2023
Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence
Wei Y, Davenport T, Collora J, Ma H, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho Y. Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence. Immunity 2023, 56: 2584-2601.e7. PMID: 37922905, PMCID: PMC10843106, DOI: 10.1016/j.immuni.2023.10.002.Peer-Reviewed Original ResearchConceptsTranscription factor accessibilityHIV-1-infected cellsFactor accessibilityHIV-1 persistenceHeterogeneous cellular statesEpigenetic programsCellular programsCellular statesLatent HIV-1-infected cellsProliferation programProtein profilingSuppressive antiretroviral therapyHIV-1 eradicationHIV-1 reservoirCell deathProtein statesHIV-1 RNAAP-1HIV-1 DNASurface proteinsMechanistic interrogationEpigeneticsAntiretroviral therapyMemory CD4Effector differentiationActivity‐based Tools for Interrogating Host Biology During Infection
Ramanathan R, Hatzios S. Activity‐based Tools for Interrogating Host Biology During Infection. Israel Journal Of Chemistry 2023, 63 PMID: 37744997, PMCID: PMC10512441, DOI: 10.1002/ijch.202200095.Peer-Reviewed Original ResearchActivity-based protein profilingPost-translational modificationsHost post-translational modificationsHost-microbe interactionsHost biologyCells senseCell signalingMicrobial mechanismsEnzyme functionProtein profilingProtein structureSide-chain reactivityChemical probesInfected cellsHost-directed therapiesPotential targetRapid modulationHost responseSignalingBiologyInfectionEnzymeProfilingPathwayPathogens
2022
Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis
Povero D, Tameda M, Eguchi A, Ren W, Kim J, Myers R, Goodman Z, Harrison S, Sanyal A, Bosch J, Ohno-Machado L, Feldstein A. Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. Scientific Reports 2022, 12: 3027. PMID: 35194091, PMCID: PMC8863778, DOI: 10.1038/s41598-022-06809-0.Peer-Reviewed Original ResearchConceptsSmall non-coding RNAsExtracellular vesiclesNon-coding RNAsNovel miRNAsControl subjectsFurther molecular characterizationMiRNA sequence analysisLiver-specific markersProtein profilingMiRNA cargoMolecular characterizationHuman diseasesCurrent serum markersNovel surrogate biomarkersPrimary sclerosing cholangitisCholestatic liver diseaseHealthy control subjectsMiRNA profilesProteinCell specificityDifferential centrifugationMiRNAsPSC patientsSclerosing cholangitisLiver disease
2021
Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler
Bergholtz H, Carter JM, Cesano A, Cheang MCU, Church SE, Divakar P, Fuhrman CA, Goel S, Gong J, Guerriero JL, Hoang ML, Hwang ES, Kuasne H, Lee J, Liang Y, Mittendorf EA, Perez J, Prat A, Pusztai L, Reeves JW, Riazalhosseini Y, Richer JK, Sahin Ö, Sato H, Schlam I, Sørlie T, Stover DG, Swain SM, Swarbrick A, Thompson EA, Tolaney SM, Warren SE, Consortium O. Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler. Cancers 2021, 13: 4456. PMID: 34503266, PMCID: PMC8431590, DOI: 10.3390/cancers13174456.Peer-Reviewed Original ResearchWhole transcriptome levelDigital Spatial ProfilerSpatial profilingTranscriptome levelRNA profilingRNA transcriptsTumor microenvironmentMolecular diversityProtein profilingCancer researchIntegration of datasetsGeoMx Digital Spatial ProfilerProfilingCell populationsMouse samplesBiomarker discoveryBreast tumor microenvironmentBreast Cancer ConsortiumCancer researchers
2018
Activity-Based Protein Profiling at the Host–Pathogen Interface
Kovalyova Y, Hatzios SK. Activity-Based Protein Profiling at the Host–Pathogen Interface. Current Topics In Microbiology And Immunology 2018, 420: 73-91. PMID: 30203396, DOI: 10.1007/82_2018_129.BooksConceptsActivity-based protein profilingHost-pathogen interfaceProtein profilingFunctional proteomePathogen interactionsMicrobial pathogenicityComplex proteomesEnzyme-mediated mechanismReactive amino acidsActive enzymeChemical probesAmino acidsMetabolic adaptationProteomeMicrobial infectionsCo-culture systemBiological systemsHost immunityEnzymeProfilingPathogenicityHostProbeAnimal modelsAdaptation
2016
The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling
Bergman J, Botling J, Fagerberg L, Hallström B, Djureinovic D, Uhlén M, Pontén F. The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling. Endocrinology 2016, 158: 239-251. PMID: 27901589, DOI: 10.1210/en.2016-1758.Peer-Reviewed Original ResearchConceptsImmunohistochemistry-based protein profilingNormal human tissue typesProtein coding genesMessenger RNA sequencingExpression levelsProtein expression patternsHuman tissue typesCoding genesProtein homologsFERM domainRelative expression levelsCorresponding proteinRNA sequencingWide transcriptomicsExpression patternsProtein profilingGreater expression levelsGenesSpecific functionsProteinMolecular landscapeTissue typesProteomeTranscriptomicsElevated expression
2015
Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands
Lu Y, Xue Q, Eisele MR, Sulistijo ES, Brower K, Han L, Amir el-AD, Pe'er D, Miller-Jensen K, Fan R. Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e607-e615. PMID: 25646488, PMCID: PMC4343126, DOI: 10.1073/pnas.1416756112.Peer-Reviewed Original ResearchConceptsSingle cellsSingle-cell genomicsSame single cellImmune effector proteinsFunctional heterogeneityToll-like receptor 4Similar cell populationsMacrophage inhibitory factorEffector proteinsCell activation processProtein profilingPopulation ArchitectureMultiplexed profilingFunctional stateDifferentiated macrophagesPrimary macrophagesCell populationsSecretion assaysPathogenic ligandsDifferent cytokine profilesProfilingPathogenic activationProteinActivation of lipopolysaccharideCells
2014
The human testis-specific proteome defined by transcriptomics and antibody-based profiling
Djureinovic D, Fagerberg L, Hallström B, Danielsson A, Lindskog C, Uhlén M, Pontén F. The human testis-specific proteome defined by transcriptomics and antibody-based profiling. Molecular Human Reproduction 2014, 20: 476-488. PMID: 24598113, DOI: 10.1093/molehr/gau018.Peer-Reviewed Original ResearchConceptsExpression patternsAntibody-based protein profilingTestis-enriched expression patternNormal human tissue typesWide transcriptomic analysisTissue-specific genesAntibody-based profilingPutative human genesList of genesHaploid germ cellsHuman tissue typesDifferent cell typesHuman reproductive biologyReproductive biologyWide analysisProtein localizationHuman genesTranscriptomic analysisCorresponding proteinStages of spermatogenesisDeep sequencingProtein profilingMolecular understandingGerm cellsGenes
2009
Actin remodeling by ADF/cofilin is required for cargo sorting at the trans-Golgi network
von Blume J, Duran JM, Forlanelli E, Alleaume AM, Egorov M, Polishchuk R, Molina H, Malhotra V. Actin remodeling by ADF/cofilin is required for cargo sorting at the trans-Golgi network. Journal Of Cell Biology 2009, 187: 1055-1069. PMID: 20026655, PMCID: PMC2806282, DOI: 10.1083/jcb.200908040.Peer-Reviewed Original ResearchConceptsTrans-Golgi networkADF/cofilinActin-depolymerizing factorSecretory proteinsSecretory cargoCofilin knockdownMass spectrometry-based protein profilingMammalian tissue culture cellsGolgi-resident proteinsSorting of proteinsEndogenous secretory proteinsIntegral membrane proteinsSoluble secretory proteinsStable isotope labelingTissue culture cellsDrosophila melanogasterActin remodelingMammalian cellsMembrane proteinsGolgi membranesProtein profilingIsotope labelingCofilinCell surfaceAmino acids
2003
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 2003, 19: 1636-1643. PMID: 12967959, DOI: 10.1093/bioinformatics/btg210.Peer-Reviewed Original Research
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