2023
NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function
Manara V, Radoani M, Belli R, Peroni D, Destefanis F, Angheben L, Tome G, Tebaldi T, Bellosta P. NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function. Frontiers In Cell And Developmental Biology 2023, 11: 1293420. PMID: 38213308, PMCID: PMC10782387, DOI: 10.3389/fcell.2023.1293420.Peer-Reviewed Original ResearchNucleolar homeostasisRRNA processingNucleolar structureDirect Myc targetsNuclear mRNA exportMYC transcription factorsProtein interactome analysisE-box sequenceCellular stress responseDirect functional linkN6-methyladenosine (m6A) methylationPotential involvementRibosome biogenesisMRNA exportSubnuclear compartmentsProtein interactomeRibosomal maturationFunctional MycRNA processingRibosomal biogenesisNucleolar proteinsRNA splicingNucleolar localizationInteractome analysisNucleolar functionALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control
Gao Y, Zimmer J, Vasic R, Liu C, Gbyli R, Zheng S, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao A, Slavoff S, Kibbey R, Flavell R, Simon M, Tebaldi T, Li H, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Reports 2023, 42: 113163. PMID: 37742191, PMCID: PMC10636609, DOI: 10.1016/j.celrep.2023.113163.Peer-Reviewed Original ResearchConceptsAlkB homolog 5Post-transcriptional regulatory mechanismsHematopoietic stemNumerous cellular processesProgenitor cell fitnessEnergy metabolismMitochondrial ATP productionMethyladenosine (m<sup>6</sup>A) RNA modificationTricarboxylic acid cycleCell energy metabolismHuman hematopoietic cellsMitochondrial energy productionCell fitnessCellular processesRNA modificationsRNA methylationRegulatory mechanismsEnzyme transcriptsATP productionHomolog 5Acid cycleΑ-ketoglutarateHematopoietic cellsMessenger RNAΑ-KGThe Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells
Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D’Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff J, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nature Cancer 2023, 4: 1102-1121. PMID: 37460872, PMCID: PMC11331482, DOI: 10.1038/s43018-023-00594-z.Peer-Reviewed Original ResearchConceptsMyeloid-derived suppressor cellsProstate cancerAvailable immunotherapiesSuppressive myeloid cellsAKT inhibitor ipatasertibAkt/mTORProstate tumor cellsDifferent genetic alterationsMDSC infiltrationSuppressor cellsImmune surveillanceMDSC migrationTherapeutic strategiesMyeloid cellsTumor growthImmunotherapyCancerTumor cellsMNK1/2 inhibitorGenetic alterationsHGFSPP1Translational levelCellsCoordinated lossAlpha-1 Adrenergic Antagonists Sensitize Neuroblastoma to Therapeutic Differentiation.
Broso F, Gatto P, Sidarovich V, Ambrosini C, De Sanctis V, Bertorelli R, Zaccheroni E, Ricci B, Destefanis E, Longhi S, Sebastiani E, Tebaldi T, Adami V, Quattrone A. Alpha-1 Adrenergic Antagonists Sensitize Neuroblastoma to Therapeutic Differentiation. Cancer Research 2023, 83: 2733-2749. PMID: 37289021, DOI: 10.1158/0008-5472.can-22-1913.Peer-Reviewed Original ResearchConceptsResidual diseaseAdrenergic antagonistsAdrenergic receptorsAlpha-1 adrenergic antagonistAdministration of doxazosinPost-consolidation therapyOverall survival probabilityPrevention of relapseHigh-risk casesMultimodal therapeutic approachPost-consolidation phaseDifferentiation of neuroblastomaNB cell viabilityAggressive childhood tumorRetinoids isotretinoinPediatric patientsΑ1B-adrenergic receptorPrevent relapseChildhood tumorsTherapeutic approachesSpecific blockadeNB cellsPharmacologic targetNeuroblastomaTumor growthVisualizing gene expression changes in time, space, and single cells with expressyouRcell
Paganin M, Tebaldi T, Lauria F, Viero G. Visualizing gene expression changes in time, space, and single cells with expressyouRcell. IScience 2023, 26: 106853. PMID: 37250782, PMCID: PMC10220493, DOI: 10.1016/j.isci.2023.106853.Peer-Reviewed Original ResearchGene expressionSingle cellsGene expression variationBulk RNA sequencingGene expression changesProtein level changesHigh-throughput techniquesGene expression datasetsProteomic datasetsRNA sequencingExpression variationExpression changesExpression datasetsProtein levelsR packageCellsExpressionTranscriptsSequencingMassive advancementVariationComplex variationsTERRA stability is regulated by RALY and polyadenylation in a telomere-specific manner
Savoca V, Rivosecchi J, Gaiatto A, Rossi A, Mosca R, Gialdini I, Zubovic L, Tebaldi T, Macchi P, Cusanelli E. TERRA stability is regulated by RALY and polyadenylation in a telomere-specific manner. Cell Reports 2023, 42: 112406. PMID: 37060569, DOI: 10.1016/j.celrep.2023.112406.Peer-Reviewed Original Research
2022
Hydrogen peroxide induced by nerve injury promotes axon regeneration via connective tissue growth factor
Negro S, Lauria F, Stazi M, Tebaldi T, D’Este G, Pirazzini M, Megighian A, Lessi F, Mazzanti C, Sales G, Romualdi C, Fillo S, Lista F, Sleigh J, Tosolini A, Schiavo G, Viero G, Rigoni M. Hydrogen peroxide induced by nerve injury promotes axon regeneration via connective tissue growth factor. Acta Neuropathologica Communications 2022, 10: 189. PMID: 36567321, PMCID: PMC9791753, DOI: 10.1186/s40478-022-01495-5.Peer-Reviewed Original ResearchConceptsConnective tissue growth factorPerisynaptic Schwann cellsMotor axon terminalsTissue growth factorPro-regenerative factorsGrowth factorInjured sciatic nervePeripheral nerve injuryMotor nerve repairMonth old miceECM remodeling processDegeneration/regenerationNerve injuryCTGF levelsSciatic nerveNeuromuscular functionAxon terminalsNerve repairSchwann cellsNerve regenerationPro-regenerative signalsAxonal growthSC migrationMuscle fibersRemodeling processRecruited monocytes/macrophages drive pulmonary neutrophilic inflammation and irreversible lung tissue remodeling in cystic fibrosis
Öz H, Cheng E, Di Pietro C, Tebaldi T, Biancon G, Zeiss C, Zhang P, Huang P, Esquibies S, Britto C, Schupp J, Murray T, Halene S, Krause D, Egan M, Bruscia E. Recruited monocytes/macrophages drive pulmonary neutrophilic inflammation and irreversible lung tissue remodeling in cystic fibrosis. Cell Reports 2022, 41: 111797. PMID: 36516754, PMCID: PMC9833830, DOI: 10.1016/j.celrep.2022.111797.Peer-Reviewed Original ResearchConceptsC motif chemokine receptor 2Monocytes/macrophagesLung tissue damageCystic fibrosisTissue damageCF lungPulmonary neutrophilic inflammationPro-inflammatory environmentChemokine receptor 2CF lung diseaseNumber of monocytesSpecific therapeutic agentsGrowth factor βCF transmembrane conductance regulatorLung hyperinflammationLung neutrophiliaNeutrophilic inflammationNeutrophil inflammationInflammation contributesLung damageNeutrophil recruitmentLung diseaseLung tissueReceptor 2Therapeutic targetDeconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
Biancon G, Busarello E, Joshi P, Lesch B, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protocols 2022, 3: 101823. PMID: 36595959, PMCID: PMC9676202, DOI: 10.1016/j.xpro.2022.101823.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsIndividual RNA-binding proteinsTranscriptome-wide analysisThousands of RNAsProtein-RNA contactsRNA-binding proteinSingle nucleotide levelComputational analysis pipelineRNA processingMulticomponent complexesRNA immunoprecipitationRead countsComplete detailsAnalysis pipelineAdditional levelProteinImmunoprecipitationRNAInteractionComplexesMODL-22. Establishment of a novel system to specifically trace and ablate quiescent/slow cycling cells in high-grade glioma
Antonica F, Santomaso L, Pernici D, Petrucci L, Aiello G, Cutarelli A, Conti L, Romanel A, Miele E, Tebaldi T, Tiberi L. MODL-22. Establishment of a novel system to specifically trace and ablate quiescent/slow cycling cells in high-grade glioma. Neuro-Oncology 2022, 24: i173-i173. DOI: 10.1093/neuonc/noac079.645.Peer-Reviewed Original ResearchSlow-cycling cellsHigh-grade gliomasBrain cancerCancer organoidsTumor infiltrationHigh-grade brain cancerAdult high-grade gliomasTumor cellsHigh-grade glioma patientsCommon malignant brain tumorCycling tumor cellsPediatric high-grade glioma patientsMalignant brain tumorsSlow cycling stem cellsCycling cellsHuman tumor samplesPoor prognosisSurgical removalMalignant featuresTumor relapseGlioma patientsMouse modelBrain tumorsTemozolomide treatmentMalignant cells
2020
Publisher Correction: Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS
Wu X, Niculite C, Preda M, Rossi A, Tebaldi T, Butoi E, White M, Tudoran O, Petrusca D, Jannasch A, Bone W, Zong X, Fang F, Burlacu A, Paulsen M, Hancock B, Sandusky G, Mitra S, Fishel M, Buechlein A, Ivan C, Oikonomopoulos S, Gorospe M, Mosley A, Radovich M, Davé U, Ragoussis J, Nephew K, Mari B, McIntyre A, Konig H, Ljungman M, Cousminer D, Macchi P, Ivan M. Publisher Correction: Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nature Communications 2020, 11: 5737. PMID: 33159065, PMCID: PMC7648073, DOI: 10.1038/s41467-020-19708-7.Peer-Reviewed Original ResearchA Computing System for Discovering Causal Relationships Among Human Genes to Improve Drug Repositioning
Blanzieri E, Tebaldi T, Cavecchia V, Asnicar F, Masera L, TomÈ G, Nigro E, Colasurdo E, Ciciani M, Mazzoni C, Pilati S. A Computing System for Discovering Causal Relationships Among Human Genes to Improve Drug Repositioning. IEEE Transactions On Emerging Topics In Computing 2020, 9: 1667-1682. DOI: 10.1109/tetc.2020.3031024.Peer-Reviewed Original Research
2014
282: p53-directed translational control can shape and expand the universe of p53 target genes
Zaccara S, Bolado C, Pederiva C, Tebaldi T, Ciribilli Y, Bisio A, Inga A. 282: p53-directed translational control can shape and expand the universe of p53 target genes. European Journal Of Cancer 2014, 50: s66-s67. DOI: 10.1016/s0959-8049(14)50250-x.Peer-Reviewed Original Researchp53-directed translational control can shape and expand the universe of p53 target genes
Zaccara S, Tebaldi T, Pederiva C, Ciribilli Y, Bisio A, Inga A. p53-directed translational control can shape and expand the universe of p53 target genes. Cell Death & Differentiation 2014, 21: 1522-1534. PMID: 24926617, PMCID: PMC4158691, DOI: 10.1038/cdd.2014.79.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCell CycleCell Line, TumorDEAD-box RNA HelicasesDNADNA-Binding ProteinsDoxorubicinGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHumansImidazolesMCF-7 CellsNuclear ProteinsPeptide Chain Elongation, TranslationalPiperazinesRNARNA InterferenceRNA-Binding ProteinsRNA, MessengerRNA, Small InterferingSerine-Arginine Splicing FactorsTumor Suppressor Protein p53Y-Box-Binding Protein 1ConceptsPost-transcriptional controlTranslational controlP53-dependent cellular responseTranslational levelGenome-wide transcriptome analysisCellular responsesRNA-binding proteinCell cycle functionP53-regulated genesGene expression responsesP53 target genesP53 transcriptional targetsDirect p53 transcriptional targetP53-dependent mannerTranscription variationTranscriptional networksPolysomal profilingRNA metabolismTranslatome analysisTranscriptome analysisCellular contextTranscriptional targetsExpression responsesMaster regulatorTarget genes
2012
107 Multi-level Gene Expression Regulation Effects of the NAMPT Inhibitor FK866 in a Model of Acute T Cell Leukemia
Zucal C, D'Agostino V, Tebaldi T, Sociali G, Bruzzone S, Quattrone A, Nencioni A, Provenzani A. 107 Multi-level Gene Expression Regulation Effects of the NAMPT Inhibitor FK866 in a Model of Acute T Cell Leukemia. European Journal Of Cancer 2012, 48: 33-34. DOI: 10.1016/s0959-8049(12)71905-6.Peer-Reviewed Original Research660 Functional Crosstalk Between the P53 and NF-kB Transcription Factors
Zamborszky J, Zaccara S, Bisio A, Lion M, Tebaldi T, Ciribilli Y, Inga A. 660 Functional Crosstalk Between the P53 and NF-kB Transcription Factors. European Journal Of Cancer 2012, 48: s156. DOI: 10.1016/s0959-8049(12)71306-0.Peer-Reviewed Original Research302 Transcriptional Cooperation Between p53 and Estrogen Receptors in a Breast Cancer Model
Lion M, Bisio A, De Sanctis V, Ciribilli Y, Tebaldi T, Menendez D, Resnick M, Inga A. 302 Transcriptional Cooperation Between p53 and Estrogen Receptors in a Breast Cancer Model. European Journal Of Cancer 2012, 48: s74. DOI: 10.1016/s0959-8049(12)70996-6.Peer-Reviewed Original Research
2011
AURA: Atlas of UTR Regulatory Activity
Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, Quattrone A. AURA: Atlas of UTR Regulatory Activity. Bioinformatics 2011, 28: 142-144. PMID: 22057158, DOI: 10.1093/bioinformatics/btr608.Peer-Reviewed Original ResearchConceptsUntranslated regionMRNA untranslated regionsRegulatory activitySingle nucleotide variationsRegulatory annotationsPhylogenetic conservationIntuitive web interfaceNucleotide variationsGene expressionRNA sequencesComprehensive catalogSupplementary dataWealth of informationWeb interfaceSpecialized databasesBioinformaticsFull accessStructure dataAtlasConservationFunctional descriptionAnnotationSupplementary informationSequenceExpression