2021
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLOS Biology 2021, 19: e3001143. PMID: 33730024, PMCID: PMC8007021, DOI: 10.1371/journal.pbio.3001143.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSARS-CoV-2Human bronchial epithelial cellsInterferon-stimulated genesCell state changesAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionSyndrome coronavirus 2 infectionCell tropismCoronavirus 2 infectionCoronavirus disease 2019Onset of infectionCell-intrinsic expressionCourse of infectionAir-liquid interface culturesHost-viral interactionsBronchial epithelial cellsSingle-cell RNA sequencingCell typesIL-1Disease 2019Human airwaysDevelopment of therapeuticsDrug AdministrationViral replicationThe aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2
Chow RD, Majety M, Chen S. The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2. Nature Communications 2021, 12: 4. PMID: 33397975, PMCID: PMC7782551, DOI: 10.1038/s41467-020-20323-9.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 infectionHuman lungCOVID-19Natural killer/T-cellAirway smooth muscle cellsSevere coronavirus diseaseSevere COVID-19Alveolar type 2 cellsMajor risk factorType 2 cellsSmooth muscle cellsSARS-CoV-2 proteomeAge-associated genesAge-associated changesDendritic cellsRisk factorsT cellsGoblet cellsAlveolar fibroblastsCoronavirus diseaseMuscle cellsOlder populationCellular landscapeEndothelial cells
2019
Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells
Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, Lam SZ, Zhou JJ, Lannin DR, Herbst RS, Chen S. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell 2019, 178: 1189-1204.e23. PMID: 31442407, PMCID: PMC6719679, DOI: 10.1016/j.cell.2019.07.044.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBreast NeoplasmsCD8-Positive T-LymphocytesCell Line, TumorClustered Regularly Interspaced Short Palindromic RepeatsCytokinesFemaleHumansImmunologic MemoryImmunotherapyMaleMiceMice, KnockoutNF-kappa BProgrammed Cell Death 1 ReceptorRNA HelicasesRNA, Guide, CRISPR-Cas SystemsTranscriptomeConceptsCRISPR screensTarget discoveryGenome-scale CRISPR screensCD8 TRNA helicase DHX37Vivo CRISPR screensGenetic screenGenome scaleTranscriptomic profilingBiochemical interrogationAntigen-specific CD8 TAnti-tumor immune responseFunctional regulatorTriple-negative breast cancerDHX37Essential roleTim-3PD-1Cytokine productionTumor infiltrationImmunotherapy targetImmunotherapy settingsRegulatorBreast cancerT cells
2017
AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma
Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, Platt RJ, Chen S. AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nature Neuroscience 2017, 20: 1329-1341. PMID: 28805815, PMCID: PMC5614841, DOI: 10.1038/nn.4620.Peer-Reviewed Original Research
2014
Global microRNA depletion suppresses tumor angiogenesis
Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA. Global microRNA depletion suppresses tumor angiogenesis. Genes & Development 2014, 28: 1054-1067. PMID: 24788094, PMCID: PMC4035535, DOI: 10.1101/gad.239681.114.Peer-Reviewed Original ResearchConceptsUntranslated regionCRISPR/Multiplexed CRISPR/HIF transcriptional activityHypoxia-inducible factor-1Tumor angiogenesisMicroRNA-binding sitesGenome engineeringExpression profilingTranscriptional activityHypoxia responseBalance of angiogenesisHIF transcriptionMicroRNA deficiencyMicroRNAsFIH1Factor 1Angiogenesis genesDeficient angiogenesisAngiogenesisVEGF productionTranscription
2012
Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila
Chen S, Spletter M, Ni X, White KP, Luo L, Long M. Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila. Cell Reports 2012, 1: 118-132. PMID: 22832161, PMCID: PMC4382513, DOI: 10.1016/j.celrep.2011.12.010.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalAgingAmino Acid SequenceAnimalsArthropod AntennaeBrainDrosophila melanogasterDrosophila ProteinsEvolution, MolecularFeeding BehaviorFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, InsectMaleMolecular Sequence DataMushroom BodiesNeuronsSelection, GeneticSex CharacteristicsSynaptic TransmissionTranscriptomeConceptsNew genesForaging behaviorMushroom bodiesYoung retrogenesAdaptive evolutionPhenotypic evolutionEvolutionary signaturesYoung genesNatural selectionGenetic basisBrain genesExpression profilingComparative behavioral analysisBrain evolutionGenesOlfactory circuitDrosophilaNew functionsAnimal behaviorNeuronal expressionExpressionRetrogenesNeural circuitsEvolutionRecent evolution