2024
The cell-type underpinnings of the human functional cortical connectome
Anderson K, Chopra S, Dhamala E, Emani P, Gerstein M, Margulies D, Holmes A. The cell-type underpinnings of the human functional cortical connectome. Nature Neuroscience 2024, 28: 150-160. PMID: 39572742, DOI: 10.1038/s41593-024-01812-2.Peer-Reviewed Original ResearchSingle-nucleus RNA sequencing dataCell-type distributionRNA sequencing dataMicroarray dataSingle-nucleusIn vivo organizationCortical sheetCortical connectomeAllen Human Brain AtlasCell typesFunctional magnetic resonance imagingCellular fingerprintsCortical tissue samplesHuman Brain AtlasOrganization of cortexFunctional organization of cortexCellular compositionBrain atlasesFunctional organizationCellsEnriched cellsAssociative territoryFunctional propertiesTissue samplesSpatial topographyTertiary Lymphoid Structures and Immunotherapy: Challenges and Opportunities
Ruddle N. Tertiary Lymphoid Structures and Immunotherapy: Challenges and Opportunities. Methods In Molecular Biology 2024, 2864: 299-312. PMID: 39527229, DOI: 10.1007/978-1-0716-4184-2_16.Peer-Reviewed Original ResearchConceptsImmune-related adverse eventsImmune checkpoint inhibitorsTertiary lymphoid structuresSecondary lymphoid organsTA-TLSSusceptibility to immune-related adverse eventsAssociated with favorable clinical outcomesPositive response to immunotherapyResponse to immunotherapyFavorable clinical outcomesCellular compositionVascular growth factorsAccumulation of lymphoid cellsCheckpoint inhibitorsLymphoid neogenesisLymphoid structuresProcess of lymphoid neogenesisClinical outcomesAdenovirus vectorLymphoid cellsTumor-associatedAdverse eventsTumor environmentOrgan rejectionChronic inflammationIs Clot Composition Associated With Cause of Stroke? A Systematic Review and Meta‐Analysis
Sujijantarat N, Templeton K, Antonios J, Renedo D, Koo A, Haynes J, Fathima B, Amllay A, Nowicki K, Huttner A, Giles J, Navaratnam D, Sansing L, Hebert R, King J, Matouk C. Is Clot Composition Associated With Cause of Stroke? A Systematic Review and Meta‐Analysis. Stroke Vascular And Interventional Neurology 2024, 4 DOI: 10.1161/svin.124.001426.Peer-Reviewed Original ResearchCause of strokeRed blood cellsWhite blood cellsBlood cellsMechanical thrombectomyCardioembolic groupHistological compositionMeta-analysisLow red blood cellQuantity of red blood cellsRandom-effects meta-analysisAcute ischemic strokeEffects meta-analysisEnglish-language articlesMean percentage differenceAdult patientsMEDLINE databaseCochrane LibraryClinical utilityIschemic strokeLanguage articlesPatientsPercentage differenceArteryCellular compositionDeciphering craniopharyngioma subtypes: Single-cell analysis of tumor microenvironment and immune networks
Matsuda T, Kono T, Taki Y, Sakuma I, Fujimoto M, Hashimoto N, Kawakami E, Fukuhara N, Nishioka H, Inoshita N, Yamada S, Nakamura Y, Horiguchi K, Miki T, Higuchi Y, Tanaka T. Deciphering craniopharyngioma subtypes: Single-cell analysis of tumor microenvironment and immune networks. IScience 2024, 27: 111068. PMID: 39483146, PMCID: PMC11525618, DOI: 10.1016/j.isci.2024.111068.Peer-Reviewed Original ResearchTumor microenvironmentAnalysis of tumor microenvironmentImmune responseOccurrence of diabetes insipidusExpression of pro-inflammatory markersCell-cell interactionsPro-inflammatory markersComprehensive cell atlasM2 macrophage ratioSquamous papillaryDiabetes insipidusTumor cellsSingle cell RNA sequencingMacrophage ratioM1 macrophagesM2 macrophagesPituitary structureCell RNA sequencingCellular compositionSingle-cell clusteringCell typesDiverse cell typesTumorGene expression patternsMolecular characteristicsInvestigation of T cell phenotypes associated with response or resistance to immune checkpoint inhibitors (ICI) through single-cell analysis of renal cell carcinoma (RCC).
Kashima S, Ye Z, Meliki A, Hugaboom M, Schindler N, Graham J, Moritz V, El Ahmar N, Nabil Laimon Y, Canniff J, Saliby R, Lee G, Machaalani M, Sun M, Xu W, Signoretti S, McGregor B, McKay R, CHOUEIRI T, Braun D. Investigation of T cell phenotypes associated with response or resistance to immune checkpoint inhibitors (ICI) through single-cell analysis of renal cell carcinoma (RCC). Journal Of Clinical Oncology 2024, 42: 4515-4515. DOI: 10.1200/jco.2024.42.16_suppl.4515.Peer-Reviewed Original ResearchImmune checkpoint inhibitorsRenal cell carcinomaCD8+ T cell infiltrationT cell infiltrationNon-respondersTumor microenvironmentT cellsRCC tumor microenvironmentResistance to immune checkpoint inhibitorsICI responseImmune checkpoint inhibitor treatmentImmune checkpoint inhibitor efficacyCD8+ T cellsExpressed PD-1ICI-treated patientsGene programGene signature scoresTumor mutation loadCellular compositionGene expression signaturesSingle-cell transcriptome analysisCheckpoint inhibitorsPD-1Partial responseSystemic therapy
2023
Posttransplant Tertiary Lymphoid Organs
Ruddle N. Posttransplant Tertiary Lymphoid Organs. Transplantation 2023, 108: 1090-1099. PMID: 37917987, PMCID: PMC11042531, DOI: 10.1097/tp.0000000000004812.Peer-Reviewed Original ResearchTertiary lymphoid organsOrgan rejectionLymphoid organsCase of immunosuppressionEctopic lymphoid structuresDevelopment of lymphomaLymphoid neogenesisLymph nodesIschemic reperfusionChronic inflammationLymphoid structuresNephrotoxic agentsTumor antigensVascular componentLymphoid cellsTherapeutic manipulationSustained exposureMicrobial infectionsCellular compositionStaging schemeCancerOrgansRejectionImmunosuppressionReperfusionTissue Biology: In Search of a New Paradigm
Adler M, Chavan A, Medzhitov R. Tissue Biology: In Search of a New Paradigm. Annual Review Of Cell And Developmental Biology 2023, 39: 67-89. PMID: 37607470, DOI: 10.1146/annurev-cellbio-120420-113830.Peer-Reviewed Original ResearchAbstract B030: Form and function in intratumoral immune organization: Understanding the cellular composition of TCF1+ CD8+ T cell niches in human cancer
Jansen C, Vo B, Sobierajska E, Greenwald R, Mullane P, Prokhnevska N, Cardenas M, Bilen M, Osunkoya A, Master V, Kissick H. Abstract B030: Form and function in intratumoral immune organization: Understanding the cellular composition of TCF1+ CD8+ T cell niches in human cancer. Cancer Research 2023, 83: b030-b030. DOI: 10.1158/1538-7445.kidney23-b030.Peer-Reviewed Original ResearchTertiary lymphoid structuresSecondary lymphoid tissuesT cell responsesT cell zonesImmune nicheB cell zonesT cell nicheLymphoid tissueT cellsTumor tissuesEffective anti-tumor T cell responsesAnti-tumor T cell responsesDevelopment of T-cell functionStem-like CD8 T cellsImmune organsCD8 T cell activationCD8 T cell infiltrationTumor-infiltrating T cellsRobust T cell responsesCellular compositionB cell presenceHuman cancersAnti-tumor immunityResponse to immunotherapyCD8 T cells
2022
Benchmarking automated cell type annotation tools for single-cell ATAC-seq data
Wang Y, Sun X, Zhao H. Benchmarking automated cell type annotation tools for single-cell ATAC-seq data. Frontiers In Genetics 2022, 13: 1063233. PMID: 36583014, PMCID: PMC9792779, DOI: 10.3389/fgene.2022.1063233.Peer-Reviewed Original ResearchCell type annotationScATAC-seq dataScRNA-seq dataScATAC-seqCell typesSingle-cell ATAC-seq dataAvailable single-cell datasetsRegulatory genomic regionsScRNA-seq data setsSingle-cell datasetsATAC-seq dataNovel cell typesSimilar cell typesSeurat v3Genomic regionsSequencing depthComplex tissuesDeep annotationAnnotationCellular compositionHuman tissuesType annotationsAnnotation toolAnnotation methodLabel transferSingle-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea.
Cortese R, Adams T, Cataldo K, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea. European Respiratory Journal 2022, 61: 2201465. PMID: 36356973, DOI: 10.1183/13993003.01465-2022.Peer-Reviewed Original ResearchConceptsObstructive sleep apnoeaSleep apnoeaImpact of OSASystemic immune functionMononuclear cell compositionMolecular signaturesCell-specific markersSystemic inflammationCardiovascular dysfunctionImmune cellsImmune functionSingle-cell transcriptomic analysisPaediatric sleep apnoeaUndescribed cell typePrevalent diseaseMajor causeCellular compositionApnoeaCell compositionRNA expression datasetsDiagnostic settingCell typesCell lineagesMolecular diagnostic settingScRNA-seqThe role of altered translation in intellectual disability and epilepsy
Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Progress In Neurobiology 2022, 213: 102267. PMID: 35364140, PMCID: PMC10583652, DOI: 10.1016/j.pneurobio.2022.102267.Peer-Reviewed Original ResearchConceptsIntellectual disabilityNeuronal stimulationLocal synaptic activityActivity-dependent changesActivity-dependent translationOverall excitabilitySynaptic activityEpileptic seizuresSynaptic componentsCellular compositionEpilepsyDisabilityIon channelsCell typesDisordersHigher proportionStimulationSeizuresStimuliWorld populationPopulationExcitabilityOriginal stimulusDiseaseMutationsCellular diversity and gene expression profiles in the male and female brain of Aedes aegypti
Cui Y, Behura SK, Franz AWE. Cellular diversity and gene expression profiles in the male and female brain of Aedes aegypti. BMC Genomics 2022, 23: 119. PMID: 35144549, PMCID: PMC8832747, DOI: 10.1186/s12864-022-08327-9.Peer-Reviewed Original ResearchConceptsFemale brainMedulla neuronsCell clustersDimorphic behaviorsCell typesBrain cell typesSingle-nucleus RNA sequencingMonoaminergic neuronsProjection neuronsMosquito brainMale brainNeuronsKenyon cellsBrainYellow feverCell atlasCellular compositionGene expression profilesFemale mosquitoesGliaMosquito vectorsType compositionType proportionsRNA sequencingAdult males
2021
929 Dissecting intratumoral immune organization: defining the comparative cellular composition of tertiary lymphoid structures T-cell supportive antigen presenting niches in renal tumors
Jansen C, Sobierajska E, Greenwald R, Carlisle J, Mullane P, Prokhnevska N, Cardenas M, Bilen M, Osunkoya A, Master V, Kissick H. 929 Dissecting intratumoral immune organization: defining the comparative cellular composition of tertiary lymphoid structures T-cell supportive antigen presenting niches in renal tumors. Journal For ImmunoTherapy Of Cancer 2021, 9: a975-a975. DOI: 10.1136/jitc-2021-sitc2021.929.Peer-Reviewed Original ResearchRole of SHH in Patterning Human Pluripotent Cells towards Ventral Forebrain Fates
Brady MV, Vaccarino FM. Role of SHH in Patterning Human Pluripotent Cells towards Ventral Forebrain Fates. Cells 2021, 10: 914. PMID: 33923415, PMCID: PMC8073580, DOI: 10.3390/cells10040914.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSonic hedgehogHuman neurodevelopmentHuman pluripotent cellsDiverse cellular compositionRole of SHHMaster regulatorPluripotent cellsCellular phenotypesVentral identityNeural organoidsExpression gradientsOrganoid systemsDisease modelingVitro systemPathway activationModel systemCellular compositionOrganoidsHuman developmentQuestions scientistsHedgehogBiologyHow well do brain organoids capture your brain?
Kim J, Sullivan GJ, Park IH. How well do brain organoids capture your brain? IScience 2021, 24: 102063. PMID: 33554067, PMCID: PMC7856464, DOI: 10.1016/j.isci.2021.102063.Peer-Reviewed Original Research
2019
Modality-Specific Circuits for Skylight Orientation in the Fly Visual System
Sancer G, Kind E, Plazaola-Sasieta H, Balke J, Pham T, Hasan A, Münch L, Courgeon M, Mathejczyk T, Wernet M. Modality-Specific Circuits for Skylight Orientation in the Fly Visual System. Current Biology 2019, 29: 2812-2825.e4. PMID: 31402302, DOI: 10.1016/j.cub.2019.07.020.Peer-Reviewed Original Research
2018
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw C, Pardiñas AF, Hu M, Jin F, Li Y, Owen M, O’Donovan M, Walters J, Posthuma D, Reimers M, Levitt P, Weinberger D, Hyde T, Kleinman J, Geschwind D, Hawrylycz M, State M, Sanders S, Sullivan P, Gerstein M, Lein E, Knowles J, Sestan N, Willsey A, Oldre A, Szafer A, Camarena A, Cherskov A, Charney A, Abyzov A, Kozlenkov A, Safi A, Jones A, Ashley-Koch A, Ebbert A, Price A, Sekijima A, Kefi A, Bernard A, Amiri A, Sboner A, Clark A, Jaffe A, Tebbenkamp A, Sodt A, Guillozet-Bongaarts A, Nairn A, Carey A, Huttner A, Chervenak A, Szekely A, Shieh A, Harmanci A, Lipska B, Carlyle B, Gregor B, Kassim B, Sheppard B, Bichsel C, Hahn C, Lee C, Chen C, Kuan C, Dang C, Lau C, Cuhaciyan C, Armoskus C, Mason C, Liu C, Slaughterbeck C, Bennet C, Pinto D, Polioudakis D, Franjic D, Miller D, Bertagnolli D, Lewis D, Feng D, Sandman D, Clarke D, Williams D, DelValle D, Fitzgerald D, Shen E, Flatow E, Zharovsky E, Burke E, Olson E, Fulfs E, Mattei E, Hadjimichael E, Deelman E, Navarro F, Wu F, Lee F, Cheng F, Goes F, Vaccarino F, Liu F, Hoffman G, Gürsoy G, Gee G, Mehta G, Coppola G, Giase G, Sedmak G, Johnson G, Wray G, Crawford G, Gu G, van Bakel H, Witt H, Yoon H, Pratt H, Zhao H, Glass I, Huey J, Arnold J, Noonan J, Bendl J, Jochim J, Goldy J, Herstein J, Wiseman J, Miller J, Mariani J, Stoll J, Moore J, Szatkiewicz J, Leng J, Zhang J, Parente J, Rozowsky J, Fullard J, Hohmann J, Morris J, Phillips J, Warrell J, Shin J, An J, Belmont J, Nyhus J, Pendergraft J, Bryois J, Roll K, Grennan K, Aiona K, White K, Aldinger K, Smith K, Girdhar K, Brouner K, Mangravite L, Brown L, Collado-Torres L, Cheng L, Gourley L, Song L, Ubieta L, Habegger L, Ng L, Hauberg M, Onorati M, Webster M, Kundakovic M, Skarica M, Reimers M, Johnson M, Chen M, Garrett M, Sarreal M, Reding M, Gu M, Peters M, Fisher M, Gandal M, Purcaro M, Smith M, Brown M, Shibata M, Brown M, Xu M, Yang M, Ray M, Shapovalova N, Francoeur N, Sjoquist N, Mastan N, Kaur N, Parikshak N, Mosqueda N, Ngo N, Dee N, Ivanov N, Devillers O, Roussos P, Parker P, Manser P, Wohnoutka P, Farnham P, Zandi P, Emani P, Dalley R, Mayani R, Tao R, Gittin R, Straub R, Lifton R, Jacobov R, Howard R, Park R, Dai R, Abramowicz S, Akbarian S, Schreiner S, Ma S, Parry S, Shapouri S, Weissman S, Caldejon S, Mane S, Ding S, Scuderi S, Dracheva S, Butler S, Lisgo S, Rhie S, Lindsay S, Datta S, Souaiaia T, Roychowdhury T, Gomez T, Naluai-Cecchini T, Beach T, Goodman T, Gao T, Dolbeare T, Fliss T, Reddy T, Chen T, Hyde T, Brunetti T, Lemon T, Desta T, Borrman T, Haroutunian V, Spitsyna V, Swarup V, Shi X, Jiang Y, Xia Y, Chen Y, Jiang Y, Wang Y, Chae Y, Yang Y, Kim Y, Riley Z, Krsnik Z, Deng Z, Weng Z, Lin Z, Li Z. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 2018, 362 PMID: 30545854, PMCID: PMC6413317, DOI: 10.1126/science.aat7615.Peer-Reviewed Original ResearchConceptsIntegrative functional genomic analysisFunctional genomic analysisCell typesGene coexpression modulesDistinct cell typesCell type-specific dynamicsGenomic basisEpigenomic reorganizationEpigenomic landscapeEpigenomic regulationGenomic analysisCoexpression modulesIntegrative analysisHuman brain developmentFetal transitionHuman neurodevelopmentGenetic associationCellular compositionNeuropsychiatric riskBrain developmentNeurodevelopmental processesGenesTraitsPostnatal developmentNeuropsychiatric disordersPotentiation of serotonin signaling protects against intestinal ischemia and reperfusion injury in mice
Tackett JJ, Gandotra N, Bamdad MC, Muise ED, Cowles RA. Potentiation of serotonin signaling protects against intestinal ischemia and reperfusion injury in mice. Neurogastroenterology & Motility 2018, 31: e13498. PMID: 30394002, DOI: 10.1111/nmo.13498.Peer-Reviewed Original ResearchConceptsSerotonin re-uptake transporterWild-type littermatesIntestinal ischemiaEnterocyte proliferationMucosal injurySuperior mesenteric artery occlusionPotentiation of serotoninMesenteric artery occlusionRe-uptake transporterChi-squared testEnteric serotoninSMA occlusionArtery occlusionR injuryReperfusion injuryEpithelial injuryMucosal protectionEnteroendocrine cellsGoblet cellsIschemiaInjurySSRIsMiceSerotoninCellular composition
2016
High Endothelial Venules and Lymphatic Vessels in Tertiary Lymphoid Organs: Characteristics, Functions, and Regulation
Ruddle NH. High Endothelial Venules and Lymphatic Vessels in Tertiary Lymphoid Organs: Characteristics, Functions, and Regulation. Frontiers In Immunology 2016, 7: 491. PMID: 27881983, PMCID: PMC5101196, DOI: 10.3389/fimmu.2016.00491.Peer-Reviewed Original ResearchTertiary lymphoid organsHigh endothelial venulesSecondary lymphoid organsLymph nodesAntigen-presenting cellsLymphoid organsEndothelial venulesLymphatic vesselsStromal cellsCentral memory cellsPrimary lymphoid organsTransport antigensGraft rejectionEffector cellsChemokine expressionChronic inflammationPeyer's patchesAntigen presentationInflammatory signalsB cellsBone marrowImmune systemReticular cellsMicrobial infectionsCellular compositionTertiary Lymphoid Tissues
Ruddle N. Tertiary Lymphoid Tissues. 2016, 480-485. DOI: 10.1016/b978-0-12-374279-7.07012-0.Peer-Reviewed Original ResearchTertiary lymphoid organsTertiary lymphoid tissueSecondary lymphoid organsLymphoid organsLymphoid tissueConventional lymphoid organsChronic graft rejectionHigh endothelial venulesChronic microbial infectionsStromal cellular compositionAntigen primingNonlymphoid organsGraft rejectionDeterminant spreadingLymph nodesChronic inflammationEndothelial venulesClinical diseaseImmune responseInfectious organismsMicrobial infectionsCellular compositionLymphatic vesselsEctopic sitesAutoimmunity
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