Bony De Kumar, PhD
Research Scientist; Director of Operations of the Yale Center for Genome AnalysisCards
About
Research
Publications
2024
The amalgam of naive CD4+ T cell transcriptional states is reconfigured by helminth infection to dampen the amplitude of the immune response
Even Z, Meli A, Tyagi A, Vidyarthi A, Briggs N, de Kouchkovsky D, Kong Y, Wang Y, Waizman D, Rice T, De Kumar B, Wang X, Palm N, Craft J, Basu M, Ghosh S, Rothlin C. The amalgam of naive CD4+ T cell transcriptional states is reconfigured by helminth infection to dampen the amplitude of the immune response. Immunity 2024, 57: 1893-1907.e6. PMID: 39096910, PMCID: PMC11421571, DOI: 10.1016/j.immuni.2024.07.006.Peer-Reviewed Original ResearchT cell receptorImmune responseNaive CD4<sup>+</sup> T cellsCD4<sup>+</sup> T cellsIFN-IHelminth infectionsNippostrongylus brasiliensis infectionDecreased immune responseType I interferonNaive TT cellsMemory-likeUnrelated antigensTranscriptional changesExtracellular matrixSPF miceCell receptorsI interferonGerm-freeResponse to certain environmental cuesInfectionMiceFunctional changesCell transcriptional statesTranscriptional heterogeneityIntranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract
Mao T, Kim J, Peña-Hernández M, Valle G, Moriyama M, Luyten S, Ott I, Gomez-Calvo M, Gehlhausen J, Baker E, Israelow B, Slade M, Sharma L, Liu W, Ryu C, Korde A, Lee C, Monteiro V, Lucas C, Dong H, Yang Y, Initiative Y, Gopinath S, Wilen C, Palm N, Dela Cruz C, Iwasaki A, Vogels C, Hahn A, Chen N, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Grubaugh N. Intranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319566121. PMID: 38648490, PMCID: PMC11067057, DOI: 10.1073/pnas.2319566121.Peer-Reviewed Original ResearchConceptsInterferon-stimulated genesRespiratory infectionsStrains of influenza A virusTreatment of respiratory viral infectionsRespiratory virus infectionsInfluenza A virusMouse model of COVID-19Respiratory viral infectionsNeomycin treatmentExpression of interferon-stimulated genesUpper respiratory infectionInterferon-stimulated gene expressionLower respiratory infectionsBroad spectrum of diseasesAdministration of neomycinRespiratory viral diseasesDisease to patientsUpper respiratory tractIntranasal deliveryCongenic miceIntranasal applicationNasal mucosaSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2A virusThe chemokine receptor CXCR3 promotes CD8+ T cell–dependent lung pathology during influenza pathogenesis
Guo K, Yombo D, Wang Z, Navaeiseddighi Z, Xu J, Schmit T, Ahamad N, Tripathi J, De Kumar B, Mathur R, Hur J, Sun J, Olszewski M, Khan N. The chemokine receptor CXCR3 promotes CD8+ T cell–dependent lung pathology during influenza pathogenesis. Science Advances 2024, 10: eadj1120. PMID: 38170765, PMCID: PMC10776024, DOI: 10.1126/sciadv.adj1120.Peer-Reviewed Original ResearchConceptsLung pathologyT cellsLung injuryCytotoxic responsePeak viral loadChemokine receptor CXCR3Wild-type CD8Robust cytotoxic responseSingle-cell RNA sequencing analysisCXCR3 blockadeAdoptive transferEffector potentialT subpopulationsT effectorsViral clearanceViral loadEffector subsetsReceptor CXCR3Influenza pathogenesisCD8Therapeutic effectMurine lungInfluenza controlCentral memoryCXCR3Hox Genes
Duraiswamy A, Senkumar L, De Kumar B. Hox Genes. 2024 DOI: 10.1016/b978-0-12-822563-9.00196-7.Peer-Reviewed Original ResearchHox genesAberrant expression of HOX genesCell fate determinationExpression of Hox genesFate determinationTissue homeostasisMetastatic behavior of tumorsCell migrationGenesDevelopmental eventsDevelopmental defectsHoxCancer progressionAberrant expressionMetastatic behaviorBehavior of tumorsCellsDisease progressionDisease prognosisProteinHomeostasisOrganogenesisPrognosis
2023
Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding
Dastidar S, De Kumar B, Lauckner B, Parrello D, Perley D, Vlasenok M, Tyagi A, Koney N, Abbas A, Nechaev S. Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding. Nature Communications 2023, 14: 7420. PMID: 37973875, PMCID: PMC10654513, DOI: 10.1038/s41467-023-43157-7.Peer-Reviewed Original ResearchMultiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival
Sun Z, Zhang Z, Banu K, Gibson I, Colvin R, Yi Z, Zhang W, De Kumar B, Reghuvaran A, Pell J, Manes T, Djamali A, Gallon L, O'Connell P, He J, Pober J, Heeger P, Menon M. Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival. Journal Of Clinical Investigation 2023, 133: e170420. PMID: 37676733, PMCID: PMC10617779, DOI: 10.1172/jci170420.Peer-Reviewed Original ResearchConceptsDeath-censored graft lossHuman leukocyte antigenExpression quantitative trait lociT cellsTGF-β1TGF-β1/Smad pathwayDonor-recipient differencesKidney allograft lossChronic allograft rejectionKidney transplant survivalDonor-recipient mismatchActive TGF-β1Allograft lossGraft lossAllograft rejectionTransplant cohortPeripheral bloodLeukocyte antigenClinical trialsImmune cellsHaplotype mismatchGenome-wide scaleTransplant survivalQuantitative trait lociSingle nucleotide polymorphism dataShared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube
Afzal Z, Lange J, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter B, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023, 150: dev201259. PMID: 37102683, PMCID: PMC10233718, DOI: 10.1242/dev.201259.Peer-Reviewed Original ResearchConceptsNascent transcriptionDynamic regulatory interactionsHox gene expressionCis-regulatory elementsRetinoic acid response elementMouse neural tubeTranscription of genesNon-coding RNAAcid response elementSingle-molecule fluorescentRetinoic acid responseMutant embryosHOXB clusterHox expressionAxial identityHoxb genesRegulatory interactionsTranscriptional mechanismsGene expressionDependent enhancersTranscriptionResponse elementResponsive enhancerNeural tubeCompetitive interactionsEnhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants
Moriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.Peer-Reviewed Original ResearchConceptsMHC-I expressionBreakthrough infectionsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variantsMajor histocompatibility complex class I expressionCell-mediated immunityInfluenza virus infectionSARS-CoV-2 VOCsMHC-I upregulationClass I expressionSARS-CoV-2T cell recognitionVirus infectionMHC II expressionSpike proteinEnhanced inhibitionInfectionCell recognitionCommon mutationsReinfectionE proteinAntibodiesViral genesSubvariantsExpressionUtility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasms
Chhoda A, Sharma A, Sailo B, Tang H, Ruzgar N, Tan W, Ying L, Khatri R, Narayanan A, Mane S, De Kumar B, Wood L, Iacobuzio-Donahue C, Wolfgang C, Kunstman J, Salem R, Farrell J, Ahuja N. Utility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasms. Clinical Epigenetics 2023, 15: 28. PMID: 36803844, PMCID: PMC9942382, DOI: 10.1186/s13148-023-01429-5.Peer-Reviewed Original ResearchConceptsPapillary mucinous neoplasmMalignant risk stratificationCACNA1G geneRisk stratificationMucinous neoplasmsBiomarker panelBackgroundIntraductal papillary mucinous neoplasmIntraductal papillary mucinous neoplasmEarly detectionPrevious case-control studyHigh-grade dysplasiaCase-control studyPancreatic cancer precursorsReceiver Operating Characteristic (ROC) curve analysisSignificant diagnostic challengeCross-sectional imagingCharacteristic curve analysisOperating Characteristic curve analysisG geneHigh diagnostic specificityPrior validation studiesSignificant procedural riskIPMN tissuesSurgical resectionAdvanced neoplasiaAge-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose
Filardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.Peer-Reviewed Original ResearchConceptsBooster doseAntibody responseNeutralization titersVirus-specific IgG titersOlder adultsAntiviral humoral immunityPlasma antibody responsesHigh-risk populationSARS-CoV-2 spikeYears of ageAge-dependent impairmentHeterologous regimensBooster dosesBooster vaccineCoronaVac vaccineIgG titersProtective immunityHumoral immunityHumoral responseCoronaVacOmicron waveBooster strategyAge groupsEarly controlVaccine