10.1016/j.microc.2021.106261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Schuurman AR, Reijnders TDY, Kullberg RFJ, Butler JM, van der Poll T, Wiersinga WJ. Sepsis: deriving biological meaning and clinical applications from high-dimensional data. Intensive Care Med Exp 2021; 9:27. [PMID: 33961170 PMCID: PMC8105470 DOI: 10.1186/s40635-021-00383-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The pathophysiology of sepsis is multi-facetted and highly complex. As sepsis is a leading cause of global mortality that still lacks targeted therapies, increased understanding of its pathogenesis is vital for improving clinical care and outcomes. An increasing number of investigations seeks to unravel the complexity of sepsis through high-dimensional data analysis, enabled by advances in -omics technologies. Here, we summarize progress in the following major -omics fields: genomics, epigenomics, transcriptomics, proteomics, lipidomics, and microbiomics. We describe what these fields can teach us about sepsis, and highlight current trends and future challenges. Finally, we focus on multi-omics integration, and discuss the challenges in deriving biological meaning and clinical applications from these types of data.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Robert F J Kullberg
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands. .,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.
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10
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Balan P, Chong YS, Lin Q, Lim TK, Suriyanarayanan T, Udawatte NS, Wong ML, Lopez V, He HG, Seneviratne CJ. Salivary Proteomic Profiling Identifies Role of Neutrophil Extracellular Traps Formation in Pregnancy Gingivitis. Immunol Invest 2021; 51:103-119. [PMID: 33902370 DOI: 10.1080/08820139.2020.1810704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Pregnancy gingivitis peaks during mid-pregnancy and resolves transiently towards the postpartum period. However, the role of maternal immune response in orchestrating gingival inflammation has not yet been fully understood. Hence, in this study, we examined the salivary protein profile during the three trimesters of pregnancy, in context to pregnancy gingivitis, employing iTRAQ-based quantitative proteomics. Unstimulated saliva was collected from 10 subjects in each trimester of pregnancy and postpartum period. Samples were analysed using iTRAQ analysis and ELISA and SEM was performed to validate results. Neutrophil mediated immune response was overrepresented in all three trimesters of pregnancy, despite the decrease in phagocytic responses during the second and third trimesters. ELISA showed a significantly higher Neutrophil Extracellular Traps (NETs) formation in the third trimester of pregnancy coinciding with the resolution of pregnancy gingivitis. The NETs-associated proteins (neutrophil elastase and myeloperoxidase) showed a positive correlation with estrogen hormones, which was also highest during the third trimester. Sex hormone-driven NETs formation could be the mainstay of defence that contributes to the remission of pregnancy gingivitis. This study has provided a new insight into the role of immune-modulation in pregnancy gingivitis, which will aid development of new therapeutics for managing pregnancy gingivitis in future.
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Affiliation(s)
- Preethi Balan
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, National Dental Center Singapore.,Oral health Academic Clinical Program, Duke NUS Medical School, Singapore
| | - Yap Seng Chong
- Department of Obstetrics and Gynecology, National University Hospital, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, National Dental Center Singapore.,Oral health Academic Clinical Program, Duke NUS Medical School, Singapore
| | - Nadeeka Shiyamalee Udawatte
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, National Dental Center Singapore
| | - Mun Loke Wong
- Discipline of Oral Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Violeta Lopez
- School of Nursing, Hubei University of Medicine, Shiyan, China
| | - Hong-Gu He
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chaminda Jayampath Seneviratne
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, National Dental Center Singapore.,Oral health Academic Clinical Program, Duke NUS Medical School, Singapore
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11
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Ge C, Feng N, Hu C, Tang Y, Li X, Wang X. Transwell isolation and difference analysis of capacitated boar sperm proteins based on the iTRAQ technique. Theriogenology 2021; 168:13-24. [PMID: 33839467 DOI: 10.1016/j.theriogenology.2021.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022]
Abstract
During capacitation, proteins in boar sperm are released to maintain the stability of their own state and membrane structure. No studies have analyzed the differences between retained proteins and released proteins during sperm capacitation. In the present study, a Transwell chamber and polycarbonate membrane were used to separate the proteins of boar sperm and their released proteins. Isotopically labeled relative and absolute quantification (iTRAQ) was used to analyze each compartment protein. A total of 108 differential proteins were identified in the upper and lower chambers of the Transwell, among which 27 were significantly upregulated (p-value≤0.05 and |log2 (fold change)|≥1) and 81 were significantly downregulated (p-value≤0.05 and |log2 (fold change)|≤1). These differential proteins were mainly involved in biological processes (e.g., the regulation of cysteine peptidase activity, transmembrane transportation, ion transportation and ATP synthesis) and major signaling pathways (e.g., glutathione/galactose metabolism, cellular adhesion and PI3K-Akt), and most of them interacted with each other to some extent. In conclusion, retained proteins and released proteins of capacitated sperm were effectively separated using a Transwell chamber, and differential proteins were successfully identified from among the proteins. Bioinformatics analysis suggested that these differential proteins affect sperm capacitation mainly by adjusting sperm energy metabolism, motion characteristics and acrosome membrane status.
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Affiliation(s)
- Chenling Ge
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Ni Feng
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Chuanhuo Hu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Yinsheng Tang
- Guangxi Work Station of Livestock & Poultry Breed Improvement, Nanning, 530001, China.
| | - Xun Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Xiaoye Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
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12
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Wang S, Wang Z, Li J, Qin J, Song J, Li Y, Zhao L, Zhang X, Guo H, Shao C, Kong B, Liu Z. Splicing factor USP39 promotes ovarian cancer malignancy through maintaining efficient splicing of oncogenic HMGA2. Cell Death Dis 2021; 12:294. [PMID: 33731694 PMCID: PMC7969951 DOI: 10.1038/s41419-021-03581-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/16/2022]
Abstract
Aberrant expression of splicing factors was found to promote tumorigenesis and the development of human malignant tumors. Nevertheless, the underlying mechanisms and functional relevance remain elusive. We here show that USP39, a component of the spliceosome, is frequently overexpressed in high-grade serous ovarian carcinoma (HGSOC) and that an elevated level of USP39 is associated with a poor prognosis. USP39 promotes proliferation/invasion in vitro and tumor growth in vivo. Importantly, USP39 was transcriptionally activated by the oncogene protein c-MYC in ovarian cancer cells. We further demonstrated that USP39 colocalizes with spliceosome components in nuclear speckles. Transcriptomic analysis revealed that USP39 deletion led to globally impaired splicing that is characterized by skipped exons and overrepresentation of introns and intergenic regions. Furthermore, RNA immunoprecipitation sequencing showed that USP39 preferentially binds to exon-intron regions near 5' and 3' splicing sites. In particular, USP39 facilitates efficient splicing of HMGA2 and thereby increases the malignancy of ovarian cancer cells. Taken together, our results indicate that USP39 functions as an oncogenic splicing factor in ovarian cancer and represents a potential target for ovarian cancer therapy.
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Affiliation(s)
- Shourong Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.,Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zixiang Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.,Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jieyin Li
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Junchao Qin
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jianping Song
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China
| | - Ling Zhao
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xiyu Zhang
- Molecular Medicine and Genetics, Cheeloo College of Medicine, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Haiyang Guo
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250012, China
| | - Changshun Shao
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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13
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Katam R, Shokri S, Murthy N, Singh SK, Suravajhala P, Khan MN, Bahmani M, Sakata K, Reddy KR. Proteomics, physiological, and biochemical analysis of cross tolerance mechanisms in response to heat and water stresses in soybean. PLoS One 2020; 15:e0233905. [PMID: 32502194 PMCID: PMC7274410 DOI: 10.1371/journal.pone.0233905] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/14/2020] [Indexed: 01/11/2023] Open
Abstract
Water stress (WS) and heat stress (HS) have a negative effect on soybean plant growth and crop productivity. Changes in the physiological characteristics, proteome, and specific metabolites investigated on molecular and cellular functions were studied in two soybean cultivars exposed to different heat and water stress conditions independently and in combination. Leaf protein composition was studied using 2-DE and complemented with MALDI TOF mass spectrometry. While the two cultivars displayed genetic variation in response to water and heat stress, thirty-nine proteins were significantly altered in their relative abundance in response to WS, HS and combined WS+HS in both cultivars. A majority of these proteins were involved in metabolism, response to heat and photosynthesis showing significant cross-tolerance mechanisms. This study revealed that MED37C, a probable mediator of RNA polymerase transcription II protein, has potential interacting partners in Arabidopsis and signified the marked impact of this on the PI-471938 cultivar. Elevated activities in antioxidant enzymes indicate that the PI-471938 cultivar can restore the oxidation levels and sustain the plant during the stress. The discovery of this plant's development of cross-stress tolerance could be used as a guide to foster ongoing genetic modifications in stress tolerance.
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Affiliation(s)
- Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, Florida, United States of America
| | - Sedigheh Shokri
- Department of Biological Sciences, Florida A&M University, Tallahassee, Florida, United States of America
- Department of Horticulture Sciences, College of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Nitya Murthy
- Department of Biological Sciences, Florida A&M University, Tallahassee, Florida, United States of America
- Kentucky College of Optometry, University of Pikeville, Pikeville, Kentucky, United States of America
| | - Shardendu K. Singh
- Mississippi State University, Mississippi, Mississippi, United States of America
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Mudassar Nawaz Khan
- Institute of Biotechnology & Genetic Engineering, University of Agriculture, Peshawar, Pakistan
| | - Mahya Bahmani
- Department of Agronomy and Plant Breeding, College of Agricultural Sciences & Engineering, University of Tehran, Tehran, Iran
| | - Katsumi Sakata
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi City, Gunma, Japan
| | - Kambham Raja Reddy
- Mississippi State University, Mississippi, Mississippi, United States of America
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14
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Liu Z, Zhou Z, Wang L, Zhang Y, Zong Y, Zheng Y, Li M, Wang W, Song L. A Signaling Pathway to Mediate the Combined Immunomodulation of Acetylcholine and Enkephalin in Oyster Crassostrea gigas. Front Immunol 2020; 11:616. [PMID: 32362893 PMCID: PMC7180215 DOI: 10.3389/fimmu.2020.00616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
Molluscs have evolved a primitive but complete neuroendocrine-immune (NEI) system with a vast array of neurotransmitters to conduct both humoral and cellular immunomodulation. Previous studies have illustrated the immune functions of several key neurotransmitters. However, the combined effects of multiple neurotransmitters and the signaling pathway to mediate such immunomodulation have not been well-understood. In the present study, iTRAQ and LC-ESI-MS/MS approaches were employed to investigate the combined immunomodulation functions of two crucial neurotransmitters, acetylcholine (ACh), and [Met5]-enkephalin (ENK), in oyster Crassostrea gigas. A total number of 5,379 proteins were identified from hemocytes of oysters after the treatments with Ach and ENK separately or simultaneously, and 1,475 of them were found to be significantly up-regulated, while 1,115 of them were significantly down-regulated. The protein expression patterns in the groups treated by ACh and ENK separately were quite similar, which were dramatically different from that in the group treated by ACh+ENK. One hundred seventy-two proteins were found to be differentially expressed in all the three neurotransmitter treatment groups. Functional validation suggested that ACh and ENK possibly modulate the immune response in oyster hemocytes by enhancing pathogen recognition, cell apoptosis, and the enzyme activities of superoxide dismutase (SOD). Moreover, GO enrichment and co-expression network analyses implied that the combined immunomodulation of ACh and ENK might be mediated by p53, EGF-R–ErbB, and Fc gamma R (FcγR) signaling pathways. These results collectively indicated that multiple neurotransmitters executed a combined and ordered immune regulation through common signaling cascades in molluscs, which was under delicate control to maintain the homeostasis.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Yukun Zhang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Yanan Zong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Yan Zheng
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Meijia Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
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15
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Zhang L, Huang J, Lin Q, Ma Y, Xia R, Zhu Y, Abudubari S. Serum Proteomic Profiling Analysis of Rats Chronically Exposed to Arsenic. Med Sci Monit 2019; 25:9923-9932. [PMID: 31874112 PMCID: PMC6941779 DOI: 10.12659/msm.918696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Arsenic (As) is an environmental contaminant, and As pollution in water and soil is a public health issue worldwide. As exposure is associated with the incidence of many disorders, such as arteriosclerosis, diabetes, neurodegenerative diseases, and renal dysfunction. However, the mechanism of As toxicity remains unclear. Material/Methods We investigated the changes in serum protein profiles of rats chronically exposed to As. Twenty healthy rats were randomly divided into 4 groups, and sodium arsenite of varying final concentrations (0, 2, 10, and 50 mg/L, respectively) was add into the drinking water for each group. The administration lasted for 3 months. Two proteomic strategies, isobaric tags for relative and absolute quantitation (iTRAQ), and 2-dimensional gel electrophoresis (2-DE), were employed to screen the differential serum proteins between control and arsenite exposure groups. Results We identified a total of 27 differentially-expressed proteins, among which 9 proteins were significantly upregulated and 18 were downregulated by As exposure. Many of the differentially-expressed proteins were related to fat digestion and absorption, including 5 apolipoproteins, which indicated lipid metabolism may be the most affected by As exposure. Conclusions This study revealed the influence of As on lipid metabolism, suggesting an increased potential risk of relevant diseases in subjects chronically exposed to As.
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Affiliation(s)
- Ling Zhang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Jia Huang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland).,School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Qin Lin
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yan Ma
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Rongxiang Xia
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yuming Zhu
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Saimaitikari Abudubari
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
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16
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Su L, Pan P, Yan P, Long Y, Zhou X, Wang X, Zhou R, Wen B, Xie L, Liu D. Role of vimentin in modulating immune cell apoptosis and inflammatory responses in sepsis. Sci Rep 2019; 9:5747. [PMID: 30952998 PMCID: PMC6451033 DOI: 10.1038/s41598-019-42287-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 03/27/2019] [Indexed: 01/04/2023] Open
Abstract
New diagnostic biomarkers or therapeutic targets for sepsis have substantial significance for critical care medicine. In this study, 192 differentially expressed proteins were selected through iTRAQ. Based on cluster analysis of protein expression dynamics and protein-protein interactions, hemopexin, vimentin, and heat shock protein 90 were selected for further investigation. It was demonstrated that serum vimentin (VIM) levels were significantly increased in patients with sepsis and septic shock compared to controls and that VIM expression was significantly increased in lymphocytes isolated from septic shock and sepsis patients compared to controls. Moreover, a nonsurvivor group had higher serum VIM levels and VIM expression in lymphocytes. Caspase-3 was significantly upregulated in Jurkat T cells lacking VIM and when exposed to LPS compared to control cells. In contrast, caspase-3 was reduced nearly 40% in cells over-expressing VIM. IL-2, IL-10 and IFN-α levels were significantly decreased in cells lacking VIM compared to control cells, whereas they were not significantly altered in cells over-expressing VIM. These findings suggest that VIM modulates lymphocyte apoptosis and inflammatory responses and that VIM could be a new target for the diagnosis and prognostic prediction of patients with sepsis or septic shock.
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Affiliation(s)
- Longxiang Su
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Pan Pan
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili the 6th, Dongcheng District, Beijing, 100050, China
| | - Peng Yan
- Department of Respiratory and Critical Care Medicine, Chinese PLA General Hospital, 28th Fuxing Rd, Haidian District, Beijing, 100853, China
| | - Yun Long
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Xiang Zhou
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Xiaoting Wang
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Ruo Zhou
- Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, 518083, Guangdong Province, China
| | - Bo Wen
- Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, 518083, Guangdong Province, China
| | - Lixin Xie
- Department of Respiratory and Critical Care Medicine, Chinese PLA General Hospital, 28th Fuxing Rd, Haidian District, Beijing, 100853, China.
| | - Dawei Liu
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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17
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He M, Luo P, Hong J, Wang X, Wu H, Zhang R, Qu F, Xiang Y, Xu W. Structural Analysis of Biomolecules through a Combination of Mobility Capillary Electrophoresis and Mass Spectrometry. ACS OMEGA 2019; 4:2377-2386. [PMID: 31459477 PMCID: PMC6648644 DOI: 10.1021/acsomega.8b03224] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/24/2019] [Indexed: 05/08/2023]
Abstract
The 3D structures of biomolecules determine their biological function. Established methods in biomolecule structure determination typically require purification, crystallization, or modification of target molecules, which limits their applications for analyzing trace amounts of biomolecules in complex matrices. Here, we developed instruments and methods of mobility capillary electrophoresis (MCE) and its coupling with MS for the 3D structural analysis of biomolecules in the liquid phase. Biomolecules in complex matrices could be separated by MCE and sequentially detected by MS. The effective radius and the aspect ratio of each separated biomolecule were simultaneously determined through the separation by MCE, which were then used as restraints in determining biomolecule conformations through modeling. Feasibility of this method was verified by analyzing a mixture of somatostatin and bradykinin, two peptides with known liquid-phase structures. Proteins could also be structurally analyzed using this method, which was demonstrated for lysozyme. The combination of MCE and MS for complex sample analysis was also demonstrated. MCE and MCE-MS would allow us to analyze trace amounts of biomolecules in complex matrices, which has the potential to be an alternative and powerful biomolecule structure analysis technique.
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Affiliation(s)
- Muyi He
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Pan Luo
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaofeng Wang
- Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haimei Wu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ye Xiang
- Beijing
Advanced Innovation Center for Structural Biology, Department of Basic
Medical Sciences, School of Medicine, Tsinghua
University, Beijing 100084, China
- E-mail: (Y.X.)
| | - Wei Xu
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
- E-mail: (W.X.)
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18
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Průcha M, Zazula R, Russwurm S. Sepsis Diagnostics in the Era of "Omics" Technologies. Prague Med Rep 2018; 119:9-29. [PMID: 29665344 DOI: 10.14712/23362936.2018.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy. Current progress in the use of systems biology technologies brings us hope that by using big data from clinical trials such biomarkers will be found.
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Affiliation(s)
- Miroslav Průcha
- Department of Clinical Biochemistry, Haematology and Immunology, Na Homolce Hospital, Prague, Czech Republic.
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Stefan Russwurm
- Department of Anesthesiology and Intensive Care, University Hospital Jena, Jena, Germany
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19
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Xia B, Meng Q, Feng X, Tang X, Jia A, Feng J, Zhang S, Zhang H. Probing the molecular regulation of lipopolysaccharide stress in piglet liver by comparative proteomics analysis. Electrophoresis 2018; 39:2321-2331. [PMID: 29569248 DOI: 10.1002/elps.201700467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/22/2018] [Accepted: 03/03/2018] [Indexed: 12/18/2022]
Abstract
Lipopolysaccharide (LPS) can induce inflammatory responses in piglets, causing immunological stress and tissue damage. However, chronic LPS infection may lead to LPS-induced immunological stress resistance. The molecular mechanisms underlying LPS stress have not been fully elucidated. Here, we conducted a global comparative proteomics analysis to investigate the molecular regulation of LPS stress using an immunological stress model of weaned piglets. A shotgun-based SWATH-MS workflow was used for global proteomes of the piglet livers after 15-day LPS treatment. Out of 3700 quantified proteins, 93 proteins showed differential changes under LPS stress. Bioinformatics analysis indicated that the differentially expressed proteins were mainly involved in inflammatory response, oxidation-redox processes and defense reactions, and were enriched in a phagosome pathway. Several key proteins associated with oxidative stress (SOD2), inflammation response (STEAP4 and S100 family) and the phagosome pathway were verified by activity and targeted-MS analyses. The observed responses appear to mitigate hepatic damage due to excessive oxidative stress, inflammation, and repression of the phagosome pathway. Our results reveal that an increased STEAP4 expression in piglets appears involved in cellular regulation by LPS stress and subsequent immunological stress resistance. This study sheds new light on the mechanism of prevention and relieving injury by LPS-induced immune responses.
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Affiliation(s)
- Bing Xia
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaohui Feng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Anfeng Jia
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Jinghai Feng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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20
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Szarvas T, Nyirády P, Ogawa O, Furuya H, Rosser CJ, Kobayashi T. Urinary Protein Markers for the Detection and Prognostication of Urothelial Carcinoma. Methods Mol Biol 2018; 1655:251-273. [PMID: 28889391 DOI: 10.1007/978-1-4939-7234-0_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bladder cancer diagnosis and surveillance is mainly based on cystoscopy and urine cytology. However, both methods have significant limitations; urine cytology has a low sensitivity for low-grade tumors, while cystoscopy is uncomfortable for the patients. Therefore, in the last decade urine analysis was the subject of intensive research resulting in the identification of many potential biomarkers for the detection, surveillance, or prognostic stratification of bladder cancer. Current trends move toward the development of multiparametric models to improve the diagnostic accuracy compared with single molecular markers. Recent technical advances for high-throughput and more sensitive measurements have led to the development of multiplex assays showing potential for more efficient tools toward future clinical application. In this review, we focus on the findings of urinary protein research in the context of detection and prognostication of bladder cancer. Furthermore, we provide an up-to-date overview on the recommendations for the quality evaluation of published studies as well as for the conduction of future urinary biomarker studies.
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Affiliation(s)
- Tibor Szarvas
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary.
| | - Péter Nyirády
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideki Furuya
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Charles J Rosser
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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21
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McGarrity S, Anuforo Ó, Halldórsson H, Bergmann A, Halldórsson S, Palsson S, Henriksen HH, Johansson PI, Rolfsson Ó. Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification. Sci Rep 2018; 8:6811. [PMID: 29717213 PMCID: PMC5931560 DOI: 10.1038/s41598-018-25015-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/13/2018] [Indexed: 12/24/2022] Open
Abstract
Endothelial dysfunction contributes to sepsis outcome. Metabolic phenotypes associated with endothelial dysfunction are not well characterised in part due to difficulties in assessing endothelial metabolism in situ. Here, we describe the construction of iEC2812, a genome scale metabolic reconstruction of endothelial cells and its application to describe metabolic changes that occur following endothelial dysfunction. Metabolic gene expression analysis of three endothelial subtypes using iEC2812 suggested their similar metabolism in culture. To mimic endothelial dysfunction, an in vitro sepsis endothelial cell culture model was established and the metabotypes associated with increased endothelial permeability and glycocalyx loss after inflammatory stimuli were quantitatively defined through metabolomics. These data and transcriptomic data were then used to parametrize iEC2812 and investigate the metabotypes of endothelial dysfunction. Glycan production and increased fatty acid metabolism accompany increased glycocalyx shedding and endothelial permeability after inflammatory stimulation. iEC2812 was then used to analyse sepsis patient plasma metabolome profiles and predict changes to endothelial derived biomarkers. These analyses revealed increased changes in glycan metabolism in sepsis non-survivors corresponding to metabolism of endothelial dysfunction in culture. The results show concordance between endothelial health and sepsis survival in particular between endothelial cell metabolism and the plasma metabolome in patients with sepsis.
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Affiliation(s)
- Sarah McGarrity
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Ósk Anuforo
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Haraldur Halldórsson
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Landspitali, Læknagarður, Hringbraut, Reykjavik, Iceland
| | - Andreas Bergmann
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Sirus Palsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Pär Ingemar Johansson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Rigshospitalet, Blegdamsvej 9, 2100, Kobenhavn O, Denmark
| | - Óttar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
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Li C, Wei X, Gao L, Chen W, Liu T, Liu B. iTRAQ-Based Proteomic Analysis of Wheat Bunt Fungi Tilletia controversa, T. caries, and T. foetida. Curr Microbiol 2018; 75:1103-1107. [PMID: 29693196 DOI: 10.1007/s00284-018-1490-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
This is the first study of proteomics of wheat bunt fungi Tilletia controversa (TCK), T. caries (TCT), and T. foetida (TFL) using the iTRAQ technique. Based on the relative quantities of specific proteins between each two pathogens, we found 50 up-regulated and 80 down-regulated protein genes in TCK compared to TFL, 62 up-regulated and 82 down-regulated protein genes in TCT compared to TFL, 47 up-regulated and 30 down-regulated protein genes in TCK compared to TCT, and there were 1 protein of up-regulated and 4 proteins of down-regulated in the three pairs. These protein data could be of great value for exploring the key proteins which play an important role in the interactions of these pathogens with their host. Some of them could be valuable for differentiating the three pathogens with monoclonal antibodies produced by the specific proteins and may enable in-site detection of the pathogens and performing routine monitoring as a diagnostic assay in wheat shipments.
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Affiliation(s)
- Chao Li
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoqing Wei
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Zhang Y, Wang Y, Li S, Zhang X, Li W, Luo S, Sun Z, Nie R. ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity. Proteome Sci 2018; 16:8. [PMID: 29692685 PMCID: PMC5905050 DOI: 10.1186/s12953-018-0136-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Euphorbia lathyris L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of Euphorbia lathyris that is commonly used in TCM practice and is obtained by removing the oil from the seed that is called paozhi, has been known to ease diarrhea. Whereas, the mechanisms of reducing intestinal toxicity have not been clearly investigated yet. Methods In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic method was applied to investigate the effects of Euphorbia lathyris L. on the protein expression involved in intestinal metabolism, in order to illustrate the potential attenuated mechanism of Euphorbia lathyris L. processing. Differentially expressed proteins (DEPs) in the intestine after treated with Semen Euphorbiae (SE), Semen Euphorbiae Pulveratum (SEP) and Euphorbiae Factor 1 (EFL1) were identified. The bioinformatics analysis including GO analysis, pathway analysis, and network analysis were done to analyze the key metabolic pathways underlying the attenuation mechanism through protein network in diarrhea. Western blot were performed to validate selected protein and the related pathways. Results A number of differentially expressed proteins that may be associated with intestinal inflammation were identified. They mainly constituted by part of the cell. The expression sites of them located within cells and organelles. G protein and Eph/Ephrin signal pathway were controlled jointly by SEP and SE. After processing, the extraction of SEP were mainly reflected in the process of cytoskeleton, glycolysis and gluconeogenesis. Conclusions These findings suggest that SE induced an inflammatory response, and activated the Interleukin signaling pathway, such as the Ang/Tie 2 and JAK2/ STAT signaling pathways, which may eventually contribute to injury result from intestinal inflammatory, while SEP could alleviate this injury by down-regulating STAT1 and activating Ang-4 that might reduce the inflammatory response. Our results demonstrated the importance of Ang-4 and STAT1 expression, which are the target proteins in the attenuated of SE after processing based on proteomic investigation. Thus iTRAQ might be a novel candidate method to study scientific connotation of hypothesis that the attenuated of SE after processing expressed lower toxicity from cellular levels.
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Affiliation(s)
- Yu Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Yingzi Wang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shaojing Li
- 2Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong cheng District, Dongzhimen Neixiang Street on the 16th, Beijing, 100700 People's Republic of China
| | - Xiuting Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Wenhua Li
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shengxiu Luo
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Zhenyang Sun
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Ruijie Nie
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
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He L, He R, Liang R, Li Y, Li X, Li C, Zhang S. Protein expression profiling in the hippocampus after focal cerebral ischemia injury in rats. J Integr Neurosci 2018. [DOI: 10.3233/jin-170047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Lichan He
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Rui He
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Ruihua Liang
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Yi Li
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Xiaoqiang Li
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Chuqiao Li
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
| | - Suping Zhang
- Department of Neurology, Guangzhou Red Cross Hospital, Medical College, Jinan University, No. 396 Tongfu Zhong Road, Guangzhou 510220, China. E-mail:
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Abstract
Sepsis is a systemic inflammatory response caused by infection whose molecular mechanisms are still not completely understood. The early detection of sepsis remains a great challenge for clinicians because no single biomarker capable of its reliable prediction, hence, delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. There are several experimental approaches used to reveal the molecular mechanism of sepsis progression. Proteomics coupled with mass spectrometry made possible to identify differentially expressed proteins in clinical samples. Recent advancement in liquid chromatography-based separation methods and mass spectrometers resolution and sensitivity with absolute quantitation methods, made possible to use proteomics as a powerful tool for study of clinical samples with higher coverage proteome profiles. In recent years, number of proteomic studies have been done under sepsis and/or in response to endotoxin and showed various signaling pathways, functions, and biomarkers. This review enlightened the proteomic progress in the last decade in sepsis.
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Dias Bastos PA, Vlahou A, Leite-Moreira A, Santos LL, Ferreira R, Vitorino R. Deciphering the disease-related molecular networks using urine proteomics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Su S, Zeng X, Bai L, Wang Y, Zhang L, Li M, Wu C. Concurrent methylation and demethylation of arsenic by fungi and their differential expression in the protoplasm proteome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 225:620-627. [PMID: 28336093 DOI: 10.1016/j.envpol.2017.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 03/04/2017] [Accepted: 03/11/2017] [Indexed: 06/06/2023]
Abstract
Microbial methylation and demethylation are central to arsenic's (As) biogeochemical cycling. Here, the transformations of monomethylarsonic acid (MMA(V)) (50 mg L-1) for 15 days in cells of As-methylating fungi, Fusarium oxysporum CZ-8F1, Penicillium janthinellum SM-12F4, and Trichoderma asperellum SM-12F1, were evaluated, and trace concentrations of As(III) and As(V) were observed in fungal cell extracts. Trace amounts of DMA(V) were also detected in MMA(V) and P. janthinellum SM-12F4 incubations. In situ X-ray absorption near edge structure (XANES) indicated that after exposure to MMA(V) (500 mg L-1) for 15 days, 28.6-48.6% of accumulated As in fungal cells was DMA(V), followed by 18.4-30.3% from As(V), 0-28.1% from As(III), and 4.8-28.9% from MMA(V). The concurrent methylation and demethylation of As occurs in fungal cells. Furthermore, a majority of proteins involved in metabolism, transport, ATP activity, biosynthesis, signal transduction, DNA activity, translation, and oxidative stress were upregulated in T. asperellum SM-12F1 cells after MMA(V) exposure compared to As(III), As(V), and DMA(V). The detoxification process of T. asperellum SM-12F1 was As species-specific. Methylenetetrahydrofolate reductase (R7YMH0) donation of a methyl group for S-adenosylmethionine (SAM) generation significantly increased following MMA(V) exposure.
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Affiliation(s)
- Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, PR China.
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, PR China.
| | - Lingyu Bai
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, PR China
| | - Yanan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, PR China
| | - Lili Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, PR China
| | - Mansheng Li
- Beijing Proteome Research Center, Beijing, PR China
| | - Cuixia Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, PR China
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Che L, Yang Z, Xu M, Xu S, Che L, Lin Y, Fang Z, Feng B, Li J, Chen D, Wu D. Maternal nutrition modulates fetal development by inducing placental efficiency changes in gilts. BMC Genomics 2017; 18:213. [PMID: 28245787 PMCID: PMC5331709 DOI: 10.1186/s12864-017-3601-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 02/22/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Intra-uterine growth restriction (IUGR) and fetal overgrowth increase risks to postnatal health. Maternal nutrition is the major intrauterine environmental factor that alters fetal weight. However, the mechanisms underlying the effects of maternal nutrition on fetal development are not entirely clear. We developed a pig model, and using isobaric tags for relative and absolute quantification (iTRAQ), we investigated alterations in the placental proteome of gilts on a normal-energy-intake (Con) and high-energy-intake (HE) diet. RESULTS In the Con group, heavy and light fetuses were found at the tubal and cervical ends of the uterus respectively at 90 d of gestation. Moreover, the heavy fetuses had a higher glucose concentration than the light fetuses. However, a higher uniformity was noted in the HE group. Placental promoters between these two positions indicated that 78 and 50 differentially expressed proteins were detected in the Con and HE groups respectively. In the Con group, these proteins were involved in lipid metabolism (HADHA, AACS, CAD), nutrient transport (GLUT, SLC27A1), and energy metabolism (NDUFV1, NDUFV2, ATP5C1). However, in the HE group they mainly participated in transcriptional and translational regulation, and intracellular vesicular transport. CONCLUSIONS Our findings revealed that maternal nutrition may alter birth weight mainly through the modulation of placental lipid and energy metabolism, which also provides a possible mechanism to explain the higher uniformity of fetal weight in gilts fed a HE diet.
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Affiliation(s)
- Long Che
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - ZhenGuo Yang
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - MengMeng Xu
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - ShengYu Xu
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - LianQiang Che
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yan Lin
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - ZhengFeng Fang
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bin Feng
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jian Li
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - DaiWen Chen
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
| | - De Wu
- Key Laboratory of Animal Disease-Resistance Nutrition and Feed Science, Ministry of Agriculture, P. R. China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 China
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Zhang J, Gao Y, Lu Q, Sa R, Zhang H. Proteome changes in the small intestinal mucosa of growing pigs with dietary supplementation of non-starch polysaccharide enzymes. Proteome Sci 2017; 15:3. [PMID: 28077931 PMCID: PMC5223414 DOI: 10.1186/s12953-016-0109-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 12/20/2016] [Indexed: 02/07/2023] Open
Abstract
Background Non-starch polysaccharide enzymes (NSPEs) have long been used in monogastric animal feed production to degrade non-starch polysaccharides (NSPs) to oligosaccharides in order to promote growth performance and gastrointestinal (GI) tract health. However, the precise molecular mechanism of NSPEs in the improvement of the mammalian small intestine remains unknown. Methods In this study, isobaric tags were applied to investigate alterations of the small intestinal mucosa proteome of growing pigs after 50 days of supplementation with 0.6% NSPEs (mixture of xylanase, β-glucanase and cellulose) in the diet. Bioinformatics analysis including gene ontology annotation was performed to determine the differentially expressed proteins. A protein fold-change of ≥ 1.2 and a P-value of < 0.05 were selected as thresholds. Results Dietary supplementation of NSPEs improved the growth performance of growing pigs. Most importantly, a total of 90 proteins were found to be differentially abundant in the small intestinal mucosa between a control group and the NSPE group. Up-regulated proteins were related to nutrient metabolism (energy, lipids, protein and mineral), immunity, redox homeostasis, detoxification and the cell cytoskeleton. Down-regulated proteins were primarily related to transcriptional and translational regulation. Our results indicate that the effect of NSPEs on the increase of nutrient availability in the intestinal lumen facilitates the efficiency of nutrient absorption and utilization, and the supplementation of NSPEs in growing pigs also modulates redox homeostasis and enhances immune response during simulating energy metabolism due to a higher uptake of nutrients in the small intestine. Conclusions These findings have important implications for understanding the mechanisms of NSPEs on the small intestine of pigs, which provides new information for the better utilization of this feed additive in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0109-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jize Zhang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010 People's Republic of China ; State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Yang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Qingping Lu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Renna Sa
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
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Wang H, Wang S, Cui D, Dong S, Tuo X, Liu Z, Liu Y. iTRAQ-based proteomic technology revealed protein perturbations in intestinal mucosa from manganese exposure in rat models. RSC Adv 2017. [DOI: 10.1039/c7ra03358c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Manganese (Mn) is an essential metal ion as a biological cofactor, but in excess, it is toxic; however, the homeostatic mechanisms of Mn at the cellular level have not been identified.
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Affiliation(s)
- Hui Wang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
| | - Shengyi Wang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
| | - Dongan Cui
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
| | - Shuwei Dong
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
| | - Xin Tuo
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
| | - Zhiqi Liu
- Institute of Agro-Products Processing Science and Technology
- Chinese Academy of Agricultural Sciences
- Beijing 100193
- China
| | - Yongming Liu
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province
- Key Lab of New Animal Drug Project of Gansu Province
- Key Lab of Veterinary Pharmaceutical Development of Ministry of Agriculture
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences
- Lanzhou 730050
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Csősz É, Kalló G, Márkus B, Deák E, Csutak A, Tőzsér J. Quantitative body fluid proteomics in medicine - A focus on minimal invasiveness. J Proteomics 2016; 153:30-43. [PMID: 27542507 DOI: 10.1016/j.jprot.2016.08.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/27/2016] [Accepted: 08/08/2016] [Indexed: 01/07/2023]
Abstract
Identification of new biomarkers specific for various pathological conditions is an important field in medical sciences. Body fluids have emerging potential in biomarker studies especially those which are continuously available and can be collected by non-invasive means. Changes in the protein composition of body fluids such as tears, saliva, sweat, etc. may provide information on both local and systemic conditions of medical relevance. In this review, our aim is to discuss the quantitative proteomics techniques used in biomarker studies, and to present advances in quantitative body fluid proteomics of non-invasively collectable body fluids with relevance to biomarker identification. The advantages and limitations of the widely used quantitative proteomics techniques are also presented. Based on the reviewed literature, we suggest an ideal pipeline for body fluid analyses aiming at biomarkers discoveries: starting from identification of biomarker candidates by shotgun quantitative proteomics or protein arrays, through verification of potential biomarkers by targeted mass spectrometry, to the antibody-based validation of biomarkers. The importance of body fluids as a rich source of biomarkers is discussed. SIGNIFICANCE Quantitative proteomics is a challenging part of proteomics applications. The body fluids collected by non-invasive means have high relevance in medicine; they are good sources for biomarkers used in establishing the diagnosis, follow up of disease progression and predicting high risk groups. The review presents the most widely used quantitative proteomics techniques in body fluid analysis and lists the potential biomarkers identified in tears, saliva, sweat, nasal mucus and urine for local and systemic diseases.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Bernadett Márkus
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Eszter Deák
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary; Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary.
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Katam R, Sakata K, Suravajhala P, Pechan T, Kambiranda DM, Naik KS, Guo B, Basha SM. Comparative leaf proteomics of drought-tolerant and -susceptible peanut in response to water stress. J Proteomics 2016; 143:209-226. [DOI: 10.1016/j.jprot.2016.05.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
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Raju M S, V J, Kamaraju RS, Sritharan V, Rajkumar K, Natarajan S, Kumar AD, Burgula S. Continuous evaluation of changes in the serum proteome from early to late stages of sepsis caused by Klebsiella pneumoniae. Mol Med Rep 2016; 13:4835-44. [PMID: 27082932 DOI: 10.3892/mmr.2016.5112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/20/2016] [Indexed: 11/06/2022] Open
Abstract
Serum protein profiles of patients with bacterial sepsis from the day of diagnosis until recovery/mortality were compared from early to late stages in response to severe sepsis using two dimensional electrophoresis. The proteins exhibiting changes during the course of sepsis (20‑28 day mortality) were selected and identified by matrix‑assisted laser desorption ionization‑time of flight‑tandem mass spectrometry. Among the proteins identified, haptoglobin (Hp), transthyretin (TTR), orosomucoid 1/α1 acid glycoprotein (ORM1), α1 antitrypsin (A1AT), serum amyloid A (SAA) and S100A9 exhibited differential expression patterns between survivors (S; n=6) and non‑survivors (NS; n=6), particularly during the early stages of sepsis. Expression factors (EFs), taken as the ratio between the NS and S during early stages, showed ratios of Hp, 0.39 (P≤0.012); TTR, 3.96 (P≤0.03); ORM1, 0.69 (P≤0.79); A1AT, 0.92 (P≤0.87) and SAA, 0.69 (P≤0.01). S100A9, an acute phase protein, exhibited an EF ratio of 1.68 (P≤0.004) during the end stages of sepsis. A delayed rise in levels was observed in Hp, A1AT, ORM1, S100A9 and SAA, whereas TTR levels increased during the early stages of sepsis in NS. Analysis of inflammatory responses in the early stages of sepsis revealed increased mRNA expression in leukocytes of interleukin (IL)‑6 (EF, 2.50), IL‑10 (EF, 1.70) and prepronociceptin (EF, 1.6), which is a precursor for nociceptin in NS compared with S, and higher Toll‑like receptor‑4 (EF, 0.30) levels in S compared with NS. Therefore, a weaker acute phase response in the early stages of sepsis in NS, combined with an inefficient inflammatory response, may contribute to sepsis mortality.
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Affiliation(s)
- Swathi Raju M
- Department of Microbiology, Osmania University, Hyderabad, Telangana 500007, India
| | - Jahnavi V
- Molecular Diagnostics and Biomarkers Department of Laboratory Medicine Global Hospitals, Hyderabad, Telangana 500004, India
| | - Ratnakar S Kamaraju
- Molecular Diagnostics and Biomarkers Department of Laboratory Medicine Global Hospitals, Hyderabad, Telangana 500004, India
| | - Venkataraman Sritharan
- Molecular Diagnostics and Biomarkers Department of Laboratory Medicine Global Hospitals, Hyderabad, Telangana 500004, India
| | - Karthik Rajkumar
- Department of Microbiology, Osmania University, Hyderabad, Telangana 500007, India
| | - Sumathi Natarajan
- Department of Biochemistry, Osmania University, Hyderabad, Telangana 500007, India
| | - Anil D Kumar
- Department of Biochemistry, Osmania University, Hyderabad, Telangana 500007, India
| | - Sandeepta Burgula
- Department of Microbiology, Osmania University, Hyderabad, Telangana 500007, India
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Zhang JH, Li Y, Song XB, Ji XH, Sun HN, Wang H, Fu SB, Zhao LJ, Sun DJ. Differential expression of serum proteins in rats subchronically exposed to arsenic identified by iTRAQ-based proteomic technology-14-3-3 ζ protein to serve as a potential biomarker. Toxicol Res (Camb) 2016; 5:651-659. [PMID: 30090378 DOI: 10.1039/c5tx00393h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/31/2016] [Indexed: 12/15/2022] Open
Abstract
Arsenic is a multi-system toxicant. However, the mechanism of arsenic toxicity is not fully clarified and few effective protein biomarkers could be used for arsenic poisoning. This study was to investigate the differentially expressed proteins in the serum of rats subchronically exposed to arsenic. Sixty male rats were randomly divided into four groups, and the dose of sodium arsenite in drinking water for each group was 0, 2, 10, and 50 mg L-1, respectively. The exposure lasted for 12 weeks. An Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic approach was used to identify the differentially expressed proteins in serum between control and 50 mg L-1 groups. A total of 201 serum proteins were identified by iTRAQ, of which 12 were significantly changed by arsenic exposure with two up-regulated and ten down-regulated proteins. One down-regulated protein 14-3-3 ζ, an abundant protein expressed in the brain, was verified by ELISA using serum samples and by immunohistochemical, real time PCR, and western blot methods using brain tissues in four groups. Our work provided valuable insight into the serum protein changes in rats exposed to arsenic, and indicated that 14-3-3 ζ may serve as a useful biomarker for nervous damage caused by arsenic poisoning.
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Affiliation(s)
- Jin Hui Zhang
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Ying Li
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Xuan Bo Song
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Xiao Hong Ji
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Hong Na Sun
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Hui Wang
- Community Health Service Center of Nanxiang Town , Jiading District , Shanghai 201802 , China
| | - Song Bin Fu
- The Laboratory of Medical Genetics , Harbin Medical University , Harbin 150081 , China
| | - Li Jun Zhao
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
| | - Dian Jun Sun
- Key Lab of Etiologic Epidemiology of National Health and Family Planning Commission , Key Lab of Etiologic Epidemiology of Education Bureau of Heilongjiang Province , The Center for Endemic Disease Control , Chinese Center for Disease Control and Prevention , Harbin Medical University , Harbin 150081 , China . ; ; ; Tel: (+86)-451-8750- 2980
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Role of Epithelial-Mesenchyme Transition in Chlamydia Pathogenesis. PLoS One 2015; 10:e0145198. [PMID: 26681200 PMCID: PMC4683008 DOI: 10.1371/journal.pone.0145198] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/01/2015] [Indexed: 12/15/2022] Open
Abstract
Chlamydia trachomatis genital infection in women causes serious adverse reproductive complications, and is a strong co-factor for human papilloma virus (HPV)-associated cervical epithelial carcinoma. We tested the hypothesis that Chlamydia induces epithelial-mesenchyme transition (EMT) involving T cell-derived TNF-alpha signaling, caspase activation, cleavage inactivation of dicer and dysregulation of micro-RNA (miRNA) in the reproductive epithelium; the pathologic process of EMT causes fibrosis and fertility-related epithelial dysfunction, and also provides the co-factor function for HPV-related cervical epithelial carcinoma. Using a combination of microarrays, immunohistochemistry and proteomics, we showed that chlamydia altered the expression of crucial miRNAs that control EMT, fibrosis and tumorigenesis; specifically, miR-15a, miR-29b, miR-382 and MiR-429 that maintain epithelial integrity were down-regulated, while miR-9, mi-R-19a, miR-22 and miR-205 that promote EMT, fibrosis and tumorigenesis were up-regulated. Chlamydia induced EMT in vitro and in vivo, marked by the suppression of normal epithelial cell markers especially E-cadherin but up-regulation of mesenchymal markers of pathological EMT, including T-cadherin, MMP9, and fibronectin. Also, Chlamydia upregulated pro-EMT regulators, including the zinc finger E-box binding homeobox protein, ZEB1, Snail1/2, and thrombospondin1 (Thbs1), but down-regulated anti-EMT and fertility promoting proteins (i.e., the major gap junction protein connexin 43 (Cx43), Mets1, Add1Scarb1 and MARCKSL1). T cell-derived TNF-alpha signaling was required for chlamydial-induced infertility and caspase inhibitors prevented both infertility and EMT. Thus, chlamydial-induced T cell-derived TNF-alpha activated caspases that inactivated dicer, causing alteration in the expression of reproductive epithelial miRNAs and induction of EMT. EMT causes epithelial malfunction, fibrosis, infertility, and the enhancement of tumorigenesis of HPV oncogene-transformed epithelial cells. These findings provide a novel understanding of the molecular pathogenesis of chlamydia-associated diseases, which may guide a rational prevention strategy.
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Abstract
The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.
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Zhang JZ, Gao Y, Lu QP, Sa RN, Zhang HF. iTRAQ-based quantitative proteomic analysis of longissimus muscle from growing pigs with dietary supplementation of non-starch polysaccharide enzymes. J Zhejiang Univ Sci B 2015; 16:465-78. [PMID: 26055908 PMCID: PMC4471598 DOI: 10.1631/jzus.b1400266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/31/2015] [Indexed: 01/13/2023]
Abstract
Non-starch polysaccharide enzymes (NSPEs) have long been used in the feed production of monogastric animals to degrade non-starch polysaccharide to oligosaccharides and promote growth performance. However, few studies have been conducted on the effect of such enzymes on skeletal muscle in monogastric animals. To elucidate the mechanism of the effect of NSPEs on skeletal muscle, an isobaric tag for relative and absolute quantification (iTRAQ) for differential proteomic quantitation was applied to investigate alterations in the proteome in the longissimus muscle (LM) of growing pigs after a 50-d period of supplementation with 0.6% NSPEs in the diet. A total of 51 proteins were found to be differentially expressed in the LM between a control group and the NSPE group. Functional analysis of the differentially expressed protein species showed an increased abundance of proteins related to energy production, protein synthesis, muscular differentiation, immunity, oxidation resistance and detoxification, and a decreased abundance of proteins related to inflammation in the LM of the pigs fed NSPEs. These findings have important implications for understanding the mechanisms whereby dietary supplementation with NSPEs enzymes can promote growth performance and improve muscular metabolism in growing pigs.
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Affiliation(s)
- Ji-ze Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yang Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Jilin University, Changchun 130062, China
| | - Qing-ping Lu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ren-na Sa
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hong-fu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Zhang J, Li C, Tang X, Lu Q, Sa R, Zhang H. High Concentrations of Atmospheric Ammonia Induce Alterations in the Hepatic Proteome of Broilers (Gallus gallus): An iTRAQ-Based Quantitative Proteomic Analysis. PLoS One 2015; 10:e0123596. [PMID: 25901992 PMCID: PMC4406733 DOI: 10.1371/journal.pone.0123596] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/20/2015] [Indexed: 12/30/2022] Open
Abstract
With the development of the poultry industry, ammonia, as a main contaminant in the air, is causing increasing problems with broiler health. To date, most studies of ammonia toxicity have focused on the nervous system and the gastrointestinal tract in mammals. However, few detailed studies have been conducted on the hepatic response to ammonia toxicity in poultry. The molecular mechanisms that underlie these effects remain unclear. In the present study, our group applied isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis to investigate changes in the protein profile change in hepatic tissue of broilers exposed to high concentrations of atmospheric ammonia, with the goal of characterizing the molecular mechanisms of chronic liver injury from exposure to high ambient levels of ammonia. Overall, 30 differentially expressed proteins that are involved in nutrient metabolism (energy, lipid, and amino acid), immune response, transcriptional and translational regulation, stress response, and detoxification were identified. In particular, two of these proteins, beta-1 galactosidase (GLB1) and a kinase (PRKA) anchor protein 8-like (AKAP8 L), were previously suggested to be potential biomarkers of chronic liver injury. In addition to the changes in the protein profile, serum parameters and histochemical analyses of hepatic tissue also showed extensive hepatic damage in ammonia-exposed broilers. Altogether, these findings suggest that longtime exposure to high concentrations of atmospheric ammonia can trigger chronic hepatic injury in broilers via different mechanisms, providing new information that can be used for intervention using nutritional strategies in the future.
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Affiliation(s)
- Jize Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cong Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingping Lu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Renna Sa
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Functional interaction of nicotinic acetylcholine receptors and Na+/K+ ATPase from Locusta migratoria manilensis (Meyen). Sci Rep 2015; 5:8849. [PMID: 25743085 PMCID: PMC4351541 DOI: 10.1038/srep08849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/28/2015] [Indexed: 01/28/2023] Open
Abstract
Associated proteins are important for the correct functioning of nicotinic acetylcholine receptors (nAChRs). In the present study, a neonicotinoid-agarose affinity column was used to isolate related proteins from a solubilized membrane preparation from the nervous system of Locusta migratoria manilensis (Meyen). 1530 peptides were identified and most of them were involved in the membranous structure, molecular interaction and cellular communication. Among these peptides, Na+/K+ ATPase had the highest MASCOT score and were involved in the molecular interaction, which suggested that Na+/K+ ATPase and nAChRs might have strong and stable interactions in insect central nervous system. In the present study, functional interactions between nAChRs and Na+/K+ ATPase were examined by heterologous expression in Xenopus oocytes. The results showed that the activated nAChRs increased pump currents of Na+/K+ ATPase, which did not require current flow through open nAChRs. In turn, Na+/K+ ATPase significantly increased agonist sensitivities of nAChRs in a pump activity-independent manner and reduced the maximum current (Imax) of nAChRs. These findings provide novel insights concerning the functional interactions between insect nAChRs and Na+/K+ ATPase.
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Zhang J, Li C, Tang X, Lu Q, Sa R, Zhang H. Proteome changes in the small intestinal mucosa of broilers (Gallus gallus) induced by high concentrations of atmospheric ammonia. Proteome Sci 2015; 13:9. [PMID: 25741220 PMCID: PMC4347970 DOI: 10.1186/s12953-015-0067-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/11/2015] [Indexed: 01/15/2023] Open
Abstract
Background Ammonia is a well-known toxicant both existing in atmospheric and aquatic system. So far, most studies of ammonia toxicity focused on mammals or aquatic animals. With the development of poultry industry, ammonia as a main source of contaminant in the air is causing more and more problems on broiler production, especially lower growth rate. The molecular mechanisms that underlie the negative effects of ammonia on the growth and intestine of broilers are yet unclear. We investigated the growth, gut morphology, and mucosal proteome of Arbor Acres broilers (Gallus gallus) exposed to high concentrations of atmospheric ammonia by performing a proteomics approach integrated with traditional methods. Results Exposure to ammonia interfered with the development of immune organ and gut villi. Meanwhile, it greatly reduced daily weight gain and feed intake, and enhanced feed conversion ratio. A total of 43 intestinal mucosal proteins were found to be differentially abundant. Up-regulated proteins are related to oxidative phosphorylation and apoptosis. Down-regulated proteins are related to cell structure and growth, transcriptional and translational regulation, immune response, oxidative stress and nutrient metabolism. These results indicated that exposure to ammonia triggered oxidative stress, and interfered with nutrient absorption and immune function in the small intestinal mucosa of broilers. Conclusions These findings have important implications for understanding the toxic mechanisms of ammonia on intestine of broilers, which provides new information that can be used for intervention using nutritional strategies in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0067-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jize Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Cong Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Qingping Lu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Renna Sa
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
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Katam R, Chibanguza K, Latinwo LM, Smith D. Proteome Biomarkers in Xylem Reveal Pierce's Disease Tolerance in Grape. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2015; 8:217-224. [PMID: 27019567 PMCID: PMC4807612 DOI: 10.4172/jpb.1000372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pierce's disease (PD) is a significant threat to grape cultivation and industry. The disease caused by bacterium Xylella fastidiosa clogs xylem vessels resulting in wilting of the plant. PD-tolerant grape genotypes are believed to produce certain novel components in xylem tissue that help them to combat invading pathogens. Research has been aimed at characterizing the uniquely expressed xylem proteins by PD-tolerant genotypes. The objectives were to i) compare and characterize Vitis xylem proteins differentially expressed in PD-tolerant and PD-susceptible cultivars and, ii) identify xylem proteins uniquely expressed in PD-tolerant genotypes. A high throughput two-dimensional gel electrophoresis of xylem proteins from three Vitis species identified more than 200 proteins with pls 3.0 to 9.0 and molecular weights of 20 to 75 kDa. The differentially expressed proteins were then excised and analyzed with MALDI/TOF mass spectrometer. The mass spectra were collected and protein identification was performed against the Viridiplantae database using Matrix Science algorithm. Proteins were mapped to the universal protein resource to study gene ontology. Comparative analysis of the xylem proteome of three species indicated the highest number of proteins in muscadine grape, followed by Florida hybrid bunch and bunch grape. These proteins were all associated with disease resistance, energy metabolism, protein processing and degradation, biosynthesis, stress related functions, cell wall biogenesis, signal transduction, and ROS detoxification. Furthermore, β-1, 3-glucanase, 10-deacetyl baccatin III-10-O-acetyl transferase-like, COP9, and aspartyl protease nepenthesin precursor proteins were found to be uniquely expressed in PD-tolerant muscadine grape, while they are absent in PD-susceptible bunch grape. Data suggests that muscadine and Florida hybrid bunch grapes express novel proteins in xylem to overcome pathogen attack while bunch grape lacks this capability, making them susceptible to PD.
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Prucha M, Bellingan G, Zazula R. Sepsis biomarkers. Clin Chim Acta 2014; 440:97-103. [PMID: 25447700 DOI: 10.1016/j.cca.2014.11.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 02/06/2023]
Abstract
Sepsis is the most frequent cause of death in non-coronary intensive care units (ICUs). In the past 10 years, progress has been made in the early identification of septic patients and in their treatment and these improvements in support and therapy mean that the mortality is gradually decreasing but it still remains unacceptably high. Leaving clinical diagnosis aside, the laboratory diagnostics represent a complex range of investigations that can place significant demands on the system given the speed of response required. There are hundreds of biomarkers which could be potentially used for diagnosis and prognosis in septic patients. The main attributes of successful markers would be high sensitivity, specificity, possibility of bed-side monitoring, and financial accessibility. Only a fraction is used in routine clinical practice because many lack sufficient sensitivity or specificity. The following review gives a short overview of the current epidemiology of sepsis, its pathogenesis and state-of-the-art knowledge on the use of specific biochemical, hematological and immunological parameters in its diagnostics. Prospective approaches towards discovery of new diagnostic biomarkers have been shortly mentioned.
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Affiliation(s)
- Miroslav Prucha
- Department of Clinical Biochemistry, Hematology and Immunology, Hospital Na Homolce, Prague, Czech Republic.
| | - Geoff Bellingan
- University College London Hospitals, 235 Euston Rd, London NW1 2PG, United Kingdom(1)
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University in Prague and Thomayer Hospital, Prague, Czech Republic
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van Swelm RPL, Kramers C, Masereeuw R, Russel FGM. Application of urine proteomics for biomarker discovery in drug-induced liver injury. Crit Rev Toxicol 2014; 44:823-41. [DOI: 10.3109/10408444.2014.931341] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kang MJ, Park YJ, You S, Yoo SA, Choi S, Kim DH, Cho CS, Yi EC, Hwang D, Kim WU. Urinary proteome profile predictive of disease activity in rheumatoid arthritis. J Proteome Res 2014; 13:5206-17. [PMID: 25222917 DOI: 10.1021/pr500467d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Current serum biomarkers for rheumatoid arthritis (RA) are not highly sensitive or specific to changes of disease activities. Thus, other complementary biomarkers have been needed to improve assessment of RA activities. In many diseases, urine has been studied as a window to provide complementary information to serum measures. Here, we conducted quantitative urinary proteome profiling using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and identified 134 differentially expressed proteins (DEPs) between RA and osteoarthritis (OA) urine samples. By integrating the DEPs with gene expression profiles in joints and mononuclear cells, we initially selected 12 biomarker candidates related to joint pathology and then tested their altered expression in independent RA and OA samples using enzyme-linked immunosorbent assay. Of the initial candidates, we selected four DEPs as final candidates that were abundant in RA patients and consistent with those observed in LC-MS/MS analysis. Among them, we further focused on urinary soluble CD14 (sCD14) and examined its diagnostic value and association with disease activity. Urinary sCD14 had a diagnostic value comparable to conventional serum measures and an even higher predictive power for disease activity when combined with serum C-reactive protein. Thus, our urinary proteome provides a diagnostic window complementary to current serum parameters for the disease activity of RA.
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Affiliation(s)
- Min Jueng Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University , Seoul 110-799, Korea
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Cao Z, Robinson RAS. The role of proteomics in understanding biological mechanisms of sepsis. Proteomics Clin Appl 2014; 8:35-52. [PMID: 24339042 DOI: 10.1002/prca.201300101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 11/10/2022]
Abstract
Sepsis is a systemic inflammatory state caused by infection. Complications of this infection with multiple organ failure lead to more lethal conditions, such as severe sepsis and septic shock. Sepsis is one of the leading causes of US deaths. Novel biomarkers with high sensitivity and specificity may be helpful for early diagnosis of sepsis and for improvement of patient outcomes through the development of new therapies. Mass spectrometry-based proteomics offers powerful tools to identify such biomarkers and furthermore to give insight to fundamental mechanisms of this clinical condition. In this review, we summarize findings from proteomics studies of sepsis and how their applications have provided more understanding into the pathogenesis of septic infection. Literatures related to "proteomics", "sepsis", "systemic inflammatory response syndrome", "severe sepsis", "septic infection", and "multiple organ dysfunction syndrome" were searched using PubMed. Findings about neonatal and adult sepsis are discussed separately. Within the adult sepsis studies, results are grouped based on the models (e.g., human or animal). Across investigations in clinical populations and in rodent and mammalian animal models, biological pathways, such as inflammatory and acute phase response, coagulation, complement, mitochondrial energy metabolism, chaperones, and oxidative stress, are altered at the protein level. These proteomics studies have discovered many novel biomarker candidates of septic infection. Validation the clinical use of these biomarker candidates may significantly impact the diagnosis and prognosis of sepsis. In addition, the molecular mechanisms revealed by these studies may also guide the development of more effective treatments.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Ji T, Liu Z, Shen J, Shen F, Liang Q, Wu L, Chen G, Corona M. Proteomics analysis reveals protein expression differences for hypopharyngeal gland activity in the honeybee, Apis mellifera carnica Pollmann. BMC Genomics 2014; 15:665. [PMID: 25103401 PMCID: PMC4141115 DOI: 10.1186/1471-2164-15-665] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 07/30/2014] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Most of the proteins contained in royal jelly (RJ) are secreted from the hypopharyngeal glands (HG) of young bees. Although generic protein composition of RJ has been investigated, little is known about how age-dependent changes on HG secretion affect RJ composition and their biological consequences. In this study, we identified differentially expressed proteins (DEPs) during HG development by using the isobaric tag for relative and absolute quantification (iTRAQ) labeling technique. This proteomic method increases the potential for new protein discovery by improving the identification of low quantity proteins. RESULTS A total of 1282 proteins were identified from five age groups of worker bees, 284 of which were differentially expressed. 43 (15.1%) of the DEPs were identified for the first time. Comparison of samples at day 6, 9, 12, and 16 of development relative to day 3 led to the unambiguous identification of 112, 117, 127, and 127 DEPs, respectively. The majority of these DEPs were up-regulated in the older worker groups, indicating a substantial change in the pattern of proteins expressed after 3 days. DEPs were identified among all the age groups, suggesting that changes in protein expression during HG ontogeny are concomitant with different states of worker development. A total of 649 proteins were mapped to canonical signaling pathways found in the Kyoto Encyclopedia of Genes and Genomes (KEGG), which were preferentially associated with metabolism and biosynthesis of secondary metabolites. More than 10 key high-abundance proteins were involved in signaling pathways related to ribosome function and protein processing in the endoplasmic reticulum. The results were validated by qPCR. CONCLUSION Our approach demonstrates that HG experienced important changes in protein expression during its ontogenic development, which supports the secretion of proteins involved in diverse functions in adult workers beyond its traditional role in royal jelly production.
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Affiliation(s)
- Ting Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.
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Zhu JY, Wu GX, Ze SZ, Stanley DW, Yang B. Parasitization by Scleroderma guani influences protein expression in Tenebrio molitor pupae. JOURNAL OF INSECT PHYSIOLOGY 2014; 66:37-44. [PMID: 24852673 DOI: 10.1016/j.jinsphys.2014.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Ectoparasitoid wasps deposit their eggs onto the surface and inject venom into their hosts. Venoms are chemically complex and they exert substantial impact on hosts, including permanent or temporary paralysis and developmental arrest. These visible venom effects are due to changes in expression of genes encoding physiologically relevant proteins. While the influence of parasitization on gene expression in several lepidopterans has been reported, the molecular details of parasitoid/beetle relationships remain mostly unknown. This shortcoming led us to pose the hypothesis that envenomation by the ectoparasitic ant-like bethylid wasp Scleroderma guani leads to changes in protein expression in the yellow mealworm beetle Tenebrio molitor. We tested our hypothesis by comparing the proteomes of non-parasitized and parasitized host pupae using iTRAQ-based proteomics. We identified 41 proteins that were differentially expressed (32↑- and 9↓-regulated) in parasitized pupae. We assigned these proteins to functional categories, including immunity, stress and detoxification, energy metabolism, development, cytoskeleton, signaling and others. We recorded parallel changes in mRNA levels and protein abundance in 14 selected proteins following parasitization. Our findings support our hypothesis by documenting changes in protein expression in parasitized hosts.
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Affiliation(s)
- Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Guo-Xing Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Sang-Zi Ze
- Yunnan Forestry Technological College, Kunming 650224, China
| | - David W Stanley
- USDA/Agricultural Research Service, Biological Control of Insects Research Laboratory, Columbia, MO 65203, USA
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
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A pro-atherogenic HDL profile in coronary heart disease patients: an iTRAQ labelling-based proteomic approach. PLoS One 2014; 9:e98368. [PMID: 24859250 PMCID: PMC4032332 DOI: 10.1371/journal.pone.0098368] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 05/01/2014] [Indexed: 12/15/2022] Open
Abstract
Objectives This study aims to compare the protein composition of high-density lipoprotein (HDL) particles in coronary heart disease (CHD) patients and controls by proteomic methods. Background HDL has been reported to exert pro-atherogenic properties in CHD patients. Accumulating evidence indicates that HDL composition, rather than the HDL-C level, determines its functions. The changes in HDL composition involved in the conversion of anti-atherogenic to pro-atherogenic properties in CHD patients are currently unknown. Methods and Results iTRAQ combined with nanoLC-MS/MS was performed to obtain a differential expression profile of the HDL pooled samples of the male age-matched CHD patients and controls (n = 10/group). Of the 196 proteins identified in the examined HDL, 12 were differentially expressed between the CHD patients and the controls, including five up-regulated proteins and seven down-regulated proteins. Using GO analysis, we determined that the up-regulated proteins were mostly involved in inflammatory reactions, displaying a potential pro-atherogenic profile. In contrast, the down-regulated proteins were mostly involved in lipid metabolism processes, displaying anti-atherogenic properties. To confirm the proteomic results, serum amyloid A (SAA) and apoC-I were selected and quantified by ELISA, in the same population as the proteomic analysis, as well as another independent population (n = 120/group). Consistent with the proteomic results, the amount of SAA was significantly increased, and apoC-I was significantly decreased in the HDL particles of CHD patients compared with those of controls (P<0.05). Conclusions Our study shows that the HDL proteome changes to a pro-atherogenic profile in CHD patients, which might compromise the protective effects of HDL. Proteomic analysis of HDL composition may provide more relevant information regarding their functional properties than steady-state HDL-C levels.
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Christaki E, Giamarellos-Bourboulis EJ. The beginning of personalized medicine in sepsis: small steps to a bright future. Clin Genet 2014; 86:56-61. [PMID: 24579691 DOI: 10.1111/cge.12368] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 02/04/2023]
Abstract
There is a growing recognition that there is a need for a more personalized approach towards sepsis care. In most clinical trials investigating novel therapeutic interventions against sepsis, patients have been considered a rather homogeneous population. However, there is probably more individual variability between septic patients than previously considered. The pathophysiology of sepsis is a complex and dynamic process that originates from the host immune response to infection and varies according to the genetic predisposition, immune status and co-morbid conditions of the host, the type of pathogen and the site and extent of infection. Until now, efforts to stratify septic patients according to their immune profile were hampered by the lack of specific biomarkers. Recent advances in molecular medicine have made it possible to develop tools that will facilitate a faster and more precise diagnosis of infection. Individual variability between each patient's responses to infection can assist in tailoring therapeutic interventions to the individual's disease profile and monitoring treatment response. In this review, we describe those recent advances in genomics and theragnostics, which are slowly entering clinical practice and which will make possible a more personalized approach to each septic patient in the next decade.
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Affiliation(s)
- E Christaki
- First Department of Internal Medicine, AHEPA University Hospital, Thessaloniki, Greece; Infectious Diseases Division, Alpert School of Medicine of Brown University, Providence, RI, USA
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Ming T, Li J, Huo P, Wei Y, Chen X. Analysis of Free Amino Acids in Russula griseocarnosa Harvested at Different Stages of Maturity Using iTRAQ®-LC-MS/MS. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9817-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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