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Article: Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death

Végvári, Ákos / Rodriguez, Jimmy E. / Zubarev, Roman A.

Analytical chemistry. 2022 June 22, v. 94, no. 26

2022

Abstract: Chemical proteomics studies the effects of drugs upon a cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus, proteome analysis at the single-cell level is needed. Here, ... ...

Abstract	Chemical proteomics studies the effects of drugs upon a cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus, proteome analysis at the single-cell level is needed. Here, we demonstrate that single-cell proteomics techniques have become quantitative enough to tackle the drug effects on target proteins, enabling single-cell chemical proteomics (SCCP). Using SCCP, we studied here the time-resolved response of individual adenocarcinoma A549 cells to anticancer drugs methotrexate, camptothecin, and tomudex, revealing the early emergence of cellular subpopulations committed and uncommitted to death. As a novel and useful approach to exploring the heterogeneous response to drugs of cancer cells, SCCP may prove to be a breakthrough application for single-cell proteomics.
Keywords	adenocarcinoma ; analytical chemistry ; death ; methotrexate ; neoplasm cells ; proteome ; proteomics
Language	English
Dates of publication	2022-0622
Size	p. 9261-9269.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00413
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Article ; Online: Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death.

Végvári, Ákos / Rodriguez, Jimmy E / Zubarev, Roman A

Analytical chemistry

2022 Volume 94, Issue 26, Page(s) 9261–9269

Abstract	Chemical proteomics studies the effects of drugs upon a cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus, proteome analysis at the single-cell level is needed. Here, we demonstrate that single-cell proteomics techniques have become quantitative enough to tackle the drug effects on target proteins, enabling single-cell chemical proteomics (SCCP). Using SCCP, we studied here the time-resolved response of individual adenocarcinoma A549 cells to anticancer drugs methotrexate, camptothecin, and tomudex, revealing the early emergence of cellular subpopulations committed and uncommitted to death. As a novel and useful approach to exploring the heterogeneous response to drugs of cancer cells, SCCP may prove to be a breakthrough application for single-cell proteomics.
MeSH term(s)	A549 Cells ; Antineoplastic Agents/pharmacology ; Camptothecin/pharmacology ; Humans ; Neoplasms ; Proteome/metabolism ; Proteomics
Chemical Substances	Antineoplastic Agents ; Proteome ; Camptothecin (XT3Z54Z28A)
Language	English
Publishing date	2022-06-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00413
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Article ; Online: Single Cell Proteomics Using Multiplexed Isobaric Labeling for Mass Spectrometric Analysis.

Végvári, Ákos / Rodriguez, Jimmy E / Zubarev, Roman A

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2386, Page(s) 113–127

Abstract: Single cell proteomics is an emerging field of bioanalysis allowing one to capture proteome profiles of isolated single cells, which is expected to yield additional biological information in comparison with bulk cell analysis. Mass spectrometry-based ... ...

Abstract	Single cell proteomics is an emerging field of bioanalysis allowing one to capture proteome profiles of isolated single cells, which is expected to yield additional biological information in comparison with bulk cell analysis. Mass spectrometry-based methods provide unbiased analysis of detectable proteins limited only by technical parameters, such as sensitivity, which necessitates the development of best-practice workflows. Here, we describe the entire experimental design of single cell proteome analysis, exemplified by cultured A549 lung adenocarcinoma cells treated with an anti-cancer drug (methotrexate) and utilizing tandem mass tag (TMTpro™) labeling strategy for mass spectrometric data acquisition.
MeSH term(s)	Proteome ; Proteomics ; Single-Cell Analysis ; Tandem Mass Spectrometry ; Workflow
Chemical Substances	Proteome
Language	English
Publishing date	2021-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1771-7_8
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Article ; Online: Naturally occurring dipeptide from elite controllers with dual anti-HIV-1 mechanism

Ceña-Diez, Rafael / Narayanan, Aswathy / Ray, Shilpa / van de Klundert, Maarten / Rodriguez, Jimmy E / Nilvebrant, Johan / Nygren, Per-Åke / Végvári, Ákos / van Domselaar, Robert / Sönnerborg, Anders

International Journal of Antimicrobial Agents. 2023 May, v. 61, no. 5 p.106792-

2023

Abstract: Enhanced levels of a dipeptide, WG-am, have been reported among elite controllers – patients who spontaneously control their HIV-1 infection. This study aimed to evaluate anti-HIV-1 activity and mechanism of action of WG-am. Drug sensitivity assays in ... ...

Abstract	Enhanced levels of a dipeptide, WG-am, have been reported among elite controllers – patients who spontaneously control their HIV-1 infection. This study aimed to evaluate anti-HIV-1 activity and mechanism of action of WG-am. Drug sensitivity assays in TZM.bl cells, PBMCs and ACH-2 cells using WT and mutated HIV-1 strainswere performed to evaluate the antiviral mechanism of WG-am. Mass spectrometry-based proteomics and Real-time PCR analysis of reverse transcription steps were performed to unravel the second anti-HIV-1 mechanism of WG-am. The data suggest that WG-am binds to the CD4 binding pocket of HIV-1 gp120 and blocks its binding to the host cell receptors. Additionally, the time course assay showed that WG-am also inhibited HIV-1 at 4–6 hours post-infection, suggesting a second antiviral mechanism. Drug sensitivity assays under acidic wash conditions confirmed the ability of WG-am to internalise into the host cell in an HIV independent manner. Proteomic studies showed a clustering of all samples treated with WG-am independent of the number of doses or presence or absence of HIV-1. Differentially expressed proteins due to the WG-am treatment indicated an effect on HIV-1 reverse transcription, which was confirmed by reverse transcriptase polymerase chain reaction (RT-PCR). Naturally occurring in HIV-1 elite controllers, WG-am stands out as a new kind of antiviral compound with two independent inhibitory mechanisms of action on HIV-1 replication. WG-am halts HIV-1 entry to the host cell by binding to HIV-1 gp120, thereby blocking the binding of HIV-1 to the host cell. WG-am also exerts a post-entry but pre-integration antiviral effect related to RT-activity.
Keywords	HIV infections ; antiviral agents ; antiviral properties ; dipeptides ; gene expression regulation ; mass spectrometry ; mechanism of action ; proteomics ; quantitative polymerase chain reaction ; reverse transcriptase polymerase chain reaction ; reverse transcription ; Antiviral ; HIV ; Dual mechanism ; Entry ; Retrotranscription ; Therapy
Language	English
Dates of publication	2023-05
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	1093977-5
ISSN	1872-7913 ; 0924-8579
ISSN (online)	1872-7913
ISSN	0924-8579
DOI	10.1016/j.ijantimicag.2023.106792
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Article ; Online: Naturally occurring dipeptide from elite controllers with dual anti-HIV-1 mechanism.

International journal of antimicrobial agents

2023 Volume 61, Issue 5, Page(s) 106792

Abstract: Background: Enhanced levels of a dipeptide, WG-am, have been reported among elite controllers - patients who spontaneously control their HIV-1 infection. This study aimed to evaluate anti-HIV-1 activity and mechanism of action of WG-am.: Methods: ... ...

Abstract	Background: Enhanced levels of a dipeptide, WG-am, have been reported among elite controllers - patients who spontaneously control their HIV-1 infection. This study aimed to evaluate anti-HIV-1 activity and mechanism of action of WG-am. Methods: Drug sensitivity assays in TZM.bl cells, PBMCs and ACH-2 cells using WT and mutated HIV-1 strainswere performed to evaluate the antiviral mechanism of WG-am. Mass spectrometry-based proteomics and Real-time PCR analysis of reverse transcription steps were performed to unravel the second anti-HIV-1 mechanism of WG-am. Results: The data suggest that WG-am binds to the CD4 binding pocket of HIV-1 gp120 and blocks its binding to the host cell receptors. Additionally, the time course assay showed that WG-am also inhibited HIV-1 at 4-6 hours post-infection, suggesting a second antiviral mechanism. Drug sensitivity assays under acidic wash conditions confirmed the ability of WG-am to internalise into the host cell in an HIV independent manner. Proteomic studies showed a clustering of all samples treated with WG-am independent of the number of doses or presence or absence of HIV-1. Differentially expressed proteins due to the WG-am treatment indicated an effect on HIV-1 reverse transcription, which was confirmed by reverse transcriptase polymerase chain reaction (RT-PCR). Conclusion: Naturally occurring in HIV-1 elite controllers, WG-am stands out as a new kind of antiviral compound with two independent inhibitory mechanisms of action on HIV-1 replication. WG-am halts HIV-1 entry to the host cell by binding to HIV-1 gp120, thereby blocking the binding of HIV-1 to the host cell. WG-am also exerts a post-entry but pre-integration antiviral effect related to RT-activity.
MeSH term(s)	Humans ; Dipeptides ; Proteomics ; HIV Infections/drug therapy ; Antiviral Agents ; HIV-1 ; Elite Controllers ; Virus Replication
Chemical Substances	Dipeptides ; Antiviral Agents
Language	English
Publishing date	2023-03-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1093977-5
ISSN	1872-7913 ; 0924-8579
ISSN (online)	1872-7913
ISSN	0924-8579
DOI	10.1016/j.ijantimicag.2023.106792
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Article ; Online: Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.

Neogi, Ujjwal / Elaldi, Nazif / Appelberg, Sofia / Ambikan, Anoop / Kennedy, Emma / Dowall, Stuart / Bagci, Binnur K / Gupta, Soham / Rodriguez, Jimmy E / Svensson-Akusjärvi, Sara / Monteil, Vanessa / Vegvari, Akos / Benfeitas, Rui / Banerjea, Akhil / Weber, Friedemann / Hewson, Roger / Mirazimi, Ali

eLife

2022 Volume 11

Abstract: The pathogenesis and host-viral interactions of the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in ... ...

Abstract	The pathogenesis and host-viral interactions of the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in elucidating the complex host-viral response, interrogates the viral pathogenesis. The present study aimed to fingerprint the system-level alterations during acute CCHFV-infection and the cellular immune responses during productive CCHFV-replication in vitro. We used system-wide network-based system biology analysis of peripheral blood mononuclear cells (PBMCs) from a longitudinal cohort of CCHF patients during the acute phase of infection and after one year of recovery (convalescent phase) followed by untargeted quantitative proteomics analysis of the most permissive CCHFV-infected Huh7 and SW13 cells. In the RNAseq analysis of the PBMCs, comparing the acute and convalescent-phase, we observed system-level host's metabolic reprogramming towards central carbon and energy metabolism (CCEM) with distinct upregulation of oxidative phosphorylation (OXPHOS) during CCHFV-infection. Upon application of network-based system biology methods, negative coordination of the biological signaling systems like FOXO/Notch axis and Akt/mTOR/HIF-1 signaling with metabolic pathways during CCHFV-infection were observed. The temporal quantitative proteomics in Huh7 showed a dynamic change in the CCEM over time and concordant with the cross-sectional proteomics in SW13 cells. By blocking the two key CCEM pathways, glycolysis and glutaminolysis, viral replication was inhibited in vitro. Activation of key interferon stimulating genes during infection suggested the role of type I and II interferon-mediated antiviral mechanisms both at the system level and during progressive replication.
MeSH term(s)	Antiviral Agents/therapeutic use ; Cross-Sectional Studies ; Hemorrhagic Fever Virus, Crimean-Congo/genetics ; Hemorrhagic Fever, Crimean ; Humans ; Interferons ; Leukocytes, Mononuclear
Chemical Substances	Antiviral Agents ; Interferons (9008-11-1)
Language	English
Publishing date	2022-04-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.76071
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Article: DiagnoProt: a tool for discovery of new molecules by mass spectrometry

Silva, André R.F / Lima, Diogo B / Leyva, Alejandro / Duran, Rosario / Batthyany, Carlos / Aquino, Priscila F / Leal, Juliana C / Rodriguez, Jimmy E / Domont, Gilberto B / Santos, Marlon D.M / Chamot-Rooke, Julia / Barbosa, Valmir C / Carvalho, Paulo C

Bioinformatics. 2017 June 15, v. 33, no. 12

2017

Abstract: Motivation: Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortlist ... ...

Abstract	Motivation: Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortlist high-quality unidentified mass spectra that are discriminative of different biological conditions. Results: We exemplify the use of DiagnoProt by shortlisting 4366 high-quality unidentified tandem mass spectra that are discriminative of different types of the Aspergillus fungus. Availability and Implementation: DiagnoProt, a demonstration video and a user tutorial are available at http://patternlabforproteomics.org/diagnoprot. Contact: andrerfsilva@gmail.com or paulo@pcarvalho.com Supplementary information: Supplementary data are available at Bioinformatics online.
Keywords	Aspergillus ; artificial intelligence ; bioinformatics ; fungi ; mass spectrometry ; proteomics
Language	English
Dates of publication	2017-0615
Size	p. 1883-1885.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4803
ISSN (online)	1460-2059
ISSN	1367-4803
DOI	10.1093/bioinformatics/btx093
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Article ; Online: Transcription of genes involved in sulfolipid and polyacyltrehalose biosynthesis of Mycobacterium tuberculosis in experimental latent tuberculosis infection.

Rodríguez, Jimmy E / Ramírez, Ana S / Salas, Laura P / Helguera-Repetto, Cecilia / Gonzalez-y-Merchand, Jorge / Soto, Carlos Y / Hernández-Pando, Rogelio

PloS one

2013 Volume 8, Issue 3, Page(s) e58378

Abstract: The Influence of trehalose-based glycolipids in the virulence of Mycobacterium tuberculosis (Mtb) is recognised; however, the actual role of these cell-wall glycolipids in latent infection is unknown. As an initial approach, we determined by two- ... ...

Abstract	The Influence of trehalose-based glycolipids in the virulence of Mycobacterium tuberculosis (Mtb) is recognised; however, the actual role of these cell-wall glycolipids in latent infection is unknown. As an initial approach, we determined by two-dimensional thin-layer chromatography the sulfolipid (SL) and diacyltrehalose/polyacyltrehalose (DAT/PAT) profile of the cell wall of hypoxic Mtb. Then, qRT-PCR was extensively conducted to determine the transcription profile of genes involved in the biosynthesis of these glycolipids in non-replicating persistent 1 (NRP1) and anaerobiosis (NRP2) models of hypoxia (Wayne model), and murine models of chronic and progressive pulmonary tuberculosis. A diminished content of SL and increased amounts of glycolipids with chromatographic profile similar to DAT were detected in Mtb grown in the NRP2 stage. A striking decrease in the transcription of mmpL8 and mmpL10 transporter genes and increased transcription of the pks (polyketidesynthase) genes involved in SL and DAT biosynthesis were detected in both the NRP2 stage and the murine model of chronic infection. All genes were found to be up-regulated in the progressive disease. These results suggest that SL production is diminished during latent infection and the DAT/PAT precursors can be accumulated inside tubercle bacilli and are possibly used in reactivation processes.
MeSH term(s)	Animals ; Cell Wall/metabolism ; Chromatography, Thin Layer ; Disease Models, Animal ; Disease Progression ; Gene Expression Regulation ; Gene Expression Regulation, Bacterial ; Lipids/biosynthesis ; Male ; Membrane Proteins/genetics ; Mice ; Mice, Inbred BALB C ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/metabolism ; Oxygen/metabolism ; Polyketide Synthases/genetics ; RNA, Ribosomal, 16S/metabolism ; Trehalose/biosynthesis ; Tuberculosis, Pulmonary/microbiology
Chemical Substances	Lipids ; Membrane Proteins ; MmpL8 protein, Mycobacterium tuberculosis ; RNA, Ribosomal, 16S ; sulfolipids ; Polyketide Synthases (79956-01-7) ; Trehalose (B8WCK70T7I) ; Oxygen (S88TT14065)
Language	English
Publishing date	2013-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0058378
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DiagnoProt: a tool for discovery of new molecules by mass spectrometry.

Silva, André R F / Lima, Diogo B / Leyva, Alejandro / Duran, Rosario / Batthyany, Carlos / Aquino, Priscila F / Leal, Juliana C / Rodriguez, Jimmy E / Domont, Gilberto B / Santos, Marlon D M / Chamot-Rooke, Julia / Barbosa, Valmir C / Carvalho, Paulo C

Bioinformatics (Oxford, England)

2017 Volume 33, Issue 12, Page(s) 1883–1885

Abstract	Motivation: Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortlist high-quality unidentified mass spectra that are discriminative of different biological conditions. Results: We exemplify the use of DiagnoProt by shortlisting 4366 high-quality unidentified tandem mass spectra that are discriminative of different types of the Aspergillus fungus. Availability and implementation: DiagnoProt, a demonstration video and a user tutorial are available at http://patternlabforproteomics.org/diagnoprot . Contact: andrerfsilva@gmail.com or paulo@pcarvalho.com. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Aspergillus/metabolism ; Fungal Proteins/analysis ; Machine Learning ; Proteomics/methods ; Sequence Analysis, Protein/methods ; Software ; Tandem Mass Spectrometry/methods
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2017-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btx093
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