2023
Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome
Ketchesin K, Becker-Krail D, Xue X, Wilson R, Lam T, Williams K, Nairn A, Tseng G, Logan R. Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome. Journal Of Proteome Research 2023, 22: 2377-2390. PMID: 37311105, PMCID: PMC10392613, DOI: 10.1021/acs.jproteome.3c00126.Peer-Reviewed Original ResearchConceptsNucleus accumbensDiurnal regulationMouse nucleus accumbensPhase-dependent regulationBrain regionsDiurnal rhythmAdministration of psychostimulantsEffects of cocaineSubstance use disordersDifferential effectsMolecular rhythmsProtein rhythmsQuantitative proteomicsProteomic dataProteomeMorphine administrationUse of substancesRhythm alterationsGlucocorticoid signalingUse disordersMorphineSubstance useProtein expressionCocaineSignificant alterationsProteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Shi G, Song C, Torres Robles J, Salichos L, Lou H, Lam T, Gerstein M, Turk B. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science Signaling 2023, 16: eabm5518. PMID: 36626580, PMCID: PMC9995140, DOI: 10.1126/scisignal.abm5518.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseDocking motifSequence motifsDocking sequenceShort linear sequence motifsLinear sequence motifsSubstrate recruitmentHuman proteomeProtein kinaseCatalytic cleftExchange mutantsEssential functionsCultured cellsScreening pipelineWide screeningInteractorsMotifSequenceLimited repertoireSelective bindingInteractomeCombinatorial librariesMKK6ProteomeMKK7
2022
Sex- and estrous-cycle dependent dorsal hippocampal phosphoproteomic changes induced by low-dose ketamine
Saland SK, Wilczak K, Voss E, Lam TT, Kabbaj M. Sex- and estrous-cycle dependent dorsal hippocampal phosphoproteomic changes induced by low-dose ketamine. Scientific Reports 2022, 12: 1820. PMID: 35110693, PMCID: PMC8810966, DOI: 10.1038/s41598-022-05937-x.Peer-Reviewed Original ResearchConceptsLow-dose ketamineFemale ratsMale ratsTherapeutic effectIntact adult male ratsNMDA receptor antagonist ketamineAcute low doseKetamine's therapeutic effectsRapid antidepressant actionsAdult male ratsKetamine-induced changesRapid actionAntidepressant actionAntidepressant ketamineHormonal milieuHormone-dependent modulationHormonal statusLow doseKetamineBrain regionsRatsSynaptic signalingPathway activationBi-directional effectsCritical modulator
2021
Cocaine self-administration induces sex-dependent protein expression in the nucleus accumbens
López AJ, Johnson AR, Euston TJ, Wilson R, Nolan SO, Brady LJ, Thibeault KC, Kelly SJ, Kondev V, Melugin P, Kutlu MG, Chuang E, Lam TT, Kiraly DD, Calipari ES. Cocaine self-administration induces sex-dependent protein expression in the nucleus accumbens. Communications Biology 2021, 4: 883. PMID: 34272455, PMCID: PMC8285523, DOI: 10.1038/s42003-021-02358-w.Peer-Reviewed Original ResearchConceptsProtein expression patternsExpression patternsQuantitative mass spectrometrySubstance use disordersCritical biological variableProteomic functionProtein regulationRegulated proteinsUnique molecular profileNucleus accumbensSexual dimorphismProteomeProtein expressionMolecular substratesDrug-induced plasticityMolecular profileChronic neuropsychiatric conditionsPreclinical evidenceBaseline differencesCocaine administrationReward-associated behaviorsUse disordersMass spectrometryMale subjectsBiological variables
2020
Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry
Franzen AD, Lam TT, Williams KR, Nairn AC, Duman RS, Sathyanesan M, Kumar V, Carpenter LL, Newton SS. Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry. BMC Psychiatry 2020, 20: 481. PMID: 32998701, PMCID: PMC7528485, DOI: 10.1186/s12888-020-02874-9.Peer-Reviewed Original ResearchMeSH KeywordsDepressive Disorder, MajorGene Expression ProfilingHumansMass SpectrometryProteomeProteomicsConceptsPR domain zinc finger protein 1Bioinformatics analysisZinc finger protein 1Quantitative mass spectrometryFinger protein 1Potential biological functionsMajor canonical pathwaysPeroxisome proliferator-activated receptor gamma coactivatorProliferator-activated receptor gamma coactivatorCellular functionsCellular movementCellular compromiseCell signalingCellular developmentOrganismal injuryBiological functionsReceptor gamma coactivatorCanonical pathwaysSignal transducerUpstream regulatorTranscription 3Protein profilesDifferential expressionProtein synthesisProteomics software
2019
Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells
Charkoftaki G, Thompson DC, Golla JP, Garcia-Milian R, Lam TT, Engel J, Vasiliou V. Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells. Chemico-Biological Interactions 2019, 304: 88-96. PMID: 30851239, PMCID: PMC7988342, DOI: 10.1016/j.cbi.2019.02.030.Peer-Reviewed Original ResearchSynovial fluid proteome changes in ACL injury-induced posttraumatic osteoarthritis: Proteomics analysis of porcine knee synovial fluid
Kiapour AM, Sieker JT, Proffen BL, Lam TT, Fleming BC, Murray MM. Synovial fluid proteome changes in ACL injury-induced posttraumatic osteoarthritis: Proteomics analysis of porcine knee synovial fluid. PLOS ONE 2019, 14: e0212662. PMID: 30822327, PMCID: PMC6396923, DOI: 10.1371/journal.pone.0212662.Peer-Reviewed Original Research
2018
Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq
Carlyle B, Kitchen RR, Zhang J, Wilson R, Lam T, Rozowsky JS, Williams KR, Sestan N, Gerstein M, Nairn AC. Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. Journal Of Proteome Research 2018, 17: 3431-3444. PMID: 30125121, PMCID: PMC6392456, DOI: 10.1021/acs.jproteome.8b00310.Peer-Reviewed Original ResearchConceptsRNA-seqProteomic dataGene expressionLiquid chromatography-tandem mass spectrometry proteomicsTandem mass spectrometry proteomicsHigh-throughput proteomic dataTranscriptomic profiling methodsDistinct amino acid sequencesTranscript-level expressionAmino acid sequenceMass spectrometry proteomicsHEK293 cell culturesTranslatome dataMost genesProfound functional implicationsProtein isoformsAlternate isoformsGene productsAcid sequenceCellular controlBiosynthetic stateGeneration of peptidesCell typesFunctional relevanceFunctional implicationsQuantification of Urinary Protein Biomarkers of Autosomal Dominant Polycystic Kidney Disease by Parallel Reaction Monitoring
Rauniyar N, Yu X, Cantley J, Voss EZ, Belcher J, Colangelo CM, Stone KL, Dahl N, Parikh C, Lam TT, Cantley LG. Quantification of Urinary Protein Biomarkers of Autosomal Dominant Polycystic Kidney Disease by Parallel Reaction Monitoring. Proteomics Clinical Applications 2018, 12: e1700157. PMID: 29573172, PMCID: PMC6736530, DOI: 10.1002/prca.201700157.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersFemaleHumansKidneyMalePolycystic Kidney, Autosomal DominantProteinsProteomeUrineConceptsAutosomal dominant polycystic kidney diseaseDominant polycystic kidney diseasePolycystic kidney diseaseCyst growthKidney diseaseUrinary proteinNormal controlsEnd-stage renal failureUrine samplesUrinary protein biomarkersLife-long diseasePresence of cystsRespective urine samplesMost patientsRenal failureADPKD patientsEarly diagnosisClinical relevanceUrinary proteomeParallel reaction monitoringPatientsCyst formationDiseaseWater intakePathogenesis
2016
Evaluation of the Nicotinic Acetylcholine Receptor-Associated Proteome at Baseline and Following Nicotine Exposure in Human and Mouse Cortex
McClure-Begley TD, Esterlis I, Stone KL, Lam TT, Grady SR, Colangelo CM, Lindstrom JM, Marks MJ, Picciotto MR. Evaluation of the Nicotinic Acetylcholine Receptor-Associated Proteome at Baseline and Following Nicotine Exposure in Human and Mouse Cortex. ENeuro 2016, 3: eneuro.0166-16.2016. PMID: 27559543, PMCID: PMC4985585, DOI: 10.1523/eneuro.0166-16.2016.Peer-Reviewed Original ResearchConceptsPutative interacting proteinsQuantitative proteomic assessmentProtein-protein interactionsTemporal cortex tissueChaperone familyMood disordersInteracting proteinProtein complexesPresynaptic neurotransmitter releaseNovel etiological mechanismsNicotine exposureProteomic assessmentProteomeNicotinic acetylcholine receptorsMouse cortexProteinHigh-affinity nAChRsΒ2 subunitCortex of miceMaintenance of smokingNew treatment targetsResult of smokingNeurotransmitter releaseAcetylcholine receptorsPrimary function
2015
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research. Genomics Proteomics & Bioinformatics 2015, 13: 25-35. PMID: 25712262, PMCID: PMC4411476, DOI: 10.1016/j.gpb.2014.11.002.Peer-Reviewed Original ResearchConceptsMultiple reaction monitoringPeptides/proteinsYale Protein Expression DatabaseReaction monitoringProteomics researchMass spectrometry-based proteomics researchMS/MSMass spectrometryDatabase search resultsPeptide identificationSpectral librarySite localizationProteomics communityGroup of laboratoriesSpectrometryProtein Expression DatabaseMS