2024
Evolving copy number gains promote tumor expansion and bolster mutational diversification
Wang Z, Xia Y, Mills L, Nikolakopoulos A, Maeser N, Dehm S, Sheltzer J, Sun R. Evolving copy number gains promote tumor expansion and bolster mutational diversification. Nature Communications 2024, 15: 2025. PMID: 38448455, PMCID: PMC10918155, DOI: 10.1038/s41467-024-46414-5.Peer-Reviewed Original ResearchConceptsSomatic copy number alterationsMutational diversificationCopy numberGenome sequenced samplesCopy number alterationsCopy number gainGenome segmentsPromote tumor expansionGenome doublingPopulation expansionSequenced samplesFitness effectsTumor typesCancer evolutionTumor expansionClonal expansionGenomeDiversification
2023
Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance
Yassine I, Rafei R, de la Gandara M, Osman M, Fabre L, Dabboussi F, Hamze M, Weill F. Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance. Microbial Genomics 2023, 9: 001157. PMID: 38100171, PMCID: PMC10763507, DOI: 10.1099/mgen.0.001157.Peer-Reviewed Original ResearchConceptsExtended-spectrum beta-lactamase genesThird-generation cephalosporinsMultidrug resistance phenotypeBeta-lactamase genesAntimicrobial resistance determinantsPrevalent serogroupsClinical isolatesQuinolone resistanceDNA gyrase genesAntimicrobial resistanceResistance determinantsCTXResistance phenotypeAmino acid substitutionsGyrase genesIsolatesNorth LebanonFirst studyAcid substitutionsPoint mutationsGenomic analysisCephalosporins
2022
Loss of PTEN phosphorylation via single point mutation alters cortical connectivity and behaviour
Binder M, Bordey A. Loss of PTEN phosphorylation via single point mutation alters cortical connectivity and behaviour. Brain 2022, 145: 3343-3344. PMID: 36148582, PMCID: PMC10233246, DOI: 10.1093/brain/awac350.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2021
Age-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity
Miazek A, Zalas M, Skrzymowska J, Bogin BA, Grzymajło K, Goszczynski TM, Levine ZA, Morrow JS, Stankewich MC. Age-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity. Scientific Reports 2021, 11: 7312. PMID: 33790315, PMCID: PMC8012654, DOI: 10.1038/s41598-021-86470-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalpainCerebellar AtaxiaCerebellumMiceMice, Inbred C57BLPoint MutationProtein BindingProteolysisSpectrinConceptsSpectrin cleavageCalpain cleavage sitesCalcium-activated proteaseGlobal neurodegenerationTraumatic encephalopathyC57BL/6J miceDendritic integrityExcessive activationNeuronal integrityProgressive ataxiaImpaired regulationCalpain activationCalpain sensitivityPhysiologic significanceNeurodegenerative diseasesNeuronal developmentCalpain proteolysisCalpain proteasesCalcium-dependent bindingAtaxiaNeurodegenerationCalpainActivated calpainSubstrate-level regulationCaM affinity
2020
Functional characterization of a novel SLC40A1 Arg88Ile mutation in a kindred with familial iron overload treated by phlebotomy
Womack J, Sukumaran A, Li X, Lozovatsky L, Gallagher PG, Seid JE, Finberg KE. Functional characterization of a novel SLC40A1 Arg88Ile mutation in a kindred with familial iron overload treated by phlebotomy. Blood Cells Molecules And Diseases 2020, 87: 102532. PMID: 33385755, PMCID: PMC8272917, DOI: 10.1016/j.bcmd.2020.102532.Peer-Reviewed Original ResearchMeSH KeywordsCation Transport ProteinsHumansIron OverloadMaleMiddle AgedModels, MolecularPhlebotomyPoint MutationAn enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins
Shon DJ, Malaker SA, Pedram K, Yang E, Krishnan V, Dorigo O, Bertozzi CR. An enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 21299-21307. PMID: 32817557, PMCID: PMC7474620, DOI: 10.1073/pnas.2012196117.Peer-Reviewed Original ResearchNovel compound heterozygous variants in NHLRC2 in a patient with FINCA syndrome
Brodsky NN, Boyarchuk O, Kovalchuk T, Hariyan T, Rice A, Ji W, Khokha M, Lakhani S, Lucas CL. Novel compound heterozygous variants in NHLRC2 in a patient with FINCA syndrome. Journal Of Human Genetics 2020, 65: 911-915. PMID: 32435055, DOI: 10.1038/s10038-020-0776-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAngiomatosisBrain NeoplasmsCardiomegalyChild, PreschoolExome SequencingFibrosisHeterozygoteHumansIntracellular Signaling Peptides and ProteinsLung DiseasesMaleModels, MolecularNeurodegenerative DiseasesPedigreePoint MutationProtein ConformationProtein DomainsSequence AlignmentSequence Homology, Amino AcidSyndromeConceptsWhole-exome sequencingNovel compound heterozygous variantsCompound heterozygous variantsUkrainian patientsClinical featuresNovel variantsNew patientsHealthy humansCompound heterozygous combinationPatientsHeterozygous variantsSyndromeFinnish childrenNHLRC2Sanger sequencingFibrosisDiseaseGnomAD databaseN-terminal thioredoxinCentral regulatorVariantsNeurodegenerationEM-mosaic detects mosaic point mutations that contribute to congenital heart disease
Hsieh A, Morton SU, Willcox JAL, Gorham JM, Tai AC, Qi H, DePalma S, McKean D, Griffin E, Manheimer KB, Bernstein D, Kim RW, Newburger JW, Porter GA, Srivastava D, Tristani-Firouzi M, Brueckner M, Lifton RP, Goldmuntz E, Gelb BD, Chung WK, Seidman CE, Seidman JG, Shen Y. EM-mosaic detects mosaic point mutations that contribute to congenital heart disease. Genome Medicine 2020, 12: 42. PMID: 32349777, PMCID: PMC7189690, DOI: 10.1186/s13073-020-00738-1.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultChildChild, PreschoolHeart Defects, CongenitalHumansInfantMosaicismPoint MutationSoftwareYoung AdultConceptsCongenital heart diseaseHigher allele fractionHeart diseaseCardiac tissueMosaic variantsAllele fractionBlood DNAHigh variant allele fractionSomatic mosaic variantsVariant allele fractionProband-parent triosCardiac malformationsOocyte fertilizationBloodHeart tissueBenign variantsMosaic mutationsExome sequencesTissue DNACardiovascular tissuesGenetic mutationsCHD probandsTrue frequencyCohortTissuePan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Pinoli P, Stamoulakatou E, Nguyen A, Martínez M, Ceri S. Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PLOS ONE 2020, 15: e0227180. PMID: 31945090, PMCID: PMC6964824, DOI: 10.1371/journal.pone.0227180.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBinding SitesCCCTC-Binding FactorChromosomes, Human, Pair 11DNA Copy Number VariationsDNA MethylationDNA Mutational AnalysisEpigenesis, GeneticExonsFemaleGene Expression Regulation, NeoplasticGenome, HumanHumansInsulator ElementsMutation RateNeoplasmsPoint MutationPromoter Regions, GeneticConceptsCTCF motifsCopy number alterationsSomatic mutationsAbnormal methylationCTCF binding sitesCopy number alteration eventsAnalysis of somatic mutationsMatched normal samplesCancer typesCTCF bindingOncogene dysregulationMutation enrichmentPan-cancer analysisPositive selectionEpigenetic alterationsIn-boundaryGenomic alterationsMotifMutational signaturesBinding sitesMutationsCTCFPan-cancerCopyNormal samplesDefining the landscape of ATP-competitive inhibitor resistance residues in protein kinases
Persky NS, Hernandez D, Do Carmo M, Brenan L, Cohen O, Kitajima S, Nayar U, Walker A, Pantel S, Lee Y, Cordova J, Sathappa M, Zhu C, Hayes TK, Ram P, Pancholi P, Mikkelsen TS, Barbie DA, Yang X, Haq R, Piccioni F, Root DE, Johannessen CM. Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases. Nature Structural & Molecular Biology 2020, 27: 92-104. PMID: 31925410, DOI: 10.1038/s41594-019-0358-z.Peer-Reviewed Original ResearchConceptsMammalian kinasesDeep mutational scanning dataDrug discovery effortsProtein kinaseMutagenesis dataMutant kinasesKinase activityDrug resistanceKinomeKinaseDiscovery effortsRelevant inhibitorsResiduesDisease developmentResistance mutationsMutationsActivation siteERK2MEK1MutantsBroader interrogationInhibitorsCSNK2A1Valuable toolTBK1
2019
Cl− and H+ coupling properties and subcellular localizations of wildtype and disease-associated variants of the voltage-gated Cl−/H+ exchanger ClC-5
Chang M, Brown M, Liu Y, Gainullin V, Harris P, Romero M, Lieske J. Cl− and H+ coupling properties and subcellular localizations of wildtype and disease-associated variants of the voltage-gated Cl−/H+ exchanger ClC-5. Journal Of Biological Chemistry 2019, 295: 1464-1473. PMID: 31852738, PMCID: PMC7008381, DOI: 10.1074/jbc.ra119.011366.Peer-Reviewed Original ResearchConceptsWT ClC-5Dent disease 1ClC-5ClC-5 transportEndosomal acidificationVoltage-gating propertiesIon-selective microelectrodesNonsense mutationDisease 1Disease-associated variantsExchange ratioSubcellular distributionEarly endosomesMutationsCo-localizationEndoplasmic reticulumVariantsTraffickingOocytesEndosomesSubcellular localizationClinical and genetic analysis in a large Chinese cohort of patients with X-linked hypophosphatemia
Zhang C, Zhao Z, Sun Y, Xu L, JiaJue R, Cui L, Pang Q, Jiang Y, Li M, Wang O, He X, He S, Nie M, Xing X, Meng X, Zhou X, Yan L, Kaplan JM, Insogna KL, Xia W. Clinical and genetic analysis in a large Chinese cohort of patients with X-linked hypophosphatemia. Bone 2019, 121: 212-220. PMID: 30682568, DOI: 10.1016/j.bone.2019.01.021.Peer-Reviewed Original ResearchAdolescentAdultChildChild, PreschoolChinaFamilial Hypophosphatemic RicketsFemaleFibroblast Growth Factor-23Fibroblast Growth FactorsGenetic Association StudiesHumansInfantMaleMiddle AgedMutationPHEX Phosphate Regulating Neutral EndopeptidasePoint MutationRetrospective StudiesSex CharacteristicsYoung Adult
2018
Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease
Ryu HY, López-Giráldez F, Knight J, Hwang SS, Renner C, Kreft SG, Hochstrasser M. Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nature Communications 2018, 9: 5417. PMID: 30575729, PMCID: PMC6303320, DOI: 10.1038/s41467-018-07836-0.Peer-Reviewed Original ResearchConceptsRibosome biogenesisSUMO modification pathwayUlp2 SUMO proteaseSmall nucleolar RNAsSUMO-specific proteasesSnoRNA genesCCR4 deadenylaseDistinct adaptive mechanismsRibosomal proteinsCellular evolutionChromosome INucleolar RNAsRibosome formationSUMO proteaseAdaptive advantageExtended passagingRapid adaptationLong-term adaptationBiogenesisAdaptive mechanismsMutationsProteaseAneuploidyDisomyRegulatory shiftA single-point mutation in the RNA-binding protein 6 generates Trypanosoma brucei metacyclics that are able to progress to bloodstream forms in vitro
Shi H, Butler K, Tschudi C. A single-point mutation in the RNA-binding protein 6 generates Trypanosoma brucei metacyclics that are able to progress to bloodstream forms in vitro. Molecular And Biochemical Parasitology 2018, 224: 50-56. PMID: 30055184, PMCID: PMC6147148, DOI: 10.1016/j.molbiopara.2018.07.011.Peer-Reviewed Original ResearchHb Adana (HBA2 or HBA1: c.179G > A) and alpha thalassemia: Genotype–phenotype correlation
Singh SA, Sarangi S, Appiah‐Kubi A, Hsu P, Smith WB, Gallagher PG, Glader B, Chui DHK. Hb Adana (HBA2 or HBA1: c.179G > A) and alpha thalassemia: Genotype–phenotype correlation. Pediatric Blood & Cancer 2018, 65: e27220. PMID: 29749692, DOI: 10.1002/pbc.27220.Peer-Reviewed Original ResearchHeterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C
Cannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene 2018, 37: 2444-2455. PMID: 29453361, DOI: 10.1038/s41388-017-0105-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAmino Acid SubstitutionAnimalsCase-Control StudiesDisease ProgressionDrug Resistance, NeoplasmFemaleGenetic HeterogeneityHigh-Throughput Nucleotide SequencingHumansMaleMiceMice, Inbred BALB CMice, NudeNeoplasmsOncogenesPoint MutationPolymorphism, Single NucleotideProto-Oncogene Proteins p21(ras)Sequence Analysis, DNAYoung AdultConceptsTime of treatmentTargeted therapyLung tumorsDe novo mutationsNew targeted therapiesPatient-derived xenograftsHighest fitness advantageKRAS G12C variantNovo mutationsEvidence of heterogeneityNovel KRAS mutationPreclinical promiseSuch therapyHigh prevalenceKRAS mutationsTreatment resistanceBRAF V600EKRASTherapyTargeted inhibitorsTumorsAssociated oncogeneRAS genesHuman cancersOncogenic mutationsAnalysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase
Wang Z, Kim MS, Martinez-Ferrando I, Koleske A, Pandey A, Cole P. Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase. Biochemistry 2018, 57: 1390-1398. PMID: 29341593, PMCID: PMC5906802, DOI: 10.1021/acs.biochem.7b01158.Peer-Reviewed Original ResearchConceptsProtein kinaseNonreceptor tyrosine kinases AblMass spectrometry-based quantitative proteomicsNovel putative substratesTyrosine kinase AblCellular tyrosine phosphorylationExtracellular growth factorsChemical rescue approachIntracellular signal transductionQuantitative phosphoproteomicsUnanticipated functionCellular physiologyGrowth factorPhosphorylation sitesPutative substratesDirect substrateDownstream substratesSignal transductionReceptor kinaseQuantitative proteomicsTyrosine phosphorylationActive Abl kinasesAbl kinaseChemical rescueKinase
2017
Two Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly
Rebane AA, Wang B, Ma L, Qu H, Coleman J, Krishnakumar S, Rothman JE, Zhang Y. Two Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly. Journal Of Molecular Biology 2017, 430: 479-490. PMID: 29056461, PMCID: PMC5805579, DOI: 10.1016/j.jmb.2017.10.012.Peer-Reviewed Original ResearchConceptsSoluble N-ethylmaleimide-sensitive factor attachment receptorSNARE assemblySynaptic exocytosisMembrane fusionSingle-molecule optical tweezersT-SNARE complexVesicle-associated SNAREsTarget plasma membraneC-terminal assemblyFour-helix bundleC-terminal regionSNARE complexPlasma membraneMolecular mechanismsZipperingMutationsNumerous diseasesAssembly energyNeurotransmitter releaseExocytosisAttachment receptorAssemblyNeurological disordersOptical tweezersComplexesCovalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography
Chan AH, Lee WG, Spasov KA, Cisneros JA, Kudalkar SN, Petrova ZO, Buckingham AB, Anderson KS, Jorgensen WL. Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 9725-9730. PMID: 28827354, PMCID: PMC5594698, DOI: 10.1073/pnas.1711463114.Peer-Reviewed Original ResearchConceptsHIV-1 reverse transcriptaseNonnucleoside RT inhibitorsDrug-resistant HIV-1 reverse transcriptaseReverse transcriptaseHIV-1 infectionTreatment of HIVT cell assaysDevelopment of resistanceRT inhibitorsAntiviral activityDrug efavirenzClass drugsInhibitorsViral polymeraseDrugsEnzyme inhibition kineticsResistant mutantsConclusive evidenceTranscriptasePoint mutationsCovalent inhibitorsHIVPatientsNevirapineEfavirenzClinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially
Luo X, Rosenfeld J, Yamamoto S, Harel T, Zuo Z, Hall M, Wierenga K, Pastore M, Bartholomew D, Delgado M, Rotenberg J, Lewis R, Emrick L, Bacino C, Eldomery M, Coban Akdemir Z, Xia F, Yang Y, Lalani S, Lotze T, Lupski J, Lee B, Bellen H, Wangler M, . Clinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially. PLOS Genetics 2017, 13: e1006905. PMID: 28742085, PMCID: PMC5557584, DOI: 10.1371/journal.pgen.1006905.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAnimalsAnimals, Genetically ModifiedCalcium ChannelsCerebellar AtaxiaChildChild, PreschoolDrosophila melanogasterFemaleGenome-Wide Association StudyGenome, HumanHumansMaleMicroscopy, Electron, TransmissionMutation, MissenseNeurodegenerative DiseasesNeuroimagingPhenotypePoint MutationConceptsNeurodegenerative phenotypeGenomic rescue constructsS4 transmembrane segmentRescue constructTransmembrane segmentsFunction phenotypesLoss of functionMissense allelesFunction allelesWild typeGlobal developmental delayToxic gainMutant clonesDominant mutationsDevelopmental delayPoint mutationsDrosophilaFunctional impactPhenotypeQ-type voltage-dependent Ca2Early-onset developmental delayNeurological phenotypeAllelesSynaptic functionNovel variants
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