2025
Transcription factor BACH2 shapes tissue-resident memory T cell programs to promote HIV-1 persistence
Wei Y, Katherine H, Wong M, Back H, Papasavvas E, Mounzer K, Aberra F, Morgenstern R, Tebas P, Konnikova L, Montaner L, Ho Y. Transcription factor BACH2 shapes tissue-resident memory T cell programs to promote HIV-1 persistence. Immunity 2025 DOI: 10.1016/j.immuni.2025.07.022.Peer-Reviewed Original ResearchCD8+ T cellsHIV-1 persistenceT cell receptorT cellsHIV-1Tissue residencyHIV-1-specific CD8+ T cellsLong-lived memoryEffector functionsTissue-resident memory T cellsHIV-1 immune evasionHIV-1-infected cellsHIV-1 DNAMemory T cellsHIV-1 RNAT cell programmingEffector memoryHIV- donorsCD4+Immune evasionMucosal immunityIn vitroSurface proteinsChromatin accessibilityTranscription factors
2024
Acute and persistent responses after H5N1 vaccination in humans
Apps R, Biancotto A, Candia J, Kotliarov Y, Perl S, Cheung F, Farmer R, Mulè M, Rachmaninoff N, Chen J, Martins A, Shi R, Zhou H, Bansal N, Schum P, Olnes M, Milanez-Almeida P, Han K, Sellers B, Cortese M, Hagan T, Rouphael N, Pulendran B, King L, Manischewitz J, Khurana S, Golding H, van der Most R, Dickler H, Germain R, Schwartzberg P, Tsang J. Acute and persistent responses after H5N1 vaccination in humans. Cell Reports 2024, 43: 114706. PMID: 39235945, PMCID: PMC11949244, DOI: 10.1016/j.celrep.2024.114706.Peer-Reviewed Original ResearchH5N1 influenza vaccineImpact vaccine responsesTime pointsAdjuvant AS03H5N1 vaccineInfluenza vaccineT cellsVaccine responseVaccinated cohortHigh antibody respondersImmune stateVaccine antigensMultiple time pointsSingle-cell profilingInitial vaccinationSystems immunologyVaccinePersistent responseSurface proteinsCell type-specific signaturesChromatin accessibilityTranscription factorsH5N1DaysAS03Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Schoelmerich M, Ly L, West-Roberts J, Shi L, Shen C, Malvankar N, Taib N, Gribaldo S, Woodcroft B, Schadt C, Al-Shayeb B, Dai X, Mozsary C, Hickey S, He C, Beaulaurier J, Juul S, Sachdeva R, Banfield J. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications 2024, 15: 5414. PMID: 38926353, PMCID: PMC11208441, DOI: 10.1038/s41467-024-49548-8.Peer-Reviewed Original ResearchConceptsExtrachromosomal elementsMethylation motifsPublished complete genomesCell surface proteinsShort readsComplete genomeConserved genesGenetic repertoireLinear genomeNanopore sequencingGenomic backboneStructure predictionGenomic signaturesGenomeMethane-oxidizing archaeaHost cellsSurface proteinsArchaeaGenesActivity in situPeatland soilsGenetic inheritanceMotifMethanoperedensHostAn immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors
Zhang X, Song B, Carlino M, Li G, Ferchen K, Chen M, Thompson E, Kain B, Schnell D, Thakkar K, Kouril M, Jin K, Hay S, Sen S, Bernardicius D, Ma S, Bennett S, Croteau J, Salvatori O, Lye M, Gillen A, Jordan C, Singh H, Krause D, Salomonis N, Grimes H. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nature Immunology 2024, 25: 703-715. PMID: 38514887, PMCID: PMC11003869, DOI: 10.1038/s41590-024-01782-4.Peer-Reviewed Original ResearchSurface markersLeukemia stem cell populationHematopoietic progenitor compartmentBone marrow cellsHuman bone marrow cellsHuman hematopoietic progenitorsCell surface markersStem cell populationCITE-seqClinical responseHematopoietic progenitorsMarrow cellsProgenitor compartmentCellular Indexing of TranscriptomesTransitional cellsCell populationsProgenitor analysisCellular indicesMultimodal approachGenomics programsProgenitor stateTranscriptome profilingSurface proteinsProgenitorsCell states
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 differentiationTracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine
de Assis F, Hoehn K, Zhang X, Kardava L, Smith C, Merhebi O, Buckner C, Trihemasava K, Wang W, Seamon C, Chen V, Schaughency P, Cheung F, Martins A, Chiang C, Li Y, Tsang J, Chun T, Kleinstein S, Moir S. Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine. Cell Reports 2023, 42: 112780. PMID: 37440409, PMCID: PMC10529190, DOI: 10.1016/j.celrep.2023.112780.Peer-Reviewed Original ResearchConceptsMemory B cellsB cell receptorB cellsAtypical memory B cellsInfection-naïve individualsTwo-dose SARSSARS-CoV-2 mRNAB cell responsesAntibody-secreting cellsMonth 6Protective immunityCell responsesCell receptorClonal expansionImmunoglobulin GEarly timepointsLater timepointsPlasmablastsVaccinationCD71TimepointsSurface proteinsCellsMultimodal single-cell analysisMRNAThe human malaria parasite Plasmodium falciparum can sense environmental changes and respond by antigenic switching
Schneider V, Visone J, Harris C, Florini F, Hadjimichael E, Zhang X, Gross M, Rhee K, Mamoun C, Kafsack B, Deitsch K. The human malaria parasite Plasmodium falciparum can sense environmental changes and respond by antigenic switching. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2302152120. PMID: 37068249, PMCID: PMC10151525, DOI: 10.1073/pnas.2302152120.Peer-Reviewed Original ResearchConceptsGene switchingGene expressionHistone methyltransferasesHuman malaria parasite Plasmodium falciparumMalaria parasite Plasmodium falciparumS-adenosylmethionineGene expression patternsMulticopy gene familiesVariant surface proteinsParasite Plasmodium falciparumHuman malaria parasiteIntracellular S-adenosylmethioninePrincipal methyl donorEpigenetic controlGene familyActive genesAntigenic switchingGene transcriptionNutrient availabilityExpression patternsMethylation modificationSAM metabolismGenetic modificationAntigenic variationSurface proteins
2020
Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus
Kotliarov Y, Sparks R, Martins A, Mulè M, Lu Y, Goswami M, Kardava L, Banchereau R, Pascual V, Biancotto A, Chen J, Schwartzberg P, Bansal N, Liu C, Cheung F, Moir S, Tsang J. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nature Medicine 2020, 26: 618-629. PMID: 32094927, PMCID: PMC8392163, DOI: 10.1038/s41591-020-0769-8.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAdolescentAdultAgedAged, 80 and overAntibody FormationB-LymphocytesChildChild, PreschoolCohort StudiesFemaleGene Expression ProfilingHumansInfluenza VaccinesInfluenza, HumanLupus Erythematosus, SystemicMaleMiddle AgedTranscriptomeVaccinationYellow FeverYellow Fever VaccineYoung AdultConceptsDisease activityVaccine responsivenessAutoimmune disease activityBlood transcriptional signaturesYellow fever vaccinationSystemic lupus erythematosusClinical quiescenceFever vaccinationLupus erythematosusCancer immunotherapyBaseline predictorsDisease outcomeHealthy subjectsImmune responseI IFNHealthy individualsVaccinationTranscriptional signatureImmune variationBaseline statePatientsExtent of activationBiological basisSurface proteinsInfection response
2019
Assessment of CD40 and CD40L expression in rheumatoid arthritis patients, association with clinical features and DAS28
Román-Fernández I, García-Chagollán M, Cerpa-Cruz S, Jave-Suárez L, Palafox-Sánchez C, García-Arellano S, Sánchez-Zuno G, Muñoz-Valle J. Assessment of CD40 and CD40L expression in rheumatoid arthritis patients, association with clinical features and DAS28. Clinical And Experimental Medicine 2019, 19: 427-437. PMID: 31313080, DOI: 10.1007/s10238-019-00568-5.Peer-Reviewed Original ResearchConceptsT cells expressing high levelsT cell subpopulationsFemale RA patientsRA patientsClinical activityCD40L expressionT cellsClinical featuresClinical features of RA patientsIncreased levels of sCD40LMarker of clinical activityCD4+ T cell subpopulationsCD4+ T cellsCell surface proteinsCD40/CD40L costimulatory pathwayExpression of CD40LRheumatoid arthritisLevels of sCD40LExpression of CD40CD40L mRNA expressionInflammatory autoimmune diseaseAssociation of CD40Surface proteinsCostimulatory pathwayRheumatoid arthritis patients
2018
Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins
Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Proteomes 2018, 6: 48. PMID: 30487426, PMCID: PMC6313906, DOI: 10.3390/proteomes6040048.Peer-Reviewed Original ResearchProximity labelingLabel-free quantitation mass spectrometryReceptor-type tyrosine-protein phosphatase zetaProximity labeling approachCell-cell contactSynaptic cleftPost-synaptic specializationsProteomic contentSynapse heterogeneitySynCAM 1Confocal microcopySurface proteinsCell surfaceProteomeSuper-resolution imagingCultured cortical neuronsMammalian brainLabeling approachMolecular compositionReporterProteinCortical neuronsFunctional organizationExcitatory synapsesDiverse set
2017
Norovirus Cell Tropism Is Determined by Combinatorial Action of a Viral Non-structural Protein and Host Cytokine
Lee S, Wilen CB, Orvedahl A, McCune BT, Kim KW, Orchard RC, Peterson ST, Nice TJ, Baldridge MT, Virgin HW. Norovirus Cell Tropism Is Determined by Combinatorial Action of a Viral Non-structural Protein and Host Cytokine. Cell Host & Microbe 2017, 22: 449-459.e4. PMID: 28966054, PMCID: PMC5679710, DOI: 10.1016/j.chom.2017.08.021.Peer-Reviewed Original ResearchConceptsIntestinal epithelial cellsViral surface proteinsCellular tropismPersistent viral infectionNon-structural protein NS1Expression of NS1MNoV infectionSurface proteinsHost cytokinesAntiviral immunityHost determinantsInterferon lambdaViral infectionKey host determinantsViral non-structural proteinsCell tropismFecal sheddingNon-structural proteinsTropism determinantsEpithelial cellsGlobal causeInfectionTropismProtein NS1MNoVHydrophilic Acylated Surface Protein A (HASPA) of Leishmania donovani: Expression, Purification and Biophysico-Chemical Characterization
Kumar M, Ranjan K, Singh V, Pathak C, Pappachan A, Singh DD. Hydrophilic Acylated Surface Protein A (HASPA) of Leishmania donovani: Expression, Purification and Biophysico-Chemical Characterization. The Protein Journal 2017, 36: 343-351. PMID: 28634775, DOI: 10.1007/s10930-017-9726-x.Peer-Reviewed Original ResearchConceptsMouse macrophage RAW264.7 cell lineRAW264.7 cell lineSurface protein AMacrophage RAW264.7 cell lineReactive oxygen species productionSurface proteinsOxygen species productionLeishmania parasitesLeishmania donovaniLeishmania proteinsDrug developmentSpecies productionCell linesCo-immunoprecipitation studiesPresent studyInfective stagesFurther researchProtein AMacrophage protein
2016
Biogenesis of the Gram-positive bacterial cell envelope
Siegel S, Liu J, Ton-That H. Biogenesis of the Gram-positive bacterial cell envelope. Current Opinion In Microbiology 2016, 34: 31-37. PMID: 27497053, PMCID: PMC5164837, DOI: 10.1016/j.mib.2016.07.015.Peer-Reviewed Original ResearchConceptsWall teichoic acidGram-positive cell envelopeCell envelopeLipoteichoic acidLytR-CpsA-Psr family proteinsPhylum of Gram-positive bacteriaSortase-assembled piliCell envelope biogenesisBacterial cell envelopeGram-negative counterpartsGram-positive bacterial cell envelopeGram-positive bacteriaEnvelope biogenesisFamily proteinsTeichoic acidGram-negative organismsSurface displaySurface proteinsFolding mechanismOxidized proteinsGram-positiveCapsular polysaccharideDivergent functionsPiliBiogenesis
2015
The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135
Stoops EH, Hull M, Olesen C, Mistry K, Harder JL, Rivera-Molina F, Toomre D, Caplan MJ. The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135. Journal Of Cell Biology 2015, 211: 287-294. PMID: 26504168, PMCID: PMC4621837, DOI: 10.1083/jcb.201502045.Peer-Reviewed Original ResearchConceptsPrimary ciliaSurface proteinsTrans-Golgi networkPolarized epithelial cellsApical surface proteinsSNAP-tag systemBasolateral plasma membraneCell surface proteinsEpithelial cellsApical proteinsPericiliary regionGolgi networkPolarized traffickingCarrier vesiclesProtein deliveryPlasma membraneApical membraneProteinGp135Basolateral membraneCiliaMembraneHot spotsCellsTraffickingClostridium Perfringens Enterotoxin (CPE) and CPE-Binding Domain (c-CPE) for the Detection and Treatment of Gynecologic Cancers
Black JD, Lopez S, Cocco E, Schwab CL, English DP, Santin AD. Clostridium Perfringens Enterotoxin (CPE) and CPE-Binding Domain (c-CPE) for the Detection and Treatment of Gynecologic Cancers. Toxins 2015, 7: 1116-1125. PMID: 25835384, PMCID: PMC4417958, DOI: 10.3390/toxins7041116.Peer-Reviewed Original ResearchConceptsClostridium perfringens enterotoxinClaudin-3Claudin-4Perfringens enterotoxinAggressive human cancer cellsGynecologic malignanciesGynecologic cancerHuman cancer cellsOperative settingHuman tumorsCancer cellsPotential roleTumorsSurface proteinsEnterotoxinTreatmentHigh affinitySurgeryMalignancyCancerCytolysisReceptors
2014
Anaplasma phagocytophilum surface protein AipA mediates invasion of mammalian host cells
Seidman D, Ojogun N, Walker NJ, Mastronunzio J, Kahlon A, Hebert KS, Karandashova S, Miller DP, Tegels BK, Marconi RT, Fikrig E, Borjesson DL, Carlyon JA. Anaplasma phagocytophilum surface protein AipA mediates invasion of mammalian host cells. Cellular Microbiology 2014, 16: 1133-1145. PMID: 24612118, PMCID: PMC4115035, DOI: 10.1111/cmi.12286.Peer-Reviewed Original ResearchConceptsGranulocytic anaplasmosisObligate intracellular bacteriumVivo infectionInfectionPhagocytophilum infectionTransmission feedingObligate intracellular pathogensInfected ticksIntracellular pathogensNon-phagocytic cellsIntracellular bacteriumHL-60 cellsHost cell invasionCell invasionAnaplasma phagocytophilumPeptide-specific antiserumOwn uptakeHost cellsAttractive targetInternalization stepMammalian cellsInvasion proteinsSurface proteinsCell morphotypesCells
2013
Claudins Overexpression in Ovarian Cancer: Potential Targets for Clostridium Perfringens Enterotoxin (CPE) Based Diagnosis and Therapy
English DP, Santin AD. Claudins Overexpression in Ovarian Cancer: Potential Targets for Clostridium Perfringens Enterotoxin (CPE) Based Diagnosis and Therapy. International Journal Of Molecular Sciences 2013, 14: 10412-10437. PMID: 23685873, PMCID: PMC3676847, DOI: 10.3390/ijms140510412.Peer-Reviewed Original ResearchConceptsClostridium perfringens enterotoxinOvarian cancerClaudin-3Chemotherapy-resistant ovarian cancerPerfringens enterotoxinAggressive solid tumorsTight junction proteinsMalignant human tissuesPotent cytolytic toxinClaudin overexpressionOvarian tumorsSolid tumorsClaudin-4CancerJunction proteinsParacellular permeabilityPotential targetExact roleTumorsAttractive targetHuman tissuesSurface proteinsCytolytic toxinEnterotoxinClaudin family
2012
SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins.
de Souza J, Galante P, de Almeida R, da Cunha J, Ohara D, Ohno-Machado L, Old L, de Souza S. SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins. Cancer Immunology Research 2012, 12: 15. PMID: 23390370, PMCID: PMC3554024.Peer-Reviewed Original ResearchConceptsCell surface proteinsSurface proteinsProtein-protein interactionsUCSC Genome BrowserImportant data repositoryUser-friendly web interfaceGene annotationProtein domainsGenome browserHuman genesGene expressionGene namesGenesSomatic mutationsProteinExcellent targetAnnotationTherapeutic reagentsWeb interfaceNCBIMutationsExpressionDomainTargetAnaplasma phagocytophilum Asp14 Is an Invasin That Interacts with Mammalian Host Cells via Its C Terminus To Facilitate Infection
Kahlon A, Ojogun N, Ragland SA, Seidman D, Troese MJ, Ottens AK, Mastronunzio JE, Truchan HK, Walker NJ, Borjesson DL, Fikrig E, Carlyon JA. Anaplasma phagocytophilum Asp14 Is an Invasin That Interacts with Mammalian Host Cells via Its C Terminus To Facilitate Infection. Infection And Immunity 2012, 81: 65-79. PMID: 23071137, PMCID: PMC3536139, DOI: 10.1128/iai.00932-12.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnaplasma phagocytophilumAnimalsBacterial Outer Membrane ProteinsBinding SitesCell AdhesionCell Line, TumorEhrlichiaEhrlichiosisGene Expression Regulation, BacterialGlutathione TransferaseHL-60 CellsHumansMembrane GlycoproteinsMembrane ProteinsMiceMolecular Sequence DataProtein BindingProtein Structure, TertiaryProteomeSequence Analysis, ProteinTranscription, GeneticUp-RegulationConceptsMammalian host cellsHost cellsReticulate cellsOuter membrane protein candidatesSurface proteinsOuter membrane protein AMembrane protein AA. phagocytophilum-infected ticksObligate intracellular bacteriumA. phagocytophilumGlutathione S-transferaseTranscriptional profilingSurface proteomeC-terminusAffinity purificationFamily AnaplasmataceaeProtein candidatesSelective biotinylationCellular invasionAsp14Transmission feedingAmino acidsS-transferaseIntracellular bacteriumP-selectin glycoprotein ligand-1Postgenomic Analyses Reveal Development of Infectious Anaplasma phagocytophilum during Transmission from Ticks to Mice
Mastronunzio JE, Kurscheid S, Fikrig E. Postgenomic Analyses Reveal Development of Infectious Anaplasma phagocytophilum during Transmission from Ticks to Mice. Journal Of Bacteriology 2012, 194: 2238-2247. PMID: 22389475, PMCID: PMC3347074, DOI: 10.1128/jb.06791-11.Peer-Reviewed Original ResearchConceptsOpen reading frameA. phagocytophilum genomeObligate intracellular bacteriaBlood-feeding arthropodsCell surface proteinsMammalian cell cultureRickettsiales orderUncharacterized proteinsRibosomal proteinsEssential proteinsTranscriptome sequencingBacterial adaptationA. phagocytophilumDNA replicationTick salivary glandsPostgenomic analysisReading frameMammalian hostsAnaplasma phagocytophilumDevelopmental transitionsDC-specific markerIntracellular bacteriaTransmission feedingSurface proteinsProtein
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