2024
Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines
Kovalchik K, Hamelin D, Kubiniok P, Bourdin B, Mostefai F, Poujol R, Paré B, Simpson S, Sidney J, Bonneil É, Courcelles M, Saini S, Shahbazy M, Kapoor S, Rajesh V, Weitzen M, Grenier J, Gharsallaoui B, Maréchal L, Wu Z, Savoie C, Sette A, Thibault P, Sirois I, Smith M, Decaluwe H, Hussin J, Lavallée-Adam M, Caron E. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines. Nature Communications 2024, 15: 10316. PMID: 39609459, PMCID: PMC11604954, DOI: 10.1038/s41467-024-54734-9.Peer-Reviewed Original ResearchConceptsT cell epitopesT cellsCD8+ T cell epitopesT cell immunityT cell epitope discoverySARS-CoV-2T-cell-directed vaccinationDesigning effective vaccinesB7 supertypePatient's proteomesSARS-CoV-2 variantsVaccine epitopesViral antigensSpike antigenVaccine developmentEffective vaccineEpitope discoveryCOVID-19 vaccineVaccineEpitopesAntigenic featuresOmicron variantAntigenCOVID-19CD8
2023
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation
Chen R, Fulton K, Tran A, Duque D, Kovalchik K, Caron E, Twine S, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Molecular & Cellular Proteomics 2023, 22: 100645. PMID: 37709257, PMCID: PMC10580047, DOI: 10.1016/j.mcpro.2023.100645.Peer-Reviewed Original ResearchSARS-CoV-2 infectionHuman leukocyte antigenAdaptive immune systemHLA allelesAntigen presentationAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionImmune systemSyndrome coronavirus 2 infectionCoronavirus disease 2019 (COVID-19) casesHost proteome changesCoronavirus 2 infectionCertain HLA allelesToll-like receptorsDifferent HLA allelesCoronavirus disease 2019Calu-3 cellsHost cellsLeukocyte antigenViral antigensDisease 2019Viral infectionDevelopment of therapeuticsInfectionClass IAlgorithms for Detection and Identification of Viruses
Landry M, Babady N, Binnicker M, Pinsky B, Tang Y. Algorithms for Detection and Identification of Viruses. 2023, 1-5. DOI: 10.1002/9781683674849.mcm0084.Peer-Reviewed Original ResearchIntroduction of nucleic acid amplification testingNucleic acid amplification testsRespiratory viral culturesSexually transmitted virusDetection of viral antigensDevelopment of antiviral therapiesImmunosuppressed hostsViral cultureAntiviral therapyRoutine cultureClinical specimensAmplification testsCentrifugation cultureViral antigensEnzyme immunoassayMonoclonal antibodiesDiagnostic virologyIdentification of virusesCapture assayCoronavirus diseaseVirusEmergence of epidemicsMedical careIncreasing numberTherapyAlgorithms for Detection and Identification of Viruses
Landry M, Babady N, Binnicker M, Pinsky B, Tang Y. Algorithms for Detection and Identification of Viruses. 2023, 1-5. DOI: 10.1002/9781683670438.mcm0084.Peer-Reviewed Original ResearchIntroduction of nucleic acid amplification testingNucleic acid amplification testsRespiratory viral culturesSexually transmitted virusDetection of viral antigensDevelopment of antiviral therapiesImmunosuppressed hostsViral cultureAntiviral therapyRoutine cultureClinical specimensAmplification testsCentrifugation cultureViral antigensEnzyme immunoassayMonoclonal antibodiesDiagnostic virologyIdentification of virusesCapture assayCoronavirus diseaseVirusEmergence of epidemicsMedical careIncreasing numberTherapy
2022
Glycan-specific B-1 cells mediate blockade of endogenous retroviruses emergence through recognition of conserved glycan epitopes
Yang Y, Treger R, Hernandez-Bird J, Iwasaki A. Glycan-specific B-1 cells mediate blockade of endogenous retroviruses emergence through recognition of conserved glycan epitopes. The Journal Of Immunology 2022, 208: 126.31-126.31. DOI: 10.4049/jimmunol.208.supp.126.31.Peer-Reviewed Original ResearchB-1 cellsB cell populationsB cellsEndogenous retrovirusesCell-intrinsic controlNatural antibodiesImmunodeficient miceUnimmunized miceGlycan-specific antibodiesClonal repertoirePleural cavityRepertoire profilingViral antigensBlockadeComplement pathwayVH genesCell compartmentAntibodiesGlycan epitopesMiceRetrovirusesAbstract Endogenous retrovirusesEpitopesSensor stimulationCellsLung Transplant Recipients with SARS-CoV-2 Infection Induce Circulating Exosomes with SARS-CoV-2 Spike Protein S2 Which Are Immunogenic in Mice
Bansal S, Fleming T, Perincheri S, Smith M, Bremner R, Mohanakumar T. Lung Transplant Recipients with SARS-CoV-2 Infection Induce Circulating Exosomes with SARS-CoV-2 Spike Protein S2 Which Are Immunogenic in Mice. The Journal Of Heart And Lung Transplantation 2022, 41: s134. PMCID: PMC8988572, DOI: 10.1016/j.healun.2022.01.314.Peer-Reviewed Original ResearchSARS-CoV-2 spike proteinSARS-CoV-2SARS-CoV-2 infectionSARS-CoV-2 spike antigenLung transplant recipientsSpike proteinTransplant recipientsSpike antigenNucleocapsid antigenSARS-CoV-2 infection inducesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Conclusion SARS-CoV-2Lungs of miceSyndrome coronavirus 2Important risk factorSARS-CoV-2 spikeSpike protein antigensC57BL/6 miceCoronavirus 2Severe inflammationInfection inducesRisk factorsViral antigens
2021
Glycan-reactive natural antibodies mediate blockade of endogenous retroviruses emergence
Yang Y, Treger R, Hernandez-Bird J, Iwasaki A. Glycan-reactive natural antibodies mediate blockade of endogenous retroviruses emergence. The Journal Of Immunology 2021, 206: 114.09-114.09. DOI: 10.4049/jimmunol.206.supp.114.09.Peer-Reviewed Original ResearchB-1 cellsB cell populationsB cellsNatural antibodiesEndogenous retrovirusesCell-intrinsic controlImmunodeficient miceSelf-antigensUnimmunized miceFetal haematopoiesisGlycan-specific antibodiesClonal repertoirePleural cavityRepertoire profilingViral antigensBlockadeComplement pathwayVH genesCell compartmentAntibodiesCell-specificAbstract Endogenous retrovirusesMiceGenetic invadersVertebrate genomes
2020
Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation
Yeh YJ, Jenike KM, Calvi RM, Chiarella J, Hoh R, Deeks SG, Ho YC. Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation. Journal Of Clinical Investigation 2020, 130: 4969-4984. PMID: 32573496, PMCID: PMC7456222, DOI: 10.1172/jci137371.Peer-Reviewed Original ResearchConceptsHIV-1 reactivationHIV-1-infected cellsT cell activationImmune activationHIV-1-induced immune activationCell activationHIV-1 RNA transcriptionHIV-1-infected individualsDrug screensEffective antiretroviral therapyHIV-1 transcriptionFilgotinib treatmentImmune exhaustionAntiretroviral therapyCell line modelsCancer-related gene expressionHIV-1 splicingViral antigensT cellsDrug treatmentHigh-throughput drug screensJAK inhibitorsFilgotinibDruggable targetsDrug candidates
2015
Clinicopathologic Characteristics and Immunolocalization of Viral Antigens in Chikungunya-Associated Fatal Cases—Puerto Rico, 2014
Sharp T, Shieh W, Levine R, Blau D, Torres J, Rivera A, Perez-Padilla J, Thomas D, Velazquez J, Bhatnagar J, Ng D, Keating M, Hunsperger E, Munoz-Jordan J, Sanabria D, Garcia B, Margolis H, Zaki S. Clinicopathologic Characteristics and Immunolocalization of Viral Antigens in Chikungunya-Associated Fatal Cases—Puerto Rico, 2014. Open Forum Infectious Diseases 2015, 2: 1975. DOI: 10.1093/ofid/ofv131.180.Peer-Reviewed Original Research
2010
Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections.
Gill JR, Sheng ZM, Ely SF, Guinee DG, Beasley MB, Suh J, Deshpande C, Mollura DJ, Morens DM, Bray M, Travis WD, Taubenberger JK. Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections. Archives Of Pathology & Laboratory Medicine 2010, 134: 235-43. PMID: 20121613, PMCID: PMC2819217, DOI: 10.5858/134.2.235.Peer-Reviewed Original ResearchConceptsPulmonary pathologic findingsPathologic findingsCardiorespiratory diseaseInfluenza A/H1N1 virusNovel pandemic influenza virusH1N1 viral infectionInfluenza viral antigensFirst influenza pandemicPandemic influenza virusReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionAlveolar epithelial cellsChief Medical ExaminerWorld Health OrganizationAlveolar damageClinicopathologic characteristicsAutopsy evidenceBacterial pneumoniaPathology findingsH1N1 virusMedical recordsMicrobiologic studiesRespiratory tractViral antigensInfluenza pandemic
2008
Dendritic cells and B cells maximize mucosal Th1 memory response to herpes simplex virus
Iijima N, Linehan MM, Zamora M, Butkus D, Dunn R, Kehry MR, Laufer TM, Iwasaki A. Dendritic cells and B cells maximize mucosal Th1 memory response to herpes simplex virus. Journal Of Experimental Medicine 2008, 205: 3041-3052. PMID: 19047439, PMCID: PMC2605233, DOI: 10.1084/jem.20082039.Peer-Reviewed Original ResearchConceptsMemory Th1 cellsDendritic cellsTh1 cellsB cellsIFN-gammaHerpes simplex virus 2 infectionAntiviral protectionSimplex virus 2 infectionMemory CD4 T cellsFurther viral replicationTh1 memory responseHSV-2 infectionCD4 T cellsLocal dendritic cellsVirus 2 infectionAntigen-presenting cellsCytotoxic T lymphocytesMHC class IISite of infectionHerpes simplex virusTh1 responseImmunized miceRecall responsesViral antigensMHC classThe Influence of Injury on Toll-Like Receptor Responses
Murphy T, Maung A, Paterson H, Lederer J. The Influence of Injury on Toll-Like Receptor Responses. 2008, 185-202. DOI: 10.1201/9781420043198-17.ChaptersToll-like receptorsToll-like receptor responsesAdaptive immune responsesInfluence of injuryStrong inflammatory responseInnate immune systemCommon microbial antigensSentinel receptorsTLR ligandsMicrobial antigensInflammatory responseViral antigensTissue injuryTLR responsesImmune responseCell injuryReceptor responsesImmune systemTissue damageInjury responseEndogenous factorsMicrobial ligandsInjuryInfectionIntracellular receptorsAutophagy and antiviral immunity
Lee HK, Iwasaki A. Autophagy and antiviral immunity. Current Opinion In Immunology 2008, 20: 23-29. PMID: 18262399, PMCID: PMC2271118, DOI: 10.1016/j.coi.2008.01.001.Peer-Reviewed Original ResearchConceptsViral infectionViral replicationAdaptive antiviral immune responsesEndogenous viral antigensCD4 T cellsMHC class II loading compartmentsAntiviral immune responseCritical effector mechanismAdaptive immune systemViral antigensEffector mechanismsT cellsImmune responseAntiviral immunityImmune systemLoading compartmentCertain virusesInfectionAutophagyRecent studiesCellsAntigenImmunityCellular homeostasis
2007
Blockade of NKG2D on NKT cells prevents hepatitis and the acute immune response to hepatitis B virus
Vilarinho S, Ogasawara K, Nishimura S, Lanier LL, Baron JL. Blockade of NKG2D on NKT cells prevents hepatitis and the acute immune response to hepatitis B virus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 18187-18192. PMID: 17991774, PMCID: PMC2084318, DOI: 10.1073/pnas.0708968104.Peer-Reviewed Original ResearchConceptsHepatitis B virusHepatitis B viral infectionB virusImmune responseAcute hepatitisNKT cellsLiver injuryViral infectionCell-mediated immune responsesBlockade of NKG2DPrimary HBV infectionAcute liver injuryAcute immune responseTransgenic mouse modelPotential therapeutic targetNKG2D-ligand interactionChronic hepatitisHBV infectionAlpha-GalCerNatural killerHepatic pathologyViral antigensMouse modelTherapeutic targetHepatitis
2004
Automated detection of immunofluorescently labeled cytomegalovirus‐infected cells in isolated peripheral blood leukocytes using decision tree analysis
Ladanyi A, Sher AC, Herlitz A, Bergsrud DE, Kraeft S, Kepros J, McDaid G, Ferguson D, Landry ML, Chen LB. Automated detection of immunofluorescently labeled cytomegalovirus‐infected cells in isolated peripheral blood leukocytes using decision tree analysis. Cytometry Part A 2004, 58A: 147-156. PMID: 15057968, DOI: 10.1002/cyto.a.20016.Peer-Reviewed Original ResearchConceptsPeripheral blood leukocytesBlood leukocytesPatient samplesDecision tree analysisImage cytometryCytomegalovirus-infected cellsCMV infectionCytomegalovirus infectionAntiviral therapyViral antigensCellular featuresCytospin preparationsLeukocytesInfectionCytometryManual microscopic analysisImage cytometerRare cellsCellsSimilar resultsPatientsCMVTherapyAntigenDiagnosis
1998
Rabies virus entry into cultured rat hippo campalneurons
Lewis P, Lentz T. Rabies virus entry into cultured rat hippo campalneurons. Brain Cell Biology 1998, 27: 559-573. PMID: 10405023, DOI: 10.1023/a:1006912610044.Peer-Reviewed Original ResearchConceptsRabies virus entryCultured hippocampal neuronsViral antigensHippocampal neuronsRabies virusVirus entryRabies virus infectionSynaptic vesicle markersAxon terminalsNerve terminalsVirus infectionLysosomotropic agent chloroquineSomatodendritic domainCell bodiesVirus-containing endosomesLucifer YellowNeuronsSynapsin IInfectionAntigenTransferrin receptorVirusWheat germ agglutininAgent chloroquineVesicle markersEffects of retinoic acid on the expression of a tumor rejection antigen (heat shock protein gp96) in human cervical cancer.
Santin AD, Hermonat PL, Ravaggi A, Chiriva-Internati M, Pecorelli S, Parham GP. Effects of retinoic acid on the expression of a tumor rejection antigen (heat shock protein gp96) in human cervical cancer. European Journal Of Gynaecological Oncology 1998, 19: 229-33. PMID: 9641219.Peer-Reviewed Original ResearchConceptsHeat shock protein gp96Shock protein gp96Tumor rejection antigensHuman cervical cancerCervical cancerRetinoic acidRejection antigensTumor cellsMajor histocompatibility complex class IPresentation of tumorHistocompatibility complex class IBiologic response modifiersCervical cancer cell linesCo-stimulation moleculesComplex class ICell linesCervical carcinoma cell linesHuman cervical carcinoma cell lineCancer cell linesCarcinoma cell linesHumoral immunityTherapeutic dosesViral antigensResponse modifiersICAM-1The effects of irradiation on the expression of a tumour rejection antigen (heat shock protein gp96) in human cervical cancer
Santin AD, Hermonat PL, Ravaggi A, Chiriva-Internati M, Hiserodt JC, Batchu RB, Pecorelli S, Parham GP. The effects of irradiation on the expression of a tumour rejection antigen (heat shock protein gp96) in human cervical cancer. International Journal Of Radiation Biology 1998, 73: 699-704. PMID: 9690688, DOI: 10.1080/095530098141951.Peer-Reviewed Original ResearchConceptsTumor rejection antigensHeat shock protein gp96Shock protein gp96Human cervical cancerCervical carcinoma cell linesRejection antigensHigh dosesHuman cervical carcinoma cell lineCervical cancerCarcinoma cell linesTumor cellsMajor histocompatibility complex class ILocal radiation therapyHistocompatibility complex class IBiologic response modifiersCo-stimulation moleculesComplex class ICell linesCervical cancer cellsDose-dependent mannerViral antigensResponse modifiersICAM-1Radiation therapyGp96 mRNA
1997
Rabies virus infection of IMR-32 human neuroblastoma cells and effect of neurochemical and other agents
Lentz T, Fu Y, Lewis P. Rabies virus infection of IMR-32 human neuroblastoma cells and effect of neurochemical and other agents. Antiviral Research 1997, 35: 29-39. PMID: 9224959, DOI: 10.1016/s0166-3542(97)01036-x.Peer-Reviewed Original ResearchConceptsIMR-32 human neuroblastoma cellsIMR-32 cellsHuman neuroblastoma cellsNeuroblastoma cellsNeuronal nicotinic acetylcholine receptorsCentral nervous system receptorsRabies virusRabies virus infectionLysosomotropic agentsReceptor alpha1 subunitNicotinic acetylcholine receptorsNerve cell lineAttachment of virusNeurotropic virusesCholinergic agonistsViral antigensVirus infectionHuman neuronsAcetylcholine receptorsSynthetic peptidesCell bodiesInfectionAlpha1 subunitCholinergic ligandsBinding receptors
1992
Infectivity and pathogenesis of iridescent virus type 22 in various insect hosts
Tesh R, Andreadis T. Infectivity and pathogenesis of iridescent virus type 22 in various insect hosts. Archives Of Virology 1992, 126: 57-65. PMID: 1355961, DOI: 10.1007/bf01309684.Peer-Reviewed Original ResearchConceptsType 22Day observation periodViral antigensInfected mosquitoesVirus replicationObservation periodTransovarial transmissionPathogenesisDifferent organsVirus particlesHost cell cytoplasmSmall percentageSand fliesSpecies of mosquitoesInfectivityMidgut epitheliumMosquitoesPhlebotomine sand fliesCell cytoplasmFat bodyMortalityTrachealAntigenInfected insectsEpithelium
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