2024
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq
Guo L, Grinko A, Olson S, Leipold A, Graveley B, Saliba A, Pyle A. Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq. RNA 2024, 30: rna.080032.124. PMID: 39174298, PMCID: PMC11482623, DOI: 10.1261/rna.080032.124.Peer-Reviewed Original ResearchNontemplated additionRNA-seqRNA sequencingGroup II self-splicing intronsTemplate-switching oligonucleotidesLong-read sequencingRNA-seq technologySelf-splicing intronsTemplate-switching reactionsLong RNA transcriptsRNA sequencing methodsWell-characterized enzymesPoly(A)-enriched RNART enzymeRNA identityNucleotide specificityEnzymatic specificityRNA librariesRNA transcriptsLong RNAsHuman RNARNA moleculesRNA referenceAccurate sequencingBinding specificitySARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity
Peña-Hernández M, Alfajaro M, Filler R, Moriyama M, Keeler E, Ranglin Z, Kong Y, Mao T, Menasche B, Mankowski M, Zhao Z, Vogels C, Hahn A, Kalinich C, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach B, Homer R, Pyle A, Martinez D, Grubaugh N, Israelow B, Iwasaki A, Wilen C. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nature Microbiology 2024, 9: 2038-2050. PMID: 39075235, DOI: 10.1038/s41564-024-01765-z.Peer-Reviewed Original ResearchBat coronavirusesRelatives of SARS-CoV-2Upper airwayUpper airways of miceEpithelial cellsHuman nasal epithelial cellsAirways of miceMajor histocompatibility complex class I.SARS-CoV-2Nasal epithelial cellsHistocompatibility complex class I.Human bronchial epithelial cellsGenetic similarityBronchial epithelial cellsInnate immune restrictionCoronavirus replicationFunctional characterizationMolecular cloningReduced pathogenesisImpaired replicationBat virusCoronavirus pathogenesisPandemic potentialHigh-risk familiesImmune restrictionThe West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles
Huston N, Tsao L, Brackney D, Pyle A. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2312080121. PMID: 38985757, PMCID: PMC11260092, DOI: 10.1073/pnas.2312080121.Peer-Reviewed Original ResearchConceptsWest Nile virus genomeWest Nile virusPositive-sense RNA virusesFunctional roleArthropod cell linesRiboregulatory elementsGenome foldingFlaviviral genomeRNA genomeIncreasing global threatVirus genomeGenomeRNA virusesStructural homologyHost-dependentSecondary structureLack of effective therapeuticsFunctional validationLocked nucleic acidStructural insightsRNA drugsCell linesArthropod-borneNucleic acidsAntisense locked nucleic acidMechanism of Action of KL-50, a Candidate Imidazotetrazine for the Treatment of Drug-Resistant Brain Cancers
Huseman E, Lo A, Fedorova O, Elia J, Gueble S, Lin K, Sundaram R, Oh J, Liu J, Menges F, Rees M, Ronan M, Roth J, Batista V, Crawford J, Pyle A, Bindra R, Herzon S. Mechanism of Action of KL-50, a Candidate Imidazotetrazine for the Treatment of Drug-Resistant Brain Cancers. Journal Of The American Chemical Society 2024, 146: 18241-18252. PMID: 38815248, PMCID: PMC11409917, DOI: 10.1021/jacs.3c06483.Peer-Reviewed Original ResearchDNA repair capacityDifferential DNA repair capacityDNA interstrand cross-linksRepair capacityInterstrand cross-linksDisplacement of fluorideDNA repairCross-linkingAberrant DNA repairLesionsHealthy tissueBrain cancerRing openingHealthy cellsMGMTSelective chemotherapyGenotoxic agentsTumorChemical DNA modificationsCancerMultistep processRepairNanoparticle Retinoic Acid-Inducible Gene I Agonist for Cancer Immunotherapy
Wang-Bishop L, Wehbe M, Pastora L, Yang J, Kimmel B, Garland K, Becker K, Carson C, Roth E, Gibson-Corley K, Ulkoski D, Krishnamurthy V, Fedorova O, Richmond A, Pyle A, Wilson J. Nanoparticle Retinoic Acid-Inducible Gene I Agonist for Cancer Immunotherapy. ACS Nano 2024, 18: 11631-11643. PMID: 38652829, PMCID: PMC11080455, DOI: 10.1021/acsnano.3c06225.Peer-Reviewed Original ResearchConceptsImmune checkpoint inhibitorsTumor microenvironmentLipid nanoparticlesBreast cancerResponse to ICIResponse to immune checkpoint inhibitorsInfiltration of CD8<sup>+</sup>Models of triple-negative breast cancerCD4<sup>+</sup> T cellsInhibition of tumor growthTriple-negative breast cancerRIG-IIonizable lipid nanoparticlesLung metastatic burdenIncrease tumor immunogenicityBreast tumor microenvironmentSignaling in vitroACTLA-4Immunogenic melanomaCheckpoint inhibitorsTumor immunogenicityImmunotherapeutic modalitiesCancer immunotherapyMetastatic burdenAPD-1Covalent Polymer‐RNA Conjugates for Potent Activation of the RIG‐I Pathway
Palmer C, Pastora L, Kimmel B, Pagendarm H, Kwiatkowski A, Stone P, Arora K, Francini N, Fedorova O, Pyle A, Wilson J. Covalent Polymer‐RNA Conjugates for Potent Activation of the RIG‐I Pathway. Advanced Healthcare Materials 2024, e2303815. PMID: 38648653, PMCID: PMC11493851, DOI: 10.1002/adhm.202303815.Peer-Reviewed Original ResearchChemical design principlesActivation of RIG-I.Retinoic acid-inducible gene ICovalent conjugationRIG-I pathwayNuclease degradationThioether linkageRIG-I.Gene IRNA ligandsElectrostatic interactionsRIG-IDevelopment of therapeuticsPotent activityOligonucleotide therapeuticsNucleaseRNAAnalog carrierNanoparticlesDrug delivery barriersConjugatePolymeric carriersImmunostimulatory activityThioethersIn vivo deliveryHighly Reactive Group I Introns Ubiquitous in Pathogenic Fungi
Liu T, Pyle A. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. Journal Of Molecular Biology 2024, 436: 168513. PMID: 38447889, DOI: 10.1016/j.jmb.2024.168513.Peer-Reviewed Original ResearchGroup I intronsAntifungal drug targetsRNA metabolismPathogenic fungiPhylogeny of fungiSelf-splicing intronsDrug targetsSystemic fungal infectionsGenetic hotspotsRiboregulatory elementsMitochondrial intronsMitochondrial genesBioinformatics pipelineC. aurisCandida aurisRelevant fungiRNA elementsAspergillus fumigatusC. albicansHousekeeping genesCandida albicansNoncoding transcriptomeCryptococcus neoformansFungal infectionsFungiA compact regulatory RNA element in mouse Hsp70 mRNA
Wang W, Liu F, Ugalde M, Pyle A. A compact regulatory RNA element in mouse Hsp70 mRNA. NAR Molecular Medicine 2024, 1: ugae002. PMID: 38318492, PMCID: PMC10840451, DOI: 10.1093/narmme/ugae002.Peer-Reviewed Original ResearchOpen reading frameRNA elementsHeat shockOpen reading frame sequenceRegulatory RNA elementsSecondary structure modelMessenger RNACap-independent mannerCap-dependent translationMolecular chaperone functionSequences of HSP70Reading frameMisfolded proteinsRNA foldingRegulate protein expressionChaperone functionMRNA sequencesUntranslated regionShort stretchSecondary structureCell stressGene expressionHSP70 gene expressionStructural basisMolecular mechanisms
2023
Structural insights into intron catalysis and dynamics during splicing
Xu L, Liu T, Chung K, Pyle A. Structural insights into intron catalysis and dynamics during splicing. Nature 2023, 624: 682-688. PMID: 37993708, PMCID: PMC10733145, DOI: 10.1038/s41586-023-06746-6.Peer-Reviewed Original ResearchThe E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization
Wang W, Götte B, Guo R, Pyle A. The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization. Nature Communications 2023, 14: 7308. PMID: 37951994, PMCID: PMC10640585, DOI: 10.1038/s41467-023-42982-0.Peer-Reviewed Original Research
2022
The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands
Wang W, Pyle AM. The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Molecular Cell 2022, 82: 4131-4144.e6. PMID: 36272408, PMCID: PMC9707737, DOI: 10.1016/j.molcel.2022.09.029.Peer-Reviewed Original ResearchConceptsRNA moleculesRNA ligandsHigh-resolution cryo-EM structuresCryo-EM structureDouble-stranded RNARIG-I receptorInduction of autoimmunityViral RNA moleculesAutoinhibited conformationInnate immune receptorsHost RNARelated RNAProtein foldsMolecular basisUnique molecular featuresHigh-affinity conformationAntiviral sensingHost cellsRNA virusesRNA releaseImmune receptorsRNAViral RNAExquisite selectivityMolecular featuresA unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs
Zhang C, Pyle AM. A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs. IScience 2022, 25: 105218. PMID: 36248743, PMCID: PMC9557024, DOI: 10.1016/j.isci.2022.105218.Peer-Reviewed Original ResearchUS-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexesChapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study
Guo R, Pyle AM. Chapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study. Methods In Enzymology 2022, 673: 39-52. PMID: 35965013, DOI: 10.1016/bs.mie.2022.03.064.Peer-Reviewed Original ResearchConceptsEnzymatic ATPase activitySuperfamily 1Nucleic acid-dependent ATPasesATPase activityRNA-dependent ATPaseSimple reporter systemNucleic acid bindingNucleic acid ligandsNucleic acidsATPase enzymeSF2 helicaseAcid ligandsKinetic parametersRNA associationSF2 helicasesRNA bindingMultitude of processesMotor proteinsBiological functionsSF1 helicasesReporter systemFunctional bindingConformational changesDirect binding assaysAcid bindingDirect tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules
Guo LT, Olson S, Patel S, Graveley BR, Pyle AM. Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules. Nucleic Acids Research 2022, 50: 6980-6989. PMID: 35713547, PMCID: PMC9262592, DOI: 10.1093/nar/gkac518.Peer-Reviewed Original ResearchA molecular beacon assay for monitoring RNA splicing
Omran QQ, Fedorova O, Liu T, Pyle AM. A molecular beacon assay for monitoring RNA splicing. Nucleic Acids Research 2022, 50: e74-e74. PMID: 35438748, PMCID: PMC9303364, DOI: 10.1093/nar/gkac242.Peer-Reviewed Original ResearchConceptsMolecular beaconsMolecular beacon assayHigher fluorescent signalHigh-throughput screening platformSmall moleculesAutocatalyzed reactionMolecular beacon approachKinetic characterizationReactionSmall molecule targetingInhibition constantsScreening platformSmall molecule inhibitorsFluorescent signalMolecule targetingMolecule inhibitorsMoleculesAMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.
Shine M, Zhang C, Pyle AM. AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics 2022 PMID: 35385068, DOI: 10.1093/bioinformatics/btac207.Peer-Reviewed Original ResearchAMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids
Shine M, Zhang C, Pyle AM. AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics 2022, 38: 2937-2939. PMID: 35561202, PMCID: PMC9113296, DOI: 10.1093/bioinformatics/btac207.Peer-Reviewed Original ResearchThe In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures
Wan H, Adams RL, Lindenbach BD, Pyle AM. The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures. Journal Of Virology 2022, 96: e01946-21. PMID: 35353000, PMCID: PMC9044954, DOI: 10.1128/jvi.01946-21.Peer-Reviewed Original ResearchConceptsSecondary structure mapRNA genomeRNA structureTertiary structureProtein-coding genesPositive-strand RNA virusesRegulatory RNA structuresFull-length structureHCV RNA genomeValuable model systemRNA structural motifsSecondary structural elementsEvolutionary functional analysisLife cycleVirus life cycleCellular contextCorresponding transcriptsImportant human pathogenLong RNAsGenomeSame RNAGenomic RNAComprehensive atlasFunctional analysisFunctional importanceDe novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report
Gandhi S, Klein J, Robertson AJ, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SAK, Catherine Muenker M, Srivathsan A, Wunder EA, Kerantzas N, Wang W, Lindenbach B, Pyle A, Wilen CB, Ogbuagu O, Greninger AL, Iwasaki A, Schulz WL, Ko AI. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nature Communications 2022, 13: 1547. PMID: 35301314, PMCID: PMC8930970, DOI: 10.1038/s41467-022-29104-y.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionVirologic responsePersistent SARS-CoV-2 infectionResistance mutationsPre-treatment specimensB-cell deficiencyRemdesivir resistanceRemdesivir therapyViral sheddingCase reportAntiviral agentsPatientsCombinatorial therapyInfectionTherapyWhole-genome sequencingTreatmentImportance of monitoringDe novo emergenceFold increaseRNA-dependent RNA polymeraseNovo emergencePotential benefitsMutationsIndolent