Featured Publications
Maturation of germinal center B cells after influenza virus vaccination in humans
McIntire K, Meng H, Lin T, Kim W, Moore N, Han J, McMahon M, Wang M, Malladi S, Mohammed B, Zhou J, Schmitz A, Hoehn K, Carreño J, Yellin T, Suessen T, Middleton W, Teefey S, Presti R, Krammer F, Turner J, Ward A, Wilson I, Kleinstein S, Ellebedy A. Maturation of germinal center B cells after influenza virus vaccination in humans. Journal Of Experimental Medicine 2024, 221: e20240668. PMID: 38935072, PMCID: PMC11211068, DOI: 10.1084/jem.20240668.Peer-Reviewed Original ResearchConceptsB cellsInfluenza vaccineGerminal centersAntigen-specific GC B cellsResponse to seasonal influenza vaccinationLong-lived bone marrow plasma cellsResponse to influenza vaccinationBone marrow plasma cellsGerminal center B cellsGC B cell clonesInfluenza virus vaccineMaturation of B cellsMarrow plasma cellsSeasonal influenza vaccineMemory B cellsHemagglutinin (HAB cell clonesGC B cellsInfluenza hemagglutinin (HAH5 HANeedle aspirationLymphoid structuresLymph nodesPlasma cellsGC reactionB cell phylogenetics in the single cell era
Hoehn K, Kleinstein S. B cell phylogenetics in the single cell era. Trends In Immunology 2023, 45: 62-74. PMID: 38151443, PMCID: PMC10872299, DOI: 10.1016/j.it.2023.11.004.Peer-Reviewed Original ResearchMulti-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients
Diray-Arce J, Fourati S, Jayavelu N, Patel R, Maguire C, Chang A, Dandekar R, Qi J, Lee B, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi J, Kho A, Chen J, Pawar S, Gonzalez-Reiche A, Hoch A, Milliren C, Overton J, Westendorf K, Network I, Abraham J, Adkisson M, Albert M, Torres L, Alvarenga B, Anderson M, Anderson E, Arnett A, Asashima H, Atkinson M, Baden L, Barton B, Beach K, Beagle E, Becker P, Bell M, Bernui M, Bime C, Kumar A, Booth L, Borresen B, Brakenridge S, Bristow L, Bryant R, Calfee C, Manuel J, Carrillo S, Chak S, Chang I, Connors J, Conway M, Corry D, Cowan D, Croen B, Dela Cruz C, Cusimano G, Eaker L, Edwards C, Ehrlich L, Elashoff D, Erickson H, Erle D, Farhadian S, Farrugia K, Fatou B, Fernandes A, Fernandez-Sesma A, Fragiadakis G, Furukawa S, Geltman J, Ghale R, Bermúdez M, Goonewardene M, Sanchez E, Guirgis F, Hafler D, Hamilton S, Harris P, Nemati A, Hendrickson C, Agudelo N, Hodder T, Holland S, Hough C, Huerta C, Hurley K, Hutton S, Iwasaki A, Jauregui A, Jha M, Johnson B, Joyner D, Kangelaris K, Kelly G, Khalil Z, Khan Z, Kheradmand F, Kim J, Kimura H, Ko A, Kohr B, Kraft M, Krummel M, Kutzler M, Lasky-Su J, Lee S, Lee D, Leipold M, Lentucci C, Leroux C, Lin E, Liu S, Love C, Lu Z, Maliskova L, Roth B, Manohar M, Martens M, McComsey G, McEnaney K, McLin R, Melamed E, Melnyk N, Mendez K, Messer W, Metcalf J, Michelotti G, Mick E, Mohanty S, Mosier J, Mulder L, Murphy M, Nadeau K, Nelson E, Nelson A, Nguyen V, Oberhaus J, Panganiban B, Pellegrini K, Pickering H, Powell D, Presnell S, Pulendran B, Rahman A, Sadeed A, Raskin A, Reed E, Pereira S, Rivera A, Rogers J, Rogers A, Rogowski B, Rooks R, Rosenberg-Hasson Y, Rothman J, Rousseau J, Salehi-Rad R, Saluvan M, Samaha H, Schaenman J, Schunk R, Semenza N, Sen S, Sevransky J, Seyfert-Margolis V, Shaheen T, Shaw A, Sieg S, Siegel S, Sigal N, Siles N, Simmons B, Simon V, Singh G, Sinko L, Smith C, Smolen K, Song L, Srivastava K, Sullivan P, Syphurs C, Tcheou J, Tegos G, Tharp G, Ally A, Tsitsiklis A, Ungaro R, Vaysman T, Viode A, Vita R, Wang X, Ward A, Ward D, Willmore A, Woloszczuk K, Wong K, Woodruff P, Xu L, van Haren S, van de Guchte A, Zhao Y, Cairns C, Rouphael N, Bosinger S, Kim-Schulze S, Krammer F, Rosen L, Grubaugh N, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier C, Levy O, Altman M, Maecker H, Montgomery R, Haddad E, Sekaly R, Esserman D, Ozonoff A, Becker P, Augustine A, Guan L, Peters B, Kleinstein S. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Reports Medicine 2023, 4: 101079. PMID: 37327781, PMCID: PMC10203880, DOI: 10.1016/j.xcrm.2023.101079.Peer-Reviewed Original ResearchConceptsDisease courseFatal COVID-19 diseaseHospitalized COVID-19 patientsSevere disease courseCOVID-19 participantsCOVID-19 patientsTrajectory groupsHost immune responseCOVID-19 diseaseImmune correlatesAcute infectionClinical courseHospital admissionClinical outcomesFatal outcomeClinical prognosisImmune responseSevere diseaseLongitudinal bloodNasal samplesBiologic stateLongitudinal studyDistinct assaysCohortMolecular signaturesBenchmarking transcriptional host response signatures for infection diagnosis
Chawla D, Cappuccio A, Tamminga A, Sealfon S, Zaslavsky E, Kleinstein S. Benchmarking transcriptional host response signatures for infection diagnosis. Cell Systems 2022, 13: 974-988.e7. PMID: 36549274, PMCID: PMC9768893, DOI: 10.1016/j.cels.2022.11.007.Peer-Reviewed Original ResearchConceptsInfection diagnosisHost response signatureNon-infectious conditionsClinical applicationResponse signatureChronic infectionPathogen of interestBacterial infectionsInfectionSignature of infectionDisease signaturesDiagnosisTranscriptional profilesStandardized methodologyDevelopment of signaturesDecreased performance
2024
Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality
Gygi J, Maguire C, Patel R, Shinde P, Konstorum A, Shannon C, Xu L, Hoch A, Jayavelu N, Haddad E, Network I, Reed E, Kraft M, McComsey G, Metcalf J, Ozonoff A, Esserman D, Cairns C, Rouphael N, Bosinger S, Kim-Schulze S, Krammer F, Rosen L, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier C, Steen H, Altman M, Montgomery R, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen K, Fragiadakis G, Becker P, Sekaly R, Ehrlich L, Fourati S, Peters B, Kleinstein S, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. Journal Of Clinical Investigation 2024, 134: e176640. PMID: 38690733, PMCID: PMC11060740, DOI: 10.1172/jci176640.Peer-Reviewed Original ResearchConceptsClinical outcomesImmune cascadeElevated levels of inflammatory cytokinesDisease severityLevels of inflammatory cytokinesFormation of neutrophil extracellular trapsAcute COVID-19 severityCritically ill patientsNeutrophil extracellular trapsDevelopment of therapiesCOVID-19 cohortCOVID-19 severityViral clearanceImmunosuppressive metabolitesDeep immunophenotypingMultiomic modelIFN-stimulated genesImmunophenotypic assessmentB cellsDisease courseEarly upregulationInflammatory cytokinesDisease progressionIFN inhibitorsExtracellular trapsA supervised Bayesian factor model for the identification of multi-omics signatures
Gygi J, Konstorum A, Pawar S, Aron E, Kleinstein S, Guan L. A supervised Bayesian factor model for the identification of multi-omics signatures. Bioinformatics 2024, 40: btae202. PMID: 38603606, PMCID: PMC11078774, DOI: 10.1093/bioinformatics/btae202.Peer-Reviewed Original ResearchConceptsMulti-omics signaturesBayesian factor modelMulti-omics dataMulti-omics integrationSupplementary dataOmics datasetsMulti-omicsProfiling datasetsR packageDiverse assaysImproved biological understandingProfiling assaysSignature discoveryBioinformaticsProfiling studiesBiological understandingDimensionality reductionBiological responsesBiological signaturesCombination of dimensionality reductionInferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.
Jensen C, Sumner J, Kleinstein S, Hoehn K. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. The Journal Of Immunology 2024, 212: 1579-1588. PMID: 38557795, PMCID: PMC11073909, DOI: 10.4049/jimmunol.2300851.Peer-Reviewed Original ResearchConceptsPhylogenetic treeL chainsBranch lengthsBCR sequencesTree-building methodsSingle-cell sequencing dataHistory of mutationsSingle-cell sequencingPhylogenetic methodsSequence dataSequencing technologiesL chain sequencesTree accuracyEvolutionary processSingle-cellPhylogenyImmune responseSomatic hypermutationSequenceClonesMutationsB cell clonesHuman immune responseTreesBCRCD23+IgG1+ memory B cells are poised to switch to pathogenic IgE production in food allergy
Ota M, Hoehn K, Fernandes-Braga W, Ota T, Aranda C, Friedman S, Miranda-Waldetario M, Redes J, Suprun M, Grishina G, Sampson H, Malbari A, Kleinstein S, Sicherer S, Curotto de Lafaille M. CD23+IgG1+ memory B cells are poised to switch to pathogenic IgE production in food allergy. Science Translational Medicine 2024, 16: eadi0673. PMID: 38324641, PMCID: PMC11008013, DOI: 10.1126/scitranslmed.adi0673.Peer-Reviewed Original ResearchConceptsMemory B cellsB cellsIgE-producing cellsPeanut allergySerum peanut-specific IgEFood allergyInterleukin-4 (IL-4)-B cell memoryPeanut-specific IgEAllergen-specific immunoglobulin EHigh-affinity B cellsPersistent IgE responsesConcentration of IgESingle-cell RNA sequencing experimentsMemory populationRNA sequencing experimentsIgE productionImmune responseImmunoglobulin ECirculating concentrationsIgE responseAllergySequencing experimentsAra h 2Long-term persistenceIgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition
Ozonoff A, Ehrlich L, Melamed E, Sesma A, Simon V, Pulendran B, Nadeau K, Davis M, McCoey G, Sekaly R, Baden L, Levy O, Schaenman J, Reed E, Shaw A, Hafler D, Montgomery R, Kleinstein S, Becker P, Augustine A, Calfee C, Erle D, DeBakey M, Corry D, Kheradmand F, Atkinson M, Brakenridge S, Higuita N, Metcalf J, Hough C, Messer W, Kraft M, Bime C, Peters B, Milliren C, Syphurs C, McEnaney K, Barton B, Lentucci C, Saluvan M, Chang A, Hoch A, Albert M, Shaheen T, Kho A, Liu S, Thomas S, Chen J, Murphy M, Cooney M, Hayati A, Bryant R, Abraham J, Jayavelu N, Presnell S, Jancsyk T, Maguire C, Qi J, Lee B, Fourati S, Esserman D, Guan L, Gygi J, Pawar S, Brito A, Fragiadakis G, Patel R, Overton J, Vita R, Westendorf K, Shannon C, Tebbutt S, Thyagarajan R, Rousseau J, Wylie D, Triplett T, Kojic E, Chinthrajah S, Ahuja N, Rogers A, Artandi M, Geng L, Yendewa G, Powell D, Kim J, Simmons B, Goonewardene I, Smith C, Martens M, Sherman A, Walsh S, Issa N, Salehi-Rad R, Dela Cruz C, Farhadian S, Iwasaki A, Ko A, Anderson E, Mehta A, Sevransky J, Seyfert-Margolis V, Leligdowicz A, Matthay M, Singer J, Kangelaris K, Hendrickson C, Krummel M, Langelier C, Woodruff P, Corry D, Kheradmand F, Anderson M, Guirgis F, Drevets D, Brown B, Siegel S, Lu Z, Mosier J, Kimura H, Khor B, van Bakel H, Rahman A, Stadlbauer D, Dutta J, Xie H, Kim-Schulze S, Gonzalez-Reiche A, van de Guchte A, Carreño J, Singh G, Raskin A, Tcheou J, Bielak D, Kawabata H, Kelly G, Patel M, Nie K, Yellin T, Fried M, Sullivan L, Morris S, Sieg S, Steen H, van Zalm P, Fatou B, Mendez K, Lasky-Su J, Hutton S, Michelotti G, Wong K, Jha M, Viode A, Kanarek N, Petrova B, Zhao Y, Bosinger S, Boddapati A, Tharp G, Pellegrini K, Beagle E, Cowan D, Hamilton S, Ribeiro S, Hodder T, Rosen L, Lee S, Wilson M, Dandekar R, Alvarenga B, Rajan J, Eckalbar W, Schroeder A, Tsitsiklis A, Mick E, Guerrero Y, Love C, Maliskova L, Adkisson M, Siles N, Geltman J, Hurley K, Saksena M, Altman D, Srivastava K, Eaker L, Bermúdez-González M, Beach K, Sominsky L, Azad A, Mulder L, Kleiner G, Lee A, Do E, Fernandes A, Manohar M, Hagan T, Blish C, Din H, Roque J, Yang S, Sigal N, Chang I, Tribout H, Harris P, Consolo M, Edwards C, Lee E, Lin E, Croen B, Semenza N, Rogowski B, Melnyk N, Bell M, Furukawa S, McLin R, Schearer P, Sheidy J, Tegos G, Nagle C, Smolen K, Desjardins M, van Haren S, Mitre X, Cauley J, Li X, Tong A, Evans B, Montesano C, Licona J, Krauss J, Chang J, Izaguirre N, Rooks R, Elashoff D, Brook J, Ramires-Sanchez E, Llamas M, Rivera A, Perdomo C, Ward D, Magyar C, Fulcher J, Pickering H, Sen S, Chaudhary O, Coppi A, Fournier J, Mohanty S, Muenker C, Nelson A, Raddassi K, Rainone M, Ruff W, Salahuddin S, Schulz W, Vijayakumar P, Wang H, Wunder E, Young H, Rothman J, Konstorum A, Chen E, Cotsapas C, Grubaugh N, Wang X, Xu L, Asashima H, Bristow L, Hussaini L, Hellmeister K, Samaha H, Wimalasena S, Cheng A, Spainhour C, Scherer E, Johnson B, Bechnak A, Ciric C, Hewitt L, Carter E, Mcnair N, Panganiban B, Huerta C, Usher J, Vaysman T, Holland S, Abe-Jones Y, Asthana S, Beagle A, Bhide S, Carrillo S, Chak S, Ghale R, Gonzalez A, Jauregui A, Jones N, Lea T, Lee D, Lota R, Milush J, Nguyen V, Pierce L, Prasad P, Rao A, Samad B, Shaw C, Sigman A, Sinha P, Ward A, Willmore A, Zhan J, Rashid S, Rodriguez N, Tang K, Altamirano L, Betancourt L, Curiel C, Sutter N, Paz M, Tietje-Ulrich G, Leroux C, Thakur N, Vasquez J, Santhosh L, Song L, Nelson E, Moldawer L, Borresen B, Roth-Manning B, Ungaro R, Oberhaus J, Booth J, Sinko L, Brunton A, Sullivan P, Strnad M, Lyski Z, Coulter F, Micheleti C, Conway M, Francisco D, Molzahn A, Erickson H, Wilson C, Schunk R, Sierra B, Hughes T. IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nature Communications 2024, 15: 404. PMID: 38195739, PMCID: PMC10776791, DOI: 10.1038/s41467-023-44211-0.Peer-Reviewed Original Research
2023
Prior cycles of anti-CD20 antibodies affect antibody responses after repeated SARS-CoV-2 mRNA vaccination
Asashima H, Kim D, Wang K, Lele N, Buitrago-Pocasangre N, Lutz R, Cruz I, Raddassi K, Ruff W, Racke M, Wilson J, Givens T, Grifoni A, Weiskopf D, Sette A, Kleinstein S, Montgomery R, Shaw A, Li F, Fan R, Hafler D, Tomayko M, Longbrake E. Prior cycles of anti-CD20 antibodies affect antibody responses after repeated SARS-CoV-2 mRNA vaccination. JCI Insight 2023, 8: e168102. PMID: 37606046, PMCID: PMC10543713, DOI: 10.1172/jci.insight.168102.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 mRNA vaccinationB-cell-depleted patientsB-cell depletionAntibody responseMRNA vaccinationThird doseCell depletionT cellsClaude D. Pepper Older Americans Independence CenterB cellsNational Multiple Sclerosis SocietyAnti-CD20 antibodySpike-specific antibodiesMultiple Sclerosis SocietyLow cumulative exposureLogistic regression modelsImportant clinical needCD20 therapyCD20 treatmentMost patientsThird vaccineSerologic responseVaccine dosesMRNA vaccinesVaccination strategiesA pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
Newton A, Chartash D, Kleinstein S, McDougal R. A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. BMC Bioinformatics 2023, 24: 292. PMID: 37474900, PMCID: PMC10357743, DOI: 10.1186/s12859-023-05397-8.Peer-Reviewed Original ResearchConceptsDomain-specific informationDocument embeddingsSVM classifierSemi-structured representationsTraining setWeb-based formKnowledge repositoryInformation modelAutomatic analysisClassifier predictionsClassifierSignature informationAutomated systemBiomedical publicationsPaper authorsEmbeddingIncomplete information modelLiterature miningIterative processSpecific informationSuch informationInformationLimited setSetQueriesTracking 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 analysisMRNAHigh-throughput single-cell profiling of B cell responses following inactivated influenza vaccination in young and older adults
Wang M, Jiang R, Mohanty S, Meng H, Shaw A, Kleinstein S. High-throughput single-cell profiling of B cell responses following inactivated influenza vaccination in young and older adults. Aging 2023, 15: 9250-9274. PMID: 37367734, PMCID: PMC10564424, DOI: 10.18632/aging.204778.Peer-Reviewed Original ResearchConceptsB cellsActivated B cellsB cell receptorOlder adultsInfluenza vaccinationAge groupsPeripheral blood B cellsYoung adultsInactivated influenza vaccineB cell responsesSubstantial disease burdenBlood B cellsMemory B cellsInfluenza vaccination responsesStrong antibody responseAge-related changesInfluenza vaccineVaccination responseSeasonal influenzaAntibody responseHospital visitsDisease burdenSomatic hypermutation frequenciesVaccinationCell responsesThe Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties
Jiang R, Roy B, Wu Q, Mohanty S, Nowak R, Shaw A, Kleinstein S, O’Connor K. The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties. ImmunoHorizons 2023, 7: 310-322. PMID: 37171806, PMCID: PMC10579972, DOI: 10.4049/immunohorizons.2200078.Peer-Reviewed Original ResearchConceptsInclusion body myositisMemory B cellsCell infiltrateBody myositisB cellsIBM muscle biopsiesB-cell infiltratesPlasma cell infiltrateClass-switched IgGMuscle tissueAdaptive immune receptor repertoire sequencingHumoral responseHealthy controlsIgA isotypePlasma cellsCell repertoireMuscle biopsyInfiltratesDegenerative disordersDisease pathologyRepertoire sequencingSkeletal muscleDermatomyositisPolymyositisMyositisPlatelet response to influenza vaccination reflects effects of aging
Konstorum A, Mohanty S, Zhao Y, Melillo A, Vander Wyk B, Nelson A, Tsang S, Blevins T, Belshe R, Chawla D, Rondina M, Gill T, Montgomery R, Allore H, Kleinstein S, Shaw A. Platelet response to influenza vaccination reflects effects of aging. Aging Cell 2023, 22: e13749. PMID: 36656789, PMCID: PMC9924941, DOI: 10.1111/acel.13749.Peer-Reviewed Original ResearchConceptsCommunity-dwelling older adultsPlatelet activationOlder adultsInfluenza vaccinationAge-associated chronic inflammationInfluence platelet functionRNA expressionPro-inflammatory diseasesAge-associated increasePlatelet activation pathwaysAge-associated differencesActivation pathwayPlatelet transcriptomeGeriatric conditionsChronic inflammationImmune responsePlatelet functionPlatelet responseSNF residentsVaccinationActivation responseYoung individualsProtein levelsAdultsYounger participantsPD-1highCXCR5–CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection
Asashima H, Mohanty S, Comi M, Ruff W, Hoehn K, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein S, Montgomery R, Iwasaki A, Dela Cruz C, Kaminski N, Shaw A, Hafler D, Sumida T. PD-1highCXCR5–CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection. Cell Reports 2023, 42: 111895. PMID: 36596303, PMCID: PMC9806868, DOI: 10.1016/j.celrep.2022.111895.Peer-Reviewed Original ResearchConceptsAcute viral infectionTph cellsViral infectionCXCR3 expressionClinical outcomesHelper TSevere viral infectionsB cell helpBetter clinical outcomesProtective humoral immunityT cell-B cell interactionsKey immune responsesPlasmablast expansionB cell differentiationCell subsetsHumoral immunityCell helpImmune responseInterferon γPlasmablast differentiationB cellsPlasmablastsCell responsesInfectionCD4
2022
Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children
Xu Q, Milanez-Almeida P, Martins A, Radtke A, Hoehn K, Oguz C, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker P, Kitakule M, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain I, McGuire P, Pittaluga S, Germain R, Apps R, Schwartz D, Sadtler K, Moir S, Chertow D, Kleinstein S, Khurana S, Tsang J, Mudd P, Schwartzberg P, Manthiram K. Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children. Nature Immunology 2022, 24: 186-199. PMID: 36536106, PMCID: PMC10777159, DOI: 10.1038/s41590-022-01367-z.Peer-Reviewed Original ResearchConceptsT cell receptorImmune responseGerminal centersPrevious SARS-CoV-2 infectionSARS-CoV-2 infectionB-cell receptor sequencingTissue-specific immunityCell receptor sequencingAdaptive immune responsesUpper respiratory tractMemory B cellsT cell clonotypesSite of infectionSARS-CoV-2Pharyngeal lymphoid tissuePeripheral bloodLymphocyte populationsLymphoid tissueRespiratory tractCell clonotypesAdaptive immunityB cellsCDR3 sequencesAdenoidsCell receptorMulti-objective optimization identifies a specific and interpretable COVID-19 host response signature
Cappuccio A, Chawla D, Chen X, Rubenstein A, Cheng W, Mao W, Burke T, Tsalik E, Petzold E, Henao R, McClain M, Woods C, Chikina M, Troyanskaya O, Sealfon S, Kleinstein S, Zaslavsky E. Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature. Cell Systems 2022, 13: 989-1001.e8. PMID: 36549275, DOI: 10.1016/j.cels.2022.11.008.Peer-Reviewed Original ResearchA curated collection of human vaccination response signatures
Smith K, Chawla D, Dhillon B, Ji Z, Vita R, van der Leest E, Weng J, Tang E, Abid A, Peters B, Hancock R, Floratos A, Kleinstein S. A curated collection of human vaccination response signatures. Scientific Data 2022, 9: 678. PMID: 36347894, PMCID: PMC9643367, DOI: 10.1038/s41597-022-01558-1.Peer-Reviewed Original ResearchTranscriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses
Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Levy O, Gottardo R, Sarwal M, Tsang J, Suárez-Fariñas M, Sékaly R, Kleinstein S, Pulendran B. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nature Immunology 2022, 23: 1788-1798. PMID: 36316475, PMCID: PMC9869360, DOI: 10.1038/s41590-022-01328-6.Peer-Reviewed Original ResearchConceptsAntibody responseDay 1Vaccine-induced antibodiesYellow fever vaccineHuman immune responseMechanisms of immunityB cell activationTranscriptional atlasFever vaccineDifferent vaccinesSystems vaccinologyImmune responseMost vaccinesDay 7Cell activationInnate immunityVaccineVaccinationImmunityCommon predictorsMolecular signaturesResponsePlasmablastsInterferonAntibodies