2023
Correlation of HER2 Protein Level With mRNA Level Quantified by RNAscope in Breast Cancer
Li X, Lee J, Gao Y, Zhang J, Bates K, Rimm D, Zhang H, Smith G, Lawson D, Meisel J, Chang J, Huo L. Correlation of HER2 Protein Level With mRNA Level Quantified by RNAscope in Breast Cancer. Modern Pathology 2023, 37: 100408. PMID: 38135153, DOI: 10.1016/j.modpat.2023.100408.Peer-Reviewed Original ResearchHER2 protein levelsHER2-low breast cancerT-DXdBreast cancerRNA levelsProtein levelsHER2 expressionEarly-stage breast cancerIHC H-scoresTrastuzumab deruxtecanTissue microarray coresClinical trialsMetastatic biopsiesImmunohistochemical assaysH-scoreDrug AdministrationResponse rateUS FoodPatientsIHC assaysCancerRNAscopeRegression analysisCell linesImmunofluorescence scoresDaily Oral HIV Pre-exposure Prophylaxis Among Young Men Who Have Sex With Men in the United States: Cost-saving at Generic Drug Price
Amick A, Eskibozkurt G, Hosek S, Flanagan C, Landovitz R, Jin E, Wilson C, Freedberg K, Weinstein M, Kazemian P, Paltiel A, Ciaranello A, Neilan A. Daily Oral HIV Pre-exposure Prophylaxis Among Young Men Who Have Sex With Men in the United States: Cost-saving at Generic Drug Price. Clinical Infectious Diseases 2023, 78: 402-410. PMID: 37823865, PMCID: PMC10874274, DOI: 10.1093/cid/ciad566.Peer-Reviewed Original ResearchPre-exposure prophylaxisHIV incidenceRisk of HIVOral PrEPAnnual screeningHuman immunodeficiency virus (HIV) pre-exposure prophylaxisOral HIV pre-exposure prophylaxisHIV pre-exposure prophylaxisIncremental cost-effectiveness ratioHIV RNA levelsYoung menCost-effectiveness ratioAnnual HIVHigher discontinuationPrEP retentionAntiretroviral therapyDrug pricesHIV careLow adherenceLifetime horizonNew infectionsHIVIncidencePrEPRNA levelsbakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling
Vock I, Simon M. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA 2023, 29: 958-976. PMID: 37028916, PMCID: PMC10275263, DOI: 10.1261/rna.079451.122.Peer-Reviewed Original ResearchConceptsBayesian hierarchical modelingAdvanced statistical modelsHierarchical modelingDifferential expression analysisStatistical modelBayesian analysisRNA synthesisExpression analysisStatistical rigorData setsR packageRNA sequencing dataCellular RNA levelsMethods addressStatistical powerKinetics of RNAImproved analysisSequencing dataModel outperformsUser-friendly softwareModelingSetRNA levelsModelDifferential kinetics
2022
Aging reduces ABHD5 protein content in the adipose tissue of mice: The reversal effect of exercise
Brícola R, Cordeiro A, Crisol B, Braga R, de Melo D, Rocha M, Gaspar R, Nakandakari S, Silva V, Anaruma C, Katashima C, Canciglieri R, Munõz V, Pavan I, Pinto A, Simabuco F, da Silva A, Moura L, Pauli J, Cintra D, Ropelle E. Aging reduces ABHD5 protein content in the adipose tissue of mice: The reversal effect of exercise. Cell Biochemistry And Function 2022, 41: 128-137. PMID: 36515301, DOI: 10.1002/cbf.3770.Peer-Reviewed Original ResearchConceptsAged miceAdipose tissueControl of lipolysisHigh-intensity interval trainingSubcutaneous white adipose tissueExperimental mouse modelAdipose tissue metabolismWhite adipose tissueMessenger RNA levelsInterval trainingMouse modelTissue metabolismLipolytic pathwayMiceRNA levelsProtein levelsScWATTranscriptomic analyzesReversal effectTissueExerciseSignificant hallmarkLipolysisABHD5Lipolytic activityInternally controlled RNA sequencing comparisons using nucleoside recoding chemistry
Courvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD. Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic Acids Research 2022, 50: e110-e110. PMID: 36018791, PMCID: PMC9638901, DOI: 10.1093/nar/gkac693.Peer-Reviewed Original ResearchConceptsBiochemical manipulationRNA polymerase II inhibitionSodium arsenite stressSet of transcriptsNew biological understandingTranscript regulationArsenite stressMRNA associationRNA transcriptsBiological insightsHeat shockMetabolic labelBiological understandingRNA contentRNA levelsTranscriptsCell culturesII inhibitionBiological variationDDX5RibosomesMCM2RNAAbundanceRegulationGenome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas
Hwang T, Kim S, Chowdhury T, Yu H, Kim K, Kang H, Won J, Park S, Shin J, Park C. Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. Communications Biology 2022, 5: 62. PMID: 35042936, PMCID: PMC8766575, DOI: 10.1038/s42003-022-03011-w.Peer-Reviewed Original ResearchConceptsCircular RNA levelsI editingGenome-wide perturbationsPost-transcriptional processesPost-transcriptional regulationRNA expressionRNA levelsAlu expressionHuman genomeRNA-seqRegulatory elementsRepeat elementsGenetic elementsAlu subfamiliesBiological processesGrade 2 oligodendrogliomaAluExpressionGliomagenesisEditingUnique patternTranscriptomeGenomeSubfamiliesNormal tissues
2021
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner
Hamelin D, Fournelle D, Grenier J, Schockaert J, Kovalchik K, Kubiniok P, Mostefai F, Duquette J, Saab F, Sirois I, Smith M, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Systems 2021, 13: 143-157.e3. PMID: 34637888, PMCID: PMC8492600, DOI: 10.1016/j.cels.2021.09.013.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 TSARS-CoV-2 variantsHLA-B allelesMutational landscapeFirst yearCell immunityCell immunosurveillanceCell epitopesMass vaccinationDelta variantCell targetsRNA levelsImmunodominant onesMutation typeEpitopesPrevalent mutantsPopulation levelCD8PandemicImmunosurveillanceVaccinationHLAYearsImmunityInvestigating the Potential Roles of SINEs in the Human Genome
Zhang X, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review Of Genomics And Human Genetics 2021, 22: 1-20. PMID: 33792357, DOI: 10.1146/annurev-genom-111620-100736.Peer-Reviewed Original ResearchConceptsShort interspersed nuclear elementsHuman genomePol II-transcribed genesFunctional regulatory elementsGene-rich regionsRNA polymerase IIIProximity to genesInterspersed nuclear elementsRegulate gene expressionPotential regulatory functionsSINE RNAsNonautonomous retrotransposonsPolymerase IIIGene regulationRegulatory elementsAutonomous retroelementsGenomeNuclear elementsGene expressionGenesRNARNA levelsPolPotential roleRetrotransposonsX Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis
Asselta R, Paraboschi E, Gerussi A, Cordell H, Mells G, Sandford R, Jones D, Nakamura M, Ueno K, Hitomi Y, Kawashima M, Nishida N, Tokunaga K, Nagasaki M, Tanaka A, Tang R, Li Z, Shi Y, Liu X, Xiong M, Hirschfield G, Siminovitch K, Consortium C, Walker E, Xie G, Mason A, Myers R, Peltekian K, Ghent C, Atkinson E, Juran B, Lazaridis K, Lu Y, Gu X, Jing K, Amos C, Group I, Affronti A, Brunetto M, Coco B, Spinzi G, Elia G, Ferrari C, Lleo A, Muratori L, Muratori P, Portincasa P, Colli A, Bruno S, Colloredo G, Azzaroli F, Andreone P, Bragazzi M, Alvaro D, Cardinale V, Cazzagon N, Rigamonti C, Floreani A, Rosina F, Ciaccio A, Cristoferi L, D’Amato D, Malinverno F, Mancuso C, Massironi S, Milani C, O’Donnell S, Ronca V, Barisani D, Lampertico P, Donato F, Fagiuoli S, Almasio P, Giannini E, Cursaro C, Colombo M, Valenti L, Miele L, Andriulli A, Niro G, Grattagliano I, Morini L, Casella G, Vinci M, Battezzati P, Crosignani A, Zuin M, Mattalia A, Calvaruso V, Colombo S, Benedetti A, Marzioni M, Galli A, Marra F, Tarocchi M, Picciotto A, Morisco F, Fabris L, Crocè L, Tiribelli C, Toniutto P, Strazzabosco M, Consortium U, Ch’ng C, Rahman M, Yapp T, Sturgess R, Healey C, Czajkowski M, Gunasekera A, Gyawali P, Premchand P, Kapur K, Marley R, Foster G, Watson A, Dias A, Subhani J, Harvey R, McCorry R, Ramanaden D, Gasem J, Evans R, Mathialahan T, Shorrock C, Lipscomb G, Southern P, Tibble J, Gorard D, Palegwala A, Jones S, Dawwas M, Alexander G, Dolwani S, Prince M, Foxton M, Elphick D, Mitchison H, Gooding I, Karmo M, Saksena S, Mendall M, Patel M, Ede R, Austin A, Sayer J, Hankey L, Hovell C, Fisher N, Carter M, Koss K, Piotrowicz A, Grimley C, Neal D, Lim G, Levi S, Ala A, Broad A, Saeed A, Wood G, Brown J, Wilkinson M, Gordon H, Ramage J, Ridpath J, Ngatchu T, Grover B, Shaukat S, Shidrawi R, Abouda G, Ali F, Rees I, Salam I, Narain M, Brown A, Taylor-Robinson S, Williams S, Grellier L, Banim P, Das D, Chilton A, Heneghan M, Curtis H, Gess M, Drake I, Aldersley M, Davies M, Jones R, McNair A, Srirajaskanthan R, Pitcher M, Sen S, Bird G, Barnardo A, Kitchen P, Yoong K, Chirag O, Sivaramakrishnan N, MacFaul G, Jones D, Shah A, Evans C, Saha S, Pollock K, Bramley P, Mukhopadhya A, Fraser A, Mills P, Shallcross C, Campbell S, Bathgate A, Shepherd A, Dillon J, Rushbrook S, Przemioslo R, Macdonald C, Metcalf J, Shmueli U, Davis A, Naqvi A, Lee T, Ryder S, Collier J, Klass H, Ninkovic M, Cramp M, Sharer N, Aspinall R, Goggin P, Ghosh D, Douds A, Hoeroldt B, Booth J, Williams E, Hussaini H, Stableforth W, Ayres R, Thorburn D, Marshall E, Burroughs A, Mann S, Lombard M, Richardson P, Patanwala I, Maltby J, Brookes M, Mathew R, Vyas S, Singhal S, Gleeson D, Misra S, Butterworth J, George K, Harding T, Douglass A, Panter S, Shearman J, Bray G, Butcher G, Forton D, Mclindon J, Cowan M, Whatley G, Mandal A, Gupta H, Sanghi P, Jain S, Pereira S, Prasad G, Watts G, Wright M, Neuberger J, Gordon F, Unitt E, Grant A, Delahooke T, Higham A, Brind A, Cox M, Ramakrishnan S, King A, Collins C, Whalley S, Li A, Fraser J, Bell A, Wong V, Singhal A, Gee I, Ang Y, Ransford R, Gotto J, Millson C, Bowles J, Thomas C, Harrison M, Galaska R, Kendall J, Whiteman J, Lawlor C, Gray C, Elliott K, Mulvaney-Jones C, Hobson L, Van Duyvenvoorde G, Loftus A, Seward K, Penn R, Maiden J, Damant R, Hails J, Cloudsdale R, Silvestre V, Glenn S, Dungca E, Wheatley N, Doyle H, Kent M, Hamilton C, Braim D, Wooldridge H, Abrahams R, Paton A, Lancaster N, Gibbins A, Hogben K, Desousa P, Muscariu F, Musselwhite J, McKay A, Tan L, Foale C, Brighton J, Flahive K, Nambela E, Townshend P, Ford C, Holder S, Palmer C, Featherstone J, Nasseri M, Sadeghian J, Williams B, Thomas C, Rolls S, Hynes A, Duggan C, Jones S, Crossey M, Stansfield G, MacNicol C, Wilkins J, Wilhelmsen E, Raymode P, Lee H, Durant E, Bishop R, Ncube N, Tripoli S, Casey R, Cowley C, Miller R, Houghton K, Ducker S, Wright F, Bird B, Baxter G, Keggans J, Hughes M, Grieve E, Young K, Williams D, Ocker K, Hines F, Martin K, Innes C, Valliani T, Fairlamb H, Thornthwaite S, Eastick A, Tanqueray E, Morrison J, Holbrook B, Browning J, Walker K, Congreave S, Verheyden J, Slininger S, Stafford L, O’Donnell D, Ainsworth M, Lord S, Kent L, March L, Dickson C, Simpson D, Longhurst B, Hayes M, Shpuza E, White N, Besley S, Pearson S, Wright A, Jones L, Gunter E, Dewhurst H, Fouracres A, Farrington L, Graves L, Marriott S, Leoni M, Tyrer D, Martin K, Dali-kemmery L, Lambourne V, Green M, Sirdefield D, Amor K, Colley J, Shinder B, Jones J, Mills M, Carnahan M, Taylor N, Boulton K, Tregonning J, Brown C, Clifford G, Archer E, Hamilton M, Curtis J, Shewan T, Walsh S, Warner K, Netherton K, Mupudzi M, Gunson B, Gitahi J, Gocher D, Batham S, Pateman H, Desmennu S, Conder J, Clement D, Gallagher S, Orpe J, Chan P, Currie L, O’Donohoe L, Oblak M, Morgan L, Quinn M, Amey I, Baird Y, Cotterill D, Cumlat L, Winter L, Greer S, Spurdle K, Allison J, Dyer S, Sweeting H, Kordula J, Consortium J, Aiba Y, Nakamura H, Abiru S, Nagaoka S, Komori A, Yatsuhashi H, Ishibashi H, Ito M, Kawai Y, Kohn S, Gervais O, Migita K, Katsushima S, Naganuma A, Sugi K, Komatsu T, Mannami T, Matsushita K, Yoshizawa K, Makita F, Nikami T, Nishimura H, Kouno H, Kouno H, Ota H, Komura T, Nakamura Y, Shimada M, Hirashima N, Komeda T, Ario K, Nakamuta M, Yamashita T, Furuta K, Kikuchi M, Naeshiro N, Takahashi H, Mano Y, Tsunematsu S, Yabuuchi I, Shimada Y, Yamauchi K, Sugimoto R, Sakai H, Mita E, Koda M, Tsuruta S, Kamitsukasa H, Sato T, Masaki N, Kobata T, Fukushima N, Higuchi N, Ohara Y, Muro T, Takesaki E, Takaki H, Yamamoto T, Kato M, Nagaoki Y, Hayashi S, Ishida J, Watanabe Y, Kobayashi M, Koga M, Saoshiro T, Yagura M, Hirata K, Takikawa H, Ohira H, Zeniya M, Abe M, Onji M, Kaneko S, Honda M, Arai K, Arinaga-Hino T, Hashimoto E, Taniai M, Umemura T, Joshita S, Nakao K, Ichikawa T, Shibata H, Yamagiwa S, Seike M, Honda K, Sakisaka S, Takeyama Y, Harada M, Senju M, Yokosuka O, Kanda T, Ueno Y, Kikuchi K, Ebinuma H, Himoto T, Yasunami M, Murata K, Mizokami M, Shimoda S, Miyake Y, Takaki A, Yamamoto K, Hirano K, Ichida T, Ido A, Tsubouchi H, Chayama K, Harada K, Nakanuma Y, Maehara Y, Taketomi A, Shirabe K, Soejima Y, Mori A, Yagi S, Uemoto S, Tanaka T, Yamashiki N, Tamura S, Sugawara Y, Kokudo N, Carbone M, Cardamone G, Duga S, Gershwin M, Seldin M, Invernizzi P. X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis. Gastroenterology 2021, 160: 2483-2495.e26. PMID: 33675743, PMCID: PMC8169555, DOI: 10.1053/j.gastro.2021.02.061.Peer-Reviewed Original ResearchMeSH KeywordsAdultAsian PeopleCarrier ProteinsCell LineageChromosomes, Human, XDNA-Binding ProteinsEndopeptidasesFemaleForkhead Transcription FactorsGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLinkage DisequilibriumLiver Cirrhosis, BiliaryMaleMitochondrial Precursor Protein Import Complex ProteinsMonosaccharide Transport ProteinsOdds RatioPolymorphism, Single NucleotideProtein Serine-Threonine KinasesProto-Oncogene ProteinsShal Potassium ChannelsWhite PeopleConceptsGenome-wide significant lociAssociation studiesSignificant lociX chromosome variantsGenome-wide association studiesWide association studyMarker association analysisLinkage disequilibrium blockGenetic architectureSuggestive signalsChromosome contributionsChromosome variantsLineage specification factorDisequilibrium blockSpecification factorAssociation analysisGenotype dataEast Asian individualsGenesOTUD5LociRNA levelsComplex autoimmune diseaseFirst comprehensive studySuperenhancersHCV Viral Load Greater Than 1000 IU/ml at Time of Virologic Failure in Direct-Acting Antiviral-Treated Patients
Morgan JR, Savinkina A, Pires dos Santos AG, Xue Z, Shilton S, Linas B. HCV Viral Load Greater Than 1000 IU/ml at Time of Virologic Failure in Direct-Acting Antiviral-Treated Patients. Advances In Therapy 2021, 38: 1690-1700. PMID: 33590445, PMCID: PMC7932931, DOI: 10.1007/s12325-021-01647-4.Peer-Reviewed Original ResearchConceptsMean HCV RNA levelHCV RNA levelsVirologic failureIU/HCV RNARNA levelsPost-treatment week 4Hepatitis C cureMean HCV RNATreatment virologic failureLevel of viremiaDirect acting antiviralsHCV viral loadTime of relapseResource-limited settingsTreatment failureViral loadElimination targetsClinical trialsWeek 4PatientsCare testOverall populationCare assaysLarger studyRoles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs
Wang C, Lin H. Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs. Genome Biology 2021, 22: 27. PMID: 33419460, PMCID: PMC7792047, DOI: 10.1186/s13059-020-02221-x.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsRole of piRNAsPIWI-piRNA pathwayRNA-binding proteinSmall noncoding RNAsGermline mRNAsGermline developmentNoncoding RNAsRegulatory relationshipsGerm cellsRNAProteinTransposonMajor classesRNA levelsRecent studiesExpressionGenomeSubfamiliesGermlineLncRNAsMajor constituentsMRNARegulation
2020
Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans
Houri-Zeevi L, Kohanim Y, Antonova O, Rechavi O. Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Cell 2020, 182: 1186-1197.e12. PMID: 32841602, PMCID: PMC7479518, DOI: 10.1016/j.cell.2020.07.022.Peer-Reviewed Original Research
2019
Association of Immunosuppression and Human Immunodeficiency Virus (HIV) Viremia With Anal Cancer Risk in Persons Living With HIV in the United States and Canada
Hernández-Ramírez RU, Qin L, Lin H, Leyden W, Neugebauer RS, Althoff KN, Hessol NA, Achenbach CJ, Brooks JT, Gill MJ, Grover S, Horberg MA, Li J, Mathews WC, Mayor AM, Patel P, Rabkin CS, Rachlis A, Justice AC, Moore RD, Engels EA, Silverberg MJ, Dubrow R, Benson C, Bosch R, Kirk G, Mayer K, Grasso C, Hogg R, Harrigan P, Montaner J, Yip B, Zhu J, Salters K, Gabler K, Buchacz K, Li J, Gebo K, Moore R, Moore R, Rodriguez B, Horberg M, Silverberg M, Thorne J, Rabkin C, Margolick J, Jacobson L, D’Souza G, Klein M, Kroch A, Burchell A, Betts A, Lindsay J, Hunter-Mellado R, Mayor A, Gill M, Deeks S, Martin J, Li J, Brooks J, Saag M, Mugavero M, Willig J, Mathews W, Eron J, Napravnik S, Kitahata M, Crane H, Drozd D, Sterling T, Haas D, Rebeiro P, Turner M, Justice A, Dubrow R, Fiellin D, Gange S, Anastos K, Moore R, Saag M, Gange S, Kitahata M, Althoff K, Horberg M, Klein M, McKaig R, Freeman A, Moore R, Freeman A, Kitahata M, Van Rompaey S, Crane H, Drozd D, Morton L, McReynolds J, Lober W, Gange S, Althoff K, Lee J, You B, Hogan B, Zhang J, Jing J, Humes E, Coburn S. Association of Immunosuppression and Human Immunodeficiency Virus (HIV) Viremia With Anal Cancer Risk in Persons Living With HIV in the United States and Canada. Clinical Infectious Diseases 2019, 70: 1176-1185. PMID: 31044245, PMCID: PMC7319056, DOI: 10.1093/cid/ciz329.Peer-Reviewed Original ResearchConceptsAnal cancer riskHIV RNA measuresCancer riskPeak CD4North American AIDS Cohort CollaborationRNA measuresHIV-1 RNA levelsHuman immunodeficiency virus (HIV) viremiaOncogenic human papillomavirus (HPV) infectionAnal cancer developmentAssociation of immunosuppressionTime-updated CD4T-cell countsHuman papillomavirus infectionHuman immunodeficiency virusCohort CollaborationPapillomavirus infectionImmunodeficiency virusImmunoregulatory controlCD4Cox modelCancer promotionUseful markerCancer developmentRNA levelsTranscriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members
Gonzalo-Gil E, Rapuano PB, Ikediobi U, Leibowitz R, Mehta S, Coskun AK, Porterfield JZ, Lampkin TD, Marconi VC, Rimland D, Walker BD, Deeks S, Sutton RE. Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members. ELife 2019, 8: e44360. PMID: 30964004, PMCID: PMC6456299, DOI: 10.7554/elife.44360.Peer-Reviewed Original ResearchConceptsAccessible chromatinActive transcriptionATAC-seqNearby genesCell surface expressionChromosome 3p21Genetic determinantsFamily membersT cell activationHost genetic determinantsResistance phenotypeChemokine receptor mRNACCR5 cell surface expressionRNA levelsCell activationPhenotypeT cellsCellsChromatinTranscriptionGenesKbMembersReceptor mRNAMRNACell Surface Notch Ligand DLL3 is a Therapeutic Target in Isocitrate Dehydrogenase–mutant Glioma
Spino M, Kurz S, Chiriboga L, Serrano J, Zeck B, Sen N, Patel S, Shen G, Vasudevaraja V, Tsirigos A, Suryadevara C, Frenster J, Tateishi K, Wakimoto H, Jain R, Riina H, Nicolaides T, Sulman E, Cahill D, Golfinos J, Isse K, Saunders L, Zagzag D, Placantonakis D, Snuderl M, S. A. Cell Surface Notch Ligand DLL3 is a Therapeutic Target in Isocitrate Dehydrogenase–mutant Glioma. Clinical Cancer Research 2019, 25: 1261-1271. PMID: 30397180, PMCID: PMC7365589, DOI: 10.1158/1078-0432.ccr-18-2312.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, Monoclonal, HumanizedBenzodiazepinonesBrainDNA MethylationFemaleGene Expression Regulation, NeoplasticGenotypeGliomaHumansImmunoconjugatesIntracellular Signaling Peptides and ProteinsIsocitrate DehydrogenaseLigandsMaleMembrane ProteinsMolecular Targeted TherapyMutationNeoplasm Recurrence, LocalReceptors, NotchRNAConceptsGlioma molecular subtypesAntibody-drug conjugatesMolecular subtypesCell surface tumor-associated antigensTumor-associated antigensWild-type glioblastomaAntigen-dependent mannerLow-grade gliomasRova-TRecurrent tumorsDLL3 expressionRovalpituzumab tesirineNontumor brain tissuesNontumor brainMutant gliomasTherapeutic strategiesCell viability assayGliomaRNA levelsDLL3TumorspheresTherapeutic targetIHCTCGA dataWild-type
2018
Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine
Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine. Wiley Interdisciplinary Reviews - RNA 2018, 10: e1513. PMID: 30370679, PMCID: PMC6768404, DOI: 10.1002/wrna.1513.Peer-Reviewed Original ResearchConceptsDifferent RNA populationsRNA populationsNumerous experimental strategiesCellular RNA levelsMetabolic labeling experimentsRNA levelsRNA metabolismRNA turnoverRNA stabilityRNA transcriptionRNA sequencingMetabolic labelingPopulation dynamicsMetabolic labelTargeted incorporationRNA analysisRNA methodWhole cellsC mutationLabeling experimentsExperimental strategiesSequencingAvailable poolGenomeCells
2017
Stress-Induced Neuronal Colony Stimulating Factor 1 Provokes Microglia-Mediated Neuronal Remodeling and Depressive-like Behavior
Wohleb ES, Terwilliger R, Duman CH, Duman RS. Stress-Induced Neuronal Colony Stimulating Factor 1 Provokes Microglia-Mediated Neuronal Remodeling and Depressive-like Behavior. Biological Psychiatry 2017, 83: 38-49. PMID: 28697890, PMCID: PMC6506225, DOI: 10.1016/j.biopsych.2017.05.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnxietyChronic DiseaseDepressive DisorderDisease Models, AnimalFemaleMacrophage Colony-Stimulating FactorMaleMice, Inbred C57BLMice, TransgenicMicrogliaNeuronal PlasticityNeuronsPhagocytosisPrefrontal CortexReceptor, Macrophage Colony-Stimulating FactorRNA, MessengerSex CharacteristicsStress, PsychologicalUncertaintyConceptsDepressive-like behaviorChronic unpredictable stressMedial prefrontal cortexDendritic spine densityNeuronal remodelingSynaptic deficitsDevelopment of anxietyMessenger RNA levelsPrefrontal cortexSpine densityFemale miceFunctional changesStress exposureNeuron-microglia interactionsRNA levelsChronic stress exposureStress-induced elevationPostmortem dorsolateral prefrontal cortexDorsolateral prefrontal cortexBehavioral consequencesNeuronal atrophyPyramidal neuronsMicroglia functionMale miceUnpredictable stress
2016
Cross-Talk Between FSH and Endoplasmic Reticulum Stress: A Mutually Suppressive Relationship
Babayev E, Lalioti MD, Favero F, Seli E. Cross-Talk Between FSH and Endoplasmic Reticulum Stress: A Mutually Suppressive Relationship. Reproductive Sciences 2016, 23: 352-364. PMID: 26342052, PMCID: PMC5933091, DOI: 10.1177/1933719115602770.Peer-Reviewed Original ResearchConceptsFollicle stimulating hormonePregnant mare serum gonadotropinMouse granulosa cellsGranulosa cellsFSH responseSerum gonadotropinFSH stimulationER stressStress-induced cellsPrimary mouse granulosa cellsUntreated granulosa cellsMessenger RNA levelsCalcium adenosine triphosphataseEndoplasmic reticulum stressEstradiol levelsMice 24Estradiol productionIntraperitoneal injectionStimulating hormoneAromatase expressionTP treatmentReticulum stressRNA levelsER stress-associated genesProtein levels
2015
Altered Expression of CDC42 Signaling Pathway Components in Cortical Layer 3 Pyramidal Cells in Schizophrenia
Datta D, Arion D, Corradi J, Lewis D. Altered Expression of CDC42 Signaling Pathway Components in Cortical Layer 3 Pyramidal Cells in Schizophrenia. Biological Psychiatry 2015, 78: 775-785. PMID: 25981171, PMCID: PMC4600637, DOI: 10.1016/j.biopsych.2015.03.030.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsAntipsychotic AgentsBenzodiazepinescdc42 GTP-Binding ProteinCytoskeletal ProteinsFemaleGene Expression RegulationGTP-Binding Protein RegulatorsHaloperidolHumansLaser Capture MicrodissectionLim KinasesMacaca fascicularisMaleMiddle AgedOlanzapinep21-Activated KinasesPrefrontal Cortexrho GTP-Binding Proteinsrho Guanine Nucleotide Dissociation Inhibitor alphaRNA-Binding ProteinsSchizophreniaSignal TransductionConceptsSerine/threonine protein kinaseThreonine protein kinaseActin cytoskeletonProtein kinaseCdc42 effector proteinsCell type-specific fashionMessenger RNA levelsCell division cycle 42Altered expressionType-specific fashionDLPFC gray matterRNA levelsEffector proteinsActin dynamicsPathway componentsSame transcriptKey organizerMessenger RNALaser microdissectionSynergistic alterationsCdc42CytoskeletonQuantitative polymerase chain reactionSpine formationKinaseAssociation between depression and nonadherence to antiretroviral therapy in pregnant women with perinatally acquired HIV
Sheth SS, Coleman J, Cannon T, Milio L, Keller J, Anderson J, Argani C. Association between depression and nonadherence to antiretroviral therapy in pregnant women with perinatally acquired HIV. AIDS Care 2015, 27: 350-354. PMID: 25616659, DOI: 10.1080/09540121.2014.998610.Peer-Reviewed Original ResearchConceptsHistory of depressionHIV RNA levelsAntiretroviral therapyThird trimesterMedication adherencePregnant womenMean HIV RNA levelUndetectable HIV RNA levelsCharts of womenHIV infection characteristicsLifelong chronic illnessRNA levelsRetrospective cohort studyPoor medication adherenceUnique psychosocial challengesOptimal medication adherenceTreatment of depressionUnstable living situationsPregnant patientsCohort studyPreconception periodPregnancy outcomesART nonadherenceHIV treatmentPrenatal care
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