2024
Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells
Mansuri M, Bathla S, Lam T, Nairn A, Williams K. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. Journal Of Proteomics 2024, 297: 105109. PMID: 38325732, PMCID: PMC10939724, DOI: 10.1016/j.jprot.2024.105109.Peer-Reviewed Original ResearchComplex proteomesProtein cleavage activityOptimal conditionsTrypsin digestion protocolReversed phase HPLC separationMass spectrometry workflowMS-based proteomicsMass spectrometric analysisC-terminal amino acid residuesTrypsin digestionChromatographic separationDigestion protocolAmino acid residuesHPLC separationMS/MS analysisGlobal proteomic analysisSingle cellsSample matrixSpectrometric analysisCleavage specificityGeneration of peptidesAcid residuesDown proteinsProteomic analysisCleavage activity
2023
Peripheral signature of altered synaptic integrity in young onset cannabis use disorder: A proteomic study of circulating extracellular vesicles
Ganesh S, Lam T, Garcia-Milian R, D'Souza D, Nairn A, Elgert K, Eitan E, Ranganathan M. Peripheral signature of altered synaptic integrity in young onset cannabis use disorder: A proteomic study of circulating extracellular vesicles. The World Journal Of Biological Psychiatry 2023, 24: 603-613. PMID: 36994633, PMCID: PMC10471733, DOI: 10.1080/15622975.2023.2197039.Peer-Reviewed Original ResearchConceptsNeuron-derived extracellular vesiclesLabel-free quantification mass spectrometryProteomic studiesCannabis use disorderExtracellular vesiclesMass spectrometry proteomic analysisDifferential proteomic profilesAdapter proteinProteomic analysisPost-synaptic densityPeripheral signatureMolecular basisProteomic profilesProteinMarkers of neuropathologyBrain tissue samplesSynaptic pathologyVesiclesSynaptic integrityImmunoaffinity methodUse disordersFunctional integrityImportant insightsNeuropathologyPilot study
2022
Proteomic profiling reveals an association between ALDH and oxidative phosphorylation and DNA damage repair pathways in human colon adenocarcinoma stem cells
Wang Y, Chen Y, Garcia-Milian R, Golla JP, Charkoftaki G, Lam TT, Thompson DC, Vasiliou V. Proteomic profiling reveals an association between ALDH and oxidative phosphorylation and DNA damage repair pathways in human colon adenocarcinoma stem cells. Chemico-Biological Interactions 2022, 368: 110175. PMID: 36162455, PMCID: PMC9891852, DOI: 10.1016/j.cbi.2022.110175.Peer-Reviewed Original ResearchConceptsCancer stem cellsProteomic profilingOxidative phosphorylationLabel-free quantitative proteomic analysisDNA damage repair pathwaysQuantitative proteomic analysisAldehyde dehydrogenase familyColon cancer stem cellsCOLO320DM cellsStem cellsNucleotide excision repairDamage repair pathwaysIngenuity Pathway AnalysisCell populationsProteomic analysisProteomic datasetsDehydrogenase familyMetabolic switchProteomic studiesRepair pathwaysCellular pathwaysALDH enzymatic activityCellular survivalExcision repairALDH activity
2017
Loss of TMEM106B Ameliorates Lysosomal and Frontotemporal Dementia-Related Phenotypes in Progranulin-Deficient Mice
Klein ZA, Takahashi H, Ma M, Stagi M, Zhou M, Lam TT, Strittmatter SM. Loss of TMEM106B Ameliorates Lysosomal and Frontotemporal Dementia-Related Phenotypes in Progranulin-Deficient Mice. Neuron 2017, 95: 281-296.e6. PMID: 28728022, PMCID: PMC5558861, DOI: 10.1016/j.neuron.2017.06.026.Peer-Reviewed Original ResearchConceptsLysosomal protein levelsFrontotemporal lobar degenerationProtein levelsMultiple lysosomal enzymesLysosomal enzymesV0 subunitsTMEM106B geneProteomic analysisProgranulin-deficient miceExtent of neurodegenerationCommon neurodegenerative disorderLysosomal acidificationLysosomal enzyme levelsProtein 1Microglial accumulationRisk modificationFTLD riskBehavioral abnormalitiesRetinal degenerationNeurodegenerative disordersFrontotemporal dementiaGRNTMEM106BFunctional relationshipEnzyme levels
2011
Functional Genomic and Proteomic Analysis Reveals Disruption of Myelin-Related Genes and Translation in a Mouse Model of Early Life Neglect
Bordner KA, George ED, Carlyle BC, Duque A, Kitchen RR, Lam TT, Colangelo CM, Stone KL, Abbott TB, Mane SM, Nairn AC, Simen AA. Functional Genomic and Proteomic Analysis Reveals Disruption of Myelin-Related Genes and Translation in a Mouse Model of Early Life Neglect. Frontiers In Psychiatry 2011, 2: 18. PMID: 21629843, PMCID: PMC3098717, DOI: 10.3389/fpsyt.2011.00018.Peer-Reviewed Original ResearchNext-generation RNA sequencingLabel-free proteomicsFunctional genomicsProtein translationProteomic analysisCDNA microarrayMethylation changesRNA sequencingPromoter regionEarly life neglectMethylation analysisGenesMolecular changesProteomicsMature oligodendrocytesGenomicsTranslationDisruption of myelinMouse modelTissue samplesMechanismMicroarrayGood animal modelDysregulation