2025
CACNA1G, A Heterotaxy Candidate Gene, Plays a Role in Ciliogenesis and Left‐Right Patterning in Xenopus tropicalis
Kostiuk V, Kabir R, Akbari R, Rushing A, González D, Kim A, Kim A, Zenisek D, Khokha M. CACNA1G, A Heterotaxy Candidate Gene, Plays a Role in Ciliogenesis and Left‐Right Patterning in Xenopus tropicalis. Genesis 2025, 63: e70009. PMID: 40008628, PMCID: PMC11867209, DOI: 10.1002/dvg.70009.Peer-Reviewed Original ResearchConceptsCongenital heart diseaseCACNA1GLow-voltage-activated calcium channelsExpression of Cacna1gCalcium channelsPatient cohortCardiac functionLR patterningHeterotaxyLR organizerChannel familyCACNA1SHeart diseaseLeft-rightG expressionXenopus tropicalisAbnormal expressionProcess of cilia formationCardiac loopingMultiple organsSignaling cascadesLR asymmetryPatientsT-typeEmbryonic development
2024
Versatility of 14-3-3 proteins and their roles in bone and joint-related diseases
Zhou R, Hu W, Ma P, Liu C. Versatility of 14-3-3 proteins and their roles in bone and joint-related diseases. Bone Research 2024, 12: 58. PMID: 39406741, PMCID: PMC11480210, DOI: 10.1038/s41413-024-00370-4.Peer-Reviewed Original ResearchLeveraging altered lipid metabolism in treating B cell malignancies
Lee J, Mani A, Shin M, Krauss R. Leveraging altered lipid metabolism in treating B cell malignancies. Progress In Lipid Research 2024, 95: 101288. PMID: 38964473, PMCID: PMC11347096, DOI: 10.1016/j.plipres.2024.101288.Peer-Reviewed Original ResearchB-cell malignanciesMalignant B cellsB cell receptorAltered lipid metabolismLipid metabolismOncogenic signalingB cellsTreating B-cell malignanciesReprogram lipid metabolismLipid raft integrityB-cell receptor activationHeterogeneous blood cancerImprove risk stratificationUncontrolled cell proliferationB cell activationRaft integrityLipid raftsMYC translocationCytotoxic therapyHeightened metabolic demandsGenetic driversSignaling cascadesMalignant subtypeRisk stratificationObese individualsModulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Edman N, Phal A, Redler R, Schlichthaerle T, Srivatsan S, Ehnes D, Etemadi A, An S, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks D, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry C, Schweppe D, Freedman B, Stewart L, Ekiert D, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell 2024, 187: 3726-3740.e43. PMID: 38861993, PMCID: PMC11246234, DOI: 10.1016/j.cell.2024.05.025.Peer-Reviewed Original ResearchConceptsIntracellular tyrosine kinase domainMitogen-activated protein kinase (MAPK) pathway activationDownstream signaling cascadesCyclic homo-oligomersTyrosine kinase domainReceptor valencyCell fateOligomeric assembliesKinase domainSignaling outcomesSignaling ligandsHomo-oligomersSplice variantsSignaling cascadesCytokine signalingExtracellular domainPathway signalingDevelopmental transitionsProtein building blocksVascular differentiationPathway activationVascular developmentComplexity of signalsModular assemblyTherapeutic applicationsSupervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer’s disease progression
Hodgson L, Li Y, Iturria-Medina Y, Stratton J, Wolf G, Krishnaswamy S, Bennett D, Bzdok D. Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer’s disease progression. Communications Biology 2024, 7: 591. PMID: 38760483, PMCID: PMC11101463, DOI: 10.1038/s42003-024-06273-8.Peer-Reviewed Original ResearchConceptsGene programAlzheimer's diseaseLate-onset Alzheimer's diseaseAD risk lociCell type-specificSingle-nucleus RNA sequencingRisk lociAD brainAlzheimer's disease progressionSnRNA-seqRNA sequencingAD pathophysiologySignaling cascadesTranscriptome modulationProgressive neurodegenerative diseaseCell-typeGWASNeurodegenerative diseasesNeuronal lossGlial cellsTranscriptomeLociGenesPseudo-trajectoriesDisease progressionEx Vivo Immunization: A Strategy for Immunization Against SARS-CoV-2
Singh H, Nuthalapati P, Yendapalli P, Sahu D. Ex Vivo Immunization: A Strategy for Immunization Against SARS-CoV-2. 2024, 258-271. DOI: 10.1039/bk9781837672813-00258.Peer-Reviewed Original ResearchPeripheral blood mononuclear cellsNatural killer cellsCell-mediated immunityBlood mononuclear cellsEnhanced immune responseNaive lymphocytesDendritic cellsKiller cellsT cellsAntigen presentationB cellsMononuclear cellsImmune responseSARS-nCoV-2Human hostSignaling cascadesSARS-CoV-2Global pandemic coronavirus diseaseVirion particlesImmunityMass immunizationAdverse effectsCoronavirus 2Pandemic coronavirus disease
2023
Functional Characterization of Novel MC4R Variants Identified in Two Unrelated Patients with Morbid Obesity in Qatar
Mohammed I, Selvaraj S, Ahmed W, Al-Barazenji T, Hammad A, Dauleh H, Saraiva L, Al-Shafai M, Hussain K. Functional Characterization of Novel MC4R Variants Identified in Two Unrelated Patients with Morbid Obesity in Qatar. International Journal Of Molecular Sciences 2023, 24: 16361. PMID: 38003551, PMCID: PMC10671262, DOI: 10.3390/ijms242216361.Peer-Reviewed Original ResearchConceptsCREB signaling pathwaysHeterozygous variantsSignaling pathwayVariants associated with obesityIn silico prediction toolsEffects of allelic variationFunctional impactIn silico analysisMonogenic obesityDownstream signaling cascadesLigand binding activityGT1-7 cellsObesity-related genesIdentified variantsAllelic variationFunctional characterizationSilico analysisSanger sequencingPathogenic variantsActivation of PKALeptin-melanocortin pathwaySignaling cascadesMonogenic forms of obesityGenesIn vitro analysisThe neuropeptidergic connectome of C. elegans
Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor S, Weinreb A, Bentley B, Hammarlund M, Miller D, Hobert O, Beets I, Vértes P, Schafer W. The neuropeptidergic connectome of C. elegans. Neuron 2023, 111: 3570-3589.e5. PMID: 37935195, PMCID: PMC7615469, DOI: 10.1016/j.neuron.2023.09.043.Peer-Reviewed Original ResearchConceptsNervous systemSynaptic wiring diagramGene expression datasetsReceptor-ligand interactionsStudied neuronsKey network hubNeuronal connectionsSignaling cascadesBrain functionInput connectivityNeuromodulatory signalingChemical synapsesPeptidergic neuromodulationBiochemical analysisEssential roleNeural basisNeuropeptidesConnectomeNetwork hubsWiring diagramSimilar patterncAMP−EPAC−PKCε−RIM1α signaling regulates presynaptic long-term potentiation and motor learning
Wang X, Zhou L, Dong B, Xu F, Wang D, Shen E, Cai X, Wang Y, Wang N, Ji S, Chen W, Schonewille M, Zhu J, De Zeeuw C, Shen Y. cAMP−EPAC−PKCε−RIM1α signaling regulates presynaptic long-term potentiation and motor learning. ELife 2023, 12: e80875. PMID: 37159499, PMCID: PMC10171863, DOI: 10.7554/elife.80875.Peer-Reviewed Original ResearchConceptsPresynaptic long-term potentiationSignaling cascadesPresynaptic plasticityRelease of synaptic vesiclesLong-term potentiationThreonine phosphorylationSynaptic vesiclesFunctional relevancePurkinje cell synapsesMotor behaviorPresynaptic formLearning mechanismCerebellar learning mechanismsCascadeLearningCell synapsesBasic performanceMotor learningThreonineMotor skillsSignalVesicles
2022
p16 Represses DNA Damage Repair via a Novel Ubiquitin-Dependent Signaling Cascade
Molkentine DP, Molkentine JM, Bridges KA, Valdecanas DR, Dhawan A, Bahri R, Hefner AJ, Kumar M, Yang L, Abdelhakiem M, Pifer PM, Sandulache V, Sheth A, Beadle BM, Thames HD, Mason KA, Pickering CR, Meyn RE, Skinner HD. p16 Represses DNA Damage Repair via a Novel Ubiquitin-Dependent Signaling Cascade. Cancer Research 2022, 82: 916-928. PMID: 34965932, PMCID: PMC9136619, DOI: 10.1158/0008-5472.can-21-2101.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Squamous CellCarrier ProteinsCyclin-Dependent Kinase Inhibitor p16DNA DamageDNA, ViralHead and Neck NeoplasmsHumansPapillomaviridaePapillomavirus InfectionsSignal TransductionSquamous Cell Carcinoma of Head and NeckTumor Suppressor ProteinsUbiquitinUbiquitin-Protein LigasesUbiquitin-Specific Peptidase 7ConceptsUbiquitin-specific protease 7DNA damage repairDamage repairHPV-positive tumorsTranscription factor Sp1Human papillomavirusFactor Sp1Neck squamous cell carcinoma cellsDNA-damaging therapiesRenders cellsHomologous recombinationSignaling cascadesHPV-negative diseaseSquamous cell carcinoma cellsHPV-negative counterpartsHPV-positive diseaseSquamous cell carcinomaUSP7 inhibitorsDNA damageHPV-negative HNSCCFunctional roleDegradation pathwayHPV positivityPathwayUndiscovered pathways
2020
Effects of nicotine on DARPP-32 and CaMKII signaling relevant to addiction
Lee AM, Picciotto MR. Effects of nicotine on DARPP-32 and CaMKII signaling relevant to addiction. Advances In Pharmacology 2020, 90: 89-115. PMID: 33706940, PMCID: PMC8008986, DOI: 10.1016/bs.apha.2020.09.002.Peer-Reviewed Original ResearchConceptsKey intracellular signaling cascadesIntracellular signaling cascadesDependent kinase IIPaul GreengardSignaling cascadesKinase IINicotine-dependent behaviorsNicotinic acetylcholine receptorsSecond messenger systemsNeuronal signalingInitial characterizationDARPP-32ProteinMessenger systemsAcetylcholine receptorsSignalingRoleCaMKIIGreengardNicotine addictionCascadeImmunohistochemical workDiscoveryReceptorsCAMPNMR in integrated biophysical drug discovery for RAS: past, present, and future
Marshall C, KleinJan F, Gebregiworgis T, Lee K, Fang Z, Eves B, Liu N, Gasmi-Seabrook G, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. Journal Of Biomolecular NMR 2020, 74: 531-554. PMID: 32804298, DOI: 10.1007/s10858-020-00338-6.Peer-Reviewed Original ResearchConceptsGTPase domainProper membrane localizationMultiple signaling cascadesOncogenic Ras mutationsKey downstream effectorDrug discoveryGTPase cycleMembrane localizationRAS proteinsGTP hydrolysisConformational selectionRAS signalingDownstream effectorsSignaling cascadesLipid modificationG12C mutantUpstream regulatorBiophysical approachesSmall proteinsRAS oncogenesDruggable pocketHuman cancersCell growthCovalent inhibitorsPeptidyl inhibitorsImpact of Monosodium Glutamate and Corticosterone in the Hippocampus: Glucocorticoid Regulation and Caspase‐3 mediated Microvascular and Neuronal Apoptosis
Mathew S, Joy K. Impact of Monosodium Glutamate and Corticosterone in the Hippocampus: Glucocorticoid Regulation and Caspase‐3 mediated Microvascular and Neuronal Apoptosis. The FASEB Journal 2020, 34: 1-1. DOI: 10.1096/fasebj.2020.34.s1.02786.Peer-Reviewed Original ResearchBlood-brain barrierExposure to monosodium glutamateGlucocorticoid receptorApoptotic signaling cascadeEnhanced glucocorticoid receptorDay 8Immediate response to stressEffects of corticosteroneResponse to stressCaspase-3Corticosterone exposureCorticosterone modelBody weightGlutamate modelGroup I control ratsMonosodium glutamate modelDentate gyrusBax-dependent apoptotic pathwayMonosodium glutamateHippocampusNeuronal apoptosisSignaling cascadesGene expressionGroup II ratsMale Wistar rats
2019
Mammalian TRP ion channels are insensitive to membrane stretch
Nikolaev YA, Cox CD, Ridone P, Rohde PR, Cordero-Morales JF, Vásquez V, Laver DR, Martinac B. Mammalian TRP ion channels are insensitive to membrane stretch. Journal Of Cell Science 2019, 132: jcs238360. PMID: 31722978, PMCID: PMC6918743, DOI: 10.1242/jcs.238360.Peer-Reviewed Original ResearchConceptsTRP channelsTouch-insensitive mutantsMembrane stretchIon channelsTRP ion channel familyIon channel familyTransient receptor potential (TRP) ion channelsTRP ion channelsMammalian subfamiliesMammalian membersPotential ion channelsArtificial bilayer systemInsensitive mutantsCytoplasmic tethersDownstream componentsMechanosensory processesSignaling cascadesChannel familyCellular componentsBlood pressure regulationCell membraneCerebrospinal fluid flowMechanical forcesStretch activationPressure regulationLipid Modifications in Cilia Biology
Roy K, Marin EP. Lipid Modifications in Cilia Biology. Journal Of Clinical Medicine 2019, 8: 921. PMID: 31252577, PMCID: PMC6678300, DOI: 10.3390/jcm8070921.BooksLipid modificationCiliary proteinsCiliary protein traffickingSpecific protein poolsDifferent lipid modificationsCilia biologyProtein traffickingProtein stabilitySignaling cascadesTransporter proteinsProtein poolProteinVariety of rolesCiliaTraffickingFinal localizationCellular structureDistinctive roleBiologyRoleAbundanceModificationRegulationPathwayCascade
2017
Neuronal expression patterns of the PlexinA family during zebrafish development
Emerson S, Light S, Ebert A. Neuronal expression patterns of the PlexinA family during zebrafish development. Gene Expression Patterns 2017, 27: 56-66. PMID: 29107805, DOI: 10.1016/j.gep.2017.10.007.Peer-Reviewed Original ResearchConceptsSignaling moleculesZebrafish developmentExpression patternsSecreted signaling moleculesRegulate many aspectsTransmembrane protein receptorIntracellular signaling cascadesNeuronal expression patternProtein receptorExpression of receptor subtypesSignaling cascadesAxon guidancePlxnsExtracellular bindingFamily membersExpression profilesDevelopmental processesNeuronal positioningAppropriate signalsSpatial expressionZebrafishReceptor subtypesPost-fertilizationExpressionNeuronal tissuePTSD Blood Transcriptome Mega-Analysis: Shared Inflammatory Pathways across Biological Sex and Modes of Trauma
Breen MS, Tylee DS, Maihofer AX, Neylan TC, Mehta D, Binder EB, Chandler SD, Hess JL, Kremen WS, Risbrough VB, Woelk CH, Baker DG, Nievergelt CM, Tsuang MT, Buxbaum JD, Glatt SJ. PTSD Blood Transcriptome Mega-Analysis: Shared Inflammatory Pathways across Biological Sex and Modes of Trauma. Neuropsychopharmacology 2017, 43: 469-481. PMID: 28925389, PMCID: PMC5770765, DOI: 10.1038/npp.2017.220.Peer-Reviewed Original ResearchConceptsDistinct gene expression perturbationsCo-expression network analysisMitogen-activated protein kinase activityCommon signaling cascadesGene expression perturbationsProtein kinase activityTranscriptome-wide screenDistinct biological pathwaysMolecular convergenceGene expression signaturesTranscriptome studiesExpression perturbationsTranscriptional dysregulationSignaling cascadesKinase activityBiological pathwaysExpression signaturesType I interferonWidespread immune dysregulationInnate immuneLipid metabolismPathwayI interferonNetwork analysisDysregulation
2016
Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling
Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R. Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling. Journal Of Proteome Research 2016, 16: 14-33. PMID: 27762135, DOI: 10.1021/acs.jproteome.6b00728.Peer-Reviewed Original ResearchConceptsTNF-α signalingProteomics researchDimeric transcription factorsComplex signaling cascadesSystems-level understandingProteome levelProteomic landscapeCellular processesTranscription factorsSignaling cascadesNF-κBSignalingLevel understandingMass spectrometryProteomeActivationProteomicsSpite of decadesCytokines IL-1βDifferentiationLimited knowledgePathwayCascadeFamilyTNFInteraction of Tumor Necrosis Factor Receptor-associated Factor 6 (TRAF6) and Vav3 in the Receptor Activator of Nuclear Factor κB (RANK) Signaling Complex Enhances Osteoclastogenesis*
Yu J, Yun H, Shin B, Kim Y, Park E, Choi S, Yu J, Amarasekara D, Kim S, Inoue J, Walsh M, Choi Y, Takami M, Rho J. Interaction of Tumor Necrosis Factor Receptor-associated Factor 6 (TRAF6) and Vav3 in the Receptor Activator of Nuclear Factor κB (RANK) Signaling Complex Enhances Osteoclastogenesis*. Journal Of Biological Chemistry 2016, 291: 20643-20660. PMID: 27507811, PMCID: PMC5034056, DOI: 10.1074/jbc.m116.728303.Peer-Reviewed Original ResearchConceptsTNF receptor-associated factor 6Signaling complexIVVY motifCross-talkDbl homology domainCoiled-coil domainFactor 6RANK-mediated osteoclastogenesisTRAF6-binding siteFunctional cross-talkUbiquitin pathwayBinding partnersCytoplasmic tailTumor necrosis factor receptor-associated factor 6Activation of nuclear factor-kBInteraction partnersNuclear factor-kBProteomic approachVav3Signaling cascadesFunctional importanceMotifCooperative signalingMutantsInteraction of tumor necrosis factor receptor-associated factor 6Oligomers of Amyloid β Prevent Physiological Activation of the Cellular Prion Protein-Metabotropic Glutamate Receptor 5 Complex by Glutamate in Alzheimer Disease*
Haas LT, Strittmatter SM. Oligomers of Amyloid β Prevent Physiological Activation of the Cellular Prion Protein-Metabotropic Glutamate Receptor 5 Complex by Glutamate in Alzheimer Disease*. Journal Of Biological Chemistry 2016, 291: 17112-17121. PMID: 27325698, PMCID: PMC5016115, DOI: 10.1074/jbc.m116.720664.Peer-Reviewed Original ResearchConceptsProtein tyrosine kinase 2Calmodulin-dependent protein kinase IICalcium/calmodulin-dependent protein kinase IICellular prion proteinProtein kinase IIBrain slicesSignaling cascadesAlzheimer's diseaseKinase IIPhysiological signalingKinase 2Mutant transgeneMetabotropic glutamate receptor 5Loss of synapsesPrion proteinGlutamate receptor 5Receptor complexWild-type slicesProtein mediatorsAmyloid-β OligomersGlutamate activationChronic expressionDementia symptomsReceptor 5Acute exposure
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