2025
Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchMeSH KeywordsBicarbonatesCarbonCarbon DioxideCupriavidus necatorGenetic EngineeringMetabolic EngineeringPromoter Regions, GeneticConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophsEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original Research
2024
Machine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cells
2023
Advancing the fitness of gut commensal bacteria
Groisman E, Han W, Krypotou E. Advancing the fitness of gut commensal bacteria. Science 2023, 382: 766-768. PMID: 37972163, PMCID: PMC10838159, DOI: 10.1126/science.adh9165.Peer-Reviewed Original ResearchAdvances in glioma models using in vivo electroporation to highjack neurodevelopmental processes
Zhang L, Bordey A. Advances in glioma models using in vivo electroporation to highjack neurodevelopmental processes. Biochimica Et Biophysica Acta (BBA) - Reviews On Cancer 2023, 1878: 188951. PMID: 37433417, DOI: 10.1016/j.bbcan.2023.188951.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrain NeoplasmsElectroporationGenetic EngineeringGliomaHumansImmune SystemTumor MicroenvironmentNovel Strategies in Transplantation: Genetic Engineering and Vascularized Composite Allotransplantation
Kauke-Navarro M, Noel O, Knoedler L, Knoedler S, Panayi A, Stoegner V, Huelsboemer L, Pomahac B. Novel Strategies in Transplantation: Genetic Engineering and Vascularized Composite Allotransplantation. Journal Of Surgical Research 2023, 291: 176-186. PMID: 37429217, DOI: 10.1016/j.jss.2023.04.028.Peer-Reviewed Original ResearchConceptsImmunosuppressive regimensAllograft rejectionComposite allotransplantationDonor-derived immune cellsDonor-derived T lymphocytesRecipient-derived T cellsPotent immunosuppressive regimensToxic immunosuppressive regimensSolid organ transplantationAntigen-presenting cellsSystemic side effectsVascularized Composite AllotransplantationCD40 knockoutChronic rejectionRejection episodesSystemic immunosuppressionMost patientsImmunomodulatory strategiesTolerance inductionImmune cellsOrgan transplantationT cellsT lymphocytesSide effectsClinical successMassively parallel base editing to map variant effects in human hematopoiesis
Martin-Rufino J, Castano N, Pang M, Grody E, Joubran S, Caulier A, Wahlster L, Li T, Qiu X, Riera-Escandell A, Newby G, Al'Khafaji A, Chaudhary S, Black S, Weng C, Munson G, Liu D, Wlodarski M, Sims K, Oakley J, Fasano R, Xavier R, Lander E, Klein D, Sankaran V. Massively parallel base editing to map variant effects in human hematopoiesis. Cell 2023, 186: 2456-2474.e24. PMID: 37137305, PMCID: PMC10225359, DOI: 10.1016/j.cell.2023.03.035.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCRISPR-Cas SystemsGene EditingGenetic EngineeringGenomeHematopoiesisHematopoietic Stem CellsHumansSingle-Cell AnalysisConceptsHuman hematopoiesisVariant effectsNon-coding variantsDisease-associated variantsSingle-cell genotypingHuman hematopoietic stemFetal hemoglobin expressionHigh-throughput variantGenome engineeringSequencing readoutHematopoietic differentiationFunctional screenHemoglobin expressionDifferentiation stateDefines mechanismsHematopoietic stemPrimary cellsGenetic variantsProgenitor cellsSpecific mutationsDiverse diseasesHuman physiologyRich phenotypingHematopoiesisImmunotherapy approachesExploiting natural riboswitches for aptamer engineering and validation
Mohsen M, Midy M, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Research 2023, 51: 966-981. PMID: 36617976, PMCID: PMC9881172, DOI: 10.1093/nar/gkac1218.Peer-Reviewed Original ResearchMeSH KeywordsAptamers, NucleotideCaffeineGenetic EngineeringGuanineLigandsNucleic Acid ConformationQuinineRiboswitchConceptsNatural riboswitchesRiboswitch aptamerReporter gene expressionSecondary structure featuresRNA poolExpression platformVivo functionGene expressionSurvival mechanismRNA sequencesStructural featuresRiboswitchAptamer selectionSmall moleculesSequenceAptamerCellsGuanineTest tubeFuture effortsSelectionSelection strategyExpressionPoolAptamer engineering
2022
Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome
Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 2022, 185: 1487-1505.e14. PMID: 35366417, PMCID: PMC10619838, DOI: 10.1016/j.cell.2022.03.008.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaBiosynthetic PathwaysEukaryotaGenetic EngineeringHost Microbial InteractionsHumansMetabolomicsMicrobiotaSynthetic BiologyConceptsSynthetic genetic elementsGenetic elementsBiosynthetic gene clusterCross-species expressionCross-species interactionsDiverse organismsGene clusterBiosynthetic machineryHeterologous expressionRegulatory regionsTRNA synthetasesBiosynthetic pathwayNative contextTranslational activityBiosynthetic capacityHuman microbiomeMetabolic capacityPositive bacteriaSmall moleculesExpressionPathwayValuable compoundsLactobacillus inersEukaryotesSynthetases
2021
VectorMOD: Method for Bottom-Up Proteomic Characterization of rAAV Capsid Post-Translational Modifications and Vector Impurities
Rumachik NG, Malaker SA, Paulk NK. VectorMOD: Method for Bottom-Up Proteomic Characterization of rAAV Capsid Post-Translational Modifications and Vector Impurities. Frontiers In Immunology 2021, 12: 657795. PMID: 33868302, PMCID: PMC8047074, DOI: 10.3389/fimmu.2021.657795.Peer-Reviewed Original ResearchYAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte‐Like Cells
Smith J, Rodríguez T, Mou H, Kwan S, Pratt H, Zhang X, Cao Y, Liang S, Ozata D, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer E, Xue W. YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte‐Like Cells. Hepatology 2021, 73: 1011-1027. PMID: 32452550, PMCID: PMC8500588, DOI: 10.1002/hep.31389.Peer-Reviewed Original ResearchConceptsYes-associated protein 1Tumor cellsTumor regressionB-cateninStage IV hepatoblastomaResidual tumor cellsPediatric liver tumorsTherapeutic targetLong-term regressionTherapeutic differentiationHepatocyte-like morphologyFunctional hepatocyte-like cellsChildren's HbHB tumorsHepatocyte gene expressionHepatocyte-like cellsTranscription factor occupancyChemotherapeutic advancesTargeted therapyTumor landscapeLiver tumorsMurine modelHepatoblastomaTumorPromote cell death
2019
Ex vivo dendritic cell generation—A critical comparison of current approaches
Han P, Hanlon D, Sobolev O, Chaudhury R, Edelson RL. Ex vivo dendritic cell generation—A critical comparison of current approaches. International Review Of Cytology 2019, 349: 251-307. PMID: 31759433, DOI: 10.1016/bs.ircmb.2019.10.003.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationDendritic CellsGenetic EngineeringHumansImmunotherapyInflammationVaccinesConceptsDendritic cellsDiscovery of DCsMemory T cell responsesProfessional antigen-presenting cellsAntigen-specific immune responsesDendritic cell generationAntigen-specific immunityT cell responsesAntigen-presenting cellsEx vivo productionMononuclear cell fractionRalph SteinmanDC therapyAutoimmune disordersImmunologic functionDC functionPoor survivalImmunologic roleImmune responsePeripheral tissuesPhysiologic productionAdaptive immunityClinical utilityTherapeutic modulationImmune systemAnimal Models: Challenges and Opportunities to Determine Optimal Experimental Models of Pancreatitis and Pancreatic Cancer.
Saloman JL, Albers KM, Cruz-Monserrate Z, Davis BM, Edderkaoui M, Eibl G, Epouhe AY, Gedeon JY, Gorelick FS, Grippo PJ, Groblewski GE, Husain SZ, Lai KKY, Pandol SJ, Uc A, Wen L, Whitcomb DC. Animal Models: Challenges and Opportunities to Determine Optimal Experimental Models of Pancreatitis and Pancreatic Cancer. Pancreas 2019, 48: 759-779. PMID: 31206467, PMCID: PMC6581211, DOI: 10.1097/mpa.0000000000001335.Peer-Reviewed Original Research
2017
Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut
Lim B, Zimmermann M, Barry NA, Goodman AL. Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell 2017, 169: 547-558.e15. PMID: 28431252, PMCID: PMC5532740, DOI: 10.1016/j.cell.2017.03.045.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteroidesGastrointestinal MicrobiomeGene ExpressionGenetic EngineeringHumansMiceNeuraminidasePromoter Regions, GeneticConceptsGene expressionModulate gene expressionAbsence of inducerCommunity assemblyAddition of inducerGenetic toolsInducible promoterGene productsExpression platformHost physiologyPromoter activityHuman commensalGenus BacteroidesSynthetic inducersGut anaerobesInducerSialidase activityExpressionNumerous aspectsGut microbiotaSialic acidGutPromoterValuable toolCommensalOptimality and sub-optimality in a bacterial growth law
Towbin B, Korem Y, Bren A, Doron S, Sorek R, Alon U. Optimality and sub-optimality in a bacterial growth law. Nature Communications 2017, 8: 14123. PMID: 28102224, PMCID: PMC5253639, DOI: 10.1038/ncomms14123.Peer-Reviewed Original Research
2016
Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains
dos Santos LV, Carazzolle MF, Nagamatsu ST, Sampaio NM, Almeida LD, Pirolla RA, Borelli G, Corrêa TL, Argueso JL, Pereira GA. Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. Scientific Reports 2016, 6: 38676. PMID: 28000736, PMCID: PMC5175268, DOI: 10.1038/srep38676.Peer-Reviewed Original ResearchConceptsXylose fermentationAdaptive evolutionSecond-generation ethanol productionDevelopment of biocatalystsXylose isomerase geneRobust industrial strainsSecond-generation ethanolIron-sulfur clustersFive-carbon sugarsEngineered SaccharomycesMetabolic engineeringEssential genesEthanol productionXylose consumptionScaffold proteinRegulatory networksXylose utilizationIsomerase geneGenetic basisViable productionIndustrial strainsEthanol/Yeast cellsPentose metabolismGenesModeling and correction of structural variations in patient-derived iPSCs using CRISPR/Cas9
Park CY, Sung JJ, Choi SH, Lee DR, Park IH, Kim DW. Modeling and correction of structural variations in patient-derived iPSCs using CRISPR/Cas9. Nature Protocols 2016, 11: 2154-2169. PMID: 27711053, DOI: 10.1038/nprot.2016.129.Peer-Reviewed Original ResearchA Modular Assembly Platform for Rapid Generation of DNA Constructs
Akama-Garren EH, Joshi NS, Tammela T, Chang GP, Wagner BL, Lee DY, Rideout III W, Papagiannakopoulos T, Xue W, Jacks T. A Modular Assembly Platform for Rapid Generation of DNA Constructs. Scientific Reports 2016, 6: 16836. PMID: 26887506, PMCID: PMC4757859, DOI: 10.1038/srep16836.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNAGene ExpressionGene Knockdown TechniquesGenetic EngineeringHEK293 CellsHumansMiceMice, KnockoutPromoter Regions, GeneticConceptsAssembly platformDNA constructsInducible lentiviral systemCollection of promotersGeneration of knockTraditional cloning methodsGenetic screenRecombinant DNA technologyRNAi constructsGenomic elementsGenetic toolsSynthetic biologySynthetic promotersDNA fragmentsCloning methodGenetic componentDNA technologyTumor initiationLentiviral systemOne-step productionViral constructsPromoterRapid generationGMAPAssemblyOptimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology 2016, 34: 184-191. PMID: 26780180, PMCID: PMC4744125, DOI: 10.1038/nbt.3437.Peer-Reviewed Original Research
2015
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Methods 2015, 12: 982-988. PMID: 26322839, PMCID: PMC4589495, DOI: 10.1038/nmeth.3543.Peer-Reviewed Original Research
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