Proteomic Profiling of Purified Rabies Virus Particles

Zhang, Yan; Wang, Yuyang; Feng, Ye; Tu, Zhongzhong; Lou, Zhiyong; Tu, Changchun

doi:10.1007/s12250-019-00157-6

Cited by 16 publications

(55 citation statements)

References 54 publications

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“…LC-MS/MS data acquisition was carried out on a Q Exactive HF-X mass spectrometer coupled with an Easy-nLC 1200 system (both Thermo Scientific) (Miao et al, 2019;Zhang et al, 2020b). Peptides were first loaded onto a C18 trap column (75 mm 3 2 cm, 3 mm particle size, 100 Å pore size, Thermo) and then separated in a C18 analytical column (75 mm 3 250 mm, 3 mm particle size, 100 Å pore size, Thermo).…”

Section: Lc-ms/ms Analysismentioning

confidence: 99%

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

et al. 2020

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The COVID-19 pandemic is a global public health crisis. However, little is known about the pathogenesis and biomarkers of COVID-19. Herein, we profiled host responses to COVID-19 by performing plasma proteomics of a cohort of COVID-19 patients including non-survivors and survivors recovered from mild or severe symptoms, and uncovered numerous COVID-19-associated alterations of plasma proteins. We developed a machine learning-based pipeline to identify 11 proteins as biomarkers and a set of biomarker combinations, which were validated by an independent cohort and accurately distinguished and predicted COVID-19 outcomes. Some of the biomarkers were further validated by ELISA using a larger cohort. These markedly altered proteins, including the biomarkers mediate pathophysiological pathways such as immune or inflammatory responses, platelet degranulation and coagulation, and metabolism, that likely contribute to the pathogenesis. Our findings provide valuable knowledge about COVID-19 biomarkers, and shed light on the pathogenesis and potential therapeutic targets of COVID-19.

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Section: Lc-ms/ms Analysismentioning

confidence: 99%

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

et al. 2020

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“…LC‐MS/MS data acquisition was carried out on an Orbitrap Exploris 480 mass spectrometer coupled with an Easy‐nLC 1200 system (Thermo Fisher Scientific). Peptides were loaded through an auto‐sampler and separated in a C18 analytical column (75 μm × 25 cm, C18, 1.9 μm, 100 A° pore size, Thermo Fisher Scientific) 20,21 . Mobile phase A (0.1% formic acid) and mobile phase B (80% acetonitrile, 0.1% formic acid) were used to establish the 60‐min separation gradient, with a constant flow rate at 300 nl/min.…”

Section: Methodsmentioning

confidence: 99%

“…Peptides were loaded through an auto-sampler and separated in a C18 analytical column (75 μm × 25 cm, C18, 1.9 μm, 100 A°pore size, Thermo Fisher Scientific). 20,21 Mobile phase A (0.1% formic acid) and mobile phase B (80% acetonitrile, 0.1% formic acid) were used to establish the 60-min separation gradient, with a constant flow rate at 300 nl/min. LC-MS/MS raw data were analyzed using the data-independent-acquisition (DIA) mode.…”

Section: Lc-ms/ms Analysismentioning

confidence: 99%

Plasma proteomic analysis reveals altered protein abundances in HIV‐infected patients with or without non‐Hodgkin lymphoma

Zhuang

Zhang

et al. 2022

Journal of Medical Virology

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The identification of circulating proteins associated with acquired immunodeficiency syndrome-related non-Hodgkin lymphoma (AIDS-NHL) may help in the development of promising biomarkers for screening, diagnosis, treatment, and prognosis.Here, we used quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins (DEPs) in plasma collected from patients with AIDS-NHL and human immunodeficiency virus (HIV)-infected patients without NHL (HIV + ). Proteins with a log2 (fold change) in abundance >0.26 and p < 0.05 were considered differentially abundant. In total, 84 DEPs were identified, among which 20 were further validated as potential biomarkers, with immunoglobulin and complement components being the most common proteins. Some of the proteins were further verified in a retrospective analysis of the medical records of patients in a larger cohort. These markedly altered proteins were found to mediate pathophysiological pathways that likely contribute to AIDS-NHL pathogenesis, such as the humoral immune response, complement activation, and complement and coagulation cascades. Our findings provide a new molecular understanding of AIDS-NHL pathogenesis and provide new evidence supporting the identification of these proteins as possible biomarkers in AIDS-NHL.

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“…Dawar et al [11] reviewed its diverse roles in infections with viruses including hepatitis B virus (HBV), vaccinia virus (VV), human immunodeficiency virus type 1 (HIV-1), [6], a related virus belonging to the genus Vesiculovirus of the family Rhabdoviridae. The recent observations by Zhang et al [12] on proteomic profiling of purified rabies virus particles have also documented the association of CypA with virus particles, emphasizing its possible role in virus replication. The cyclophilins are known for their high binding affinity for CsA [10].…”

Section: Introductionmentioning

confidence: 95%

Cyclophilin A: a possible host modulator in Chandipura virus infection

et al. 2021

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Chandipura virus (CHPV), belonging to the genus Vesiculovirus of the family Rhabdoviridae, has been identified as one of the causes of pediatric encephalitis in India. Currently, neither vaccines nor therapeutic drugs are available against this agent. Considering that the disease progresses very fast with a high mortality rate, working towards the development of potential therapeutics against it will have a public health impact. Although the use of viral inhibitors as antiviral agents is the most common way to curb virus replication, the mutation-prone nature of viruses results in the development of resistance to antiviral agents. The recent development of proteomic platforms for analysis of purified viral agents has allowed certain upregulated host proteins that are involved in the morphogenesis and replication of viruses to be identified. Thus, the alternative approach of inhibition of host proteins involved in the regulation of virus replication could be explored for their therapeutic effectiveness. In the current study, we have evaluated the effect of inhibition of cyclophilin A (CypA), an immunophilin with peptidyl-prolyl cis/trans-isomerase activity, on the replication of CHPV. Treatment with cyclosporin A, used in vitro for the inhibition of CypA, resulted in a 3-log reduction in CHPV titer and an undetectable level of CypA in comparison to an untreated control. An in silico analysis of the interaction of the CHPV nucleoprotein with the human CypA protein showed stable interaction in molecular docking and molecular dynamics simulations. Overall, the results of this study suggest a possible role of CypA in facilitating CHPV replication, thus making it one of the potential host factors to be explored in future antiviral studies.

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Proteomic Profiling of Purified Rabies Virus Particles

Cited by 16 publications

References 54 publications

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

Plasma proteomic analysis reveals altered protein abundances in HIV‐infected patients with or without non‐Hodgkin lymphoma

Cyclophilin A: a possible host modulator in Chandipura virus infection

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