Life Sciences Data and Application Integration with B-Fabric

Türker, Can; Akal, Fuat; Schlapbach, Ralph

doi:10.1515/jib-2011-159

Cited by 9 publications

(7 citation statements)

References 2 publications

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“…Hybridization on Affymetrix HG‐U133 Plus 2 chip was performed at the Functional Genomic Centre Zurich. Data quality control and extraction were performed in the B‐Fabric platform, which uses several R scripts based on bioConductor . RMA algorithm was used for summarization and standard RMA .…”

Section: Methodsmentioning

confidence: 99%

Early gene expression changes by Epstein‐Barr virus infection of B‐cells indicate CDKs and survivin as therapeutic targets for post‐transplant lymphoproliferative diseases

Bernasconi

Ueda

Krukowski

et al. 2013

Intl Journal of Cancer

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Lymphoproliferative diseases (LPDs) associated with Epstein-Barr virus (EBV) infection cause significant morbidity and mortality in bone marrow and solid organ transplant recipients. To gain insight into LPD pathogenesis and to identify potential effective therapeutic approaches, we investigated early molecular events leading to B-cell transformation by gene expression profiling of EBV-infected B-cells from tonsils by Affymetrix microarray 72 hr postinfection when the B-cells hyperproliferation phase starts. Cell cycle and apoptosis were the most significantly affected pathways and enriched gene sets. In particular, we found significantly increased expression of cyclin-dependent kinase (CDK)1 and CCNB1 (cyclin B1) and of one of their downstream targets BIRC5 (survivin). Importantly, the strong upregulation of the antiapoptotic protein survivin was confirmed in lymphoblastoid cell lines (LCLs) and 71% of EBV-positive post-transplant EBV-LPD lesions scored positive for survivin. The validity of early transforming events for the identification of therapeutic targets for EBV-LPD was confirmed by the marked antiproliferative effect of the CDK inhibitor flavopiridol on LCLs and by the strong induction of apoptosis by survivin inhibition with YM155 or terameprocol. Our results suggest that targeting of CDKs and/or survivin in post-transplant EBV-LPD by specific inhibitors might be an important approach to control and eliminate EBV-transformed B-cells that should be further considered.Lymphoproliferative disease (LPD) associated with the B-cell tropic Epstein-Barr virus (EBV) causes significant morbidity and mortality in solid organ transplant (SOT) 1 or bone marrow transplant (BMT) 2 recipients. The risk to develop EBV-LPD is greatest in EBV-seronegative transplant recipients, i.e., upon primary EBV infection, and in patients with extensive iatrogenic immunosuppression. 3 EBV-associated B-cell lymphoma in the setting of post-transplant LPD (PTLD) is

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Section: Methodsmentioning

confidence: 99%

Early gene expression changes by Epstein‐Barr virus infection of B‐cells indicate CDKs and survivin as therapeutic targets for post‐transplant lymphoproliferative diseases

Bernasconi

Ueda

Krukowski

et al. 2013

Intl Journal of Cancer

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“…Mass spectrometry data were handled using the local laboratory information management system (LIMS) [ 31 ]. The in-house database and mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD026971.…”

Section: Methodsmentioning

confidence: 99%

Proteomic Characterization of the Oral Pathogen Filifactor alocis Reveals Key Inter-Protein Interactions of Its RTX Toxin: FtxA

et al. 2022

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Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod that has been isolated from a variety of oral infections including periodontitis, peri-implantitis, and odontogenic abscesses. As a newly emerging pathogen, its type strain has been investigated for pathogenic properties, yet little is known about its virulence variations among strains. We previously screened the whole genome of nine clinical oral isolates and a reference strain of F. alocis, and they expressed a novel RTX toxin, FtxA. In the present study, we aimed to use label-free quantification proteomics to characterize the full proteome of those ten F. alocis strains. A total of 872 proteins were quantified, and 97 among them were differentially expressed in FtxA-positive strains compared with the negative strains. In addition, 44 of these differentially expressed proteins formed 66 pairs of associations based on their predicted functions, which included clusters of proteins with DNA repair/mediated transformation and catalytic activity-related function, indicating different biosynthetic activities among strains. FtxA displayed specific interactions with another six intracellular proteins, forming a functional cluster that could discriminate between FtxA-producing and non-producing strains. Among them were FtxB and FtxD, predicted to be encoded by the same operon as FtxA. While revealing the broader qualitative and quantitative proteomic landscape of F. alocis, this study also sheds light on the deeper functional inter-relationships of FtxA, thus placing this RTX family member into context as a major virulence factor of this species.

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“…Data Deposit-The mass spectrometry proteomics data, from tier 3 measurements, were handled using the local laboratory information management system (LIMS) (49) and all relevant data have been deposited to the ProteomeXchange Consortium via the PRIDE (http://www.ebi.ac.uk/pride) partner repository with the data set identifier PXD006435 (Username: reviewer63730@ebi.ac.uk; Password: h7qCP1Jk).…”

Section: Methodsmentioning

confidence: 99%

“…The mass spectrometry proteomics data, from tier 3 measurements, were handled using the local laboratory information management system (LIMS) (49)…”

Section: Data Availabilitymentioning

confidence: 99%

Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae

Poljak

Selevsek

Ngwa

et al. 2018

Molecular & Cellular Proteomics

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Asparagine-linked glycosylation is a common posttranslational protein modification regulating the structure, stability and function of many proteins. The -linked glycosylation machinery involves enzymes responsible for the assembly of the lipid-linked oligosaccharide (LLO), which is then transferred to the asparagine residues on the polypeptides by the enzyme oligosaccharyltransferase (OST). A major goal in the study of protein glycosylation is to establish quantitative methods for the analysis of site-specific extent of glycosylation. We developed a sensitive approach to examine glycosylation site occupancy in by coupling stable isotope labeling (SILAC) approach to parallel reaction monitoring (PRM) mass spectrometry (MS). We combined the method with genetic tools and validated the approach with the identification of novel glycosylation sites dependent on the Ost3p and Ost6p regulatory subunits of OST. Based on the observations that alternations in LLO substrate structure and OST subunits activity differentially alter the systemic output of OST, we conclude that sequon recognition is a direct property of the catalytic subunit Stt3p, auxiliary subunits such as Ost3p and Ost6p extend the OST substrate range by modulating interfering pathways such as protein folding. In addition, our proteomics approach revealed a novel regulatory network that connects isoprenoid lipid biosynthesis and LLO substrate assembly.

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Life Sciences Data and Application Integration with B-Fabric

Cited by 9 publications

References 2 publications

Early gene expression changes by Epstein‐Barr virus infection of B‐cells indicate CDKs and survivin as therapeutic targets for post‐transplant lymphoproliferative diseases

Early gene expression changes by Epstein‐Barr virus infection of B‐cells indicate CDKs and survivin as therapeutic targets for post‐transplant lymphoproliferative diseases

Proteomic Characterization of the Oral Pathogen Filifactor alocis Reveals Key Inter-Protein Interactions of Its RTX Toxin: FtxA

Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae

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