2022
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022, 55: 1013-1031.e7. PMID: 35320704, PMCID: PMC9203927, DOI: 10.1016/j.immuni.2022.03.004.Peer-Reviewed Original ResearchConceptsHIV-1 eradicationHIV-1 RNAHIV-1Effector memory Th1 cellsHIV-1-infected individualsHIV-1-infected CD4Clonal expansionCell clonesMemory Th1 cellsCell clonal expansionPersistent antigenAntiretroviral therapyViral suppressionCytotoxic CD4Cytotoxic TTh1 cellsAntigen stimulationClonal expansion dynamicsUninfected individualsSurface protein expressionTNF responseUnstimulated conditionsTCR sequencesProtein expressionCD4
2010
Inference of Surface Membrane Factors of HIV-1 Infection through Functional Interaction Networks
Jaeger S, Ertaylan G, van Dijk D, Leser U, Sloot P. Inference of Surface Membrane Factors of HIV-1 Infection through Functional Interaction Networks. PLOS ONE 2010, 5: e13139. PMID: 20967291, PMCID: PMC2953485, DOI: 10.1371/journal.pone.0013139.Peer-Reviewed Original ResearchConceptsSurface membrane proteinsMembrane factorsBioinformatics techniquesNovel cell surface proteinCell/tissue typesSurface proteinsFunctional interaction networkDifferent cell/tissue typesSimilar cellular processesCell surface proteinsCellular surface proteinsCellular processesMembrane proteinsInteraction networksFunctional similarityCell typesCommon functionPatient-specific disease progressionDirect interactionProteinSpecific disease progressionTissue typesExcellent targetNetwork centrality analysisComprehensive networkIdentifying potential survival strategies of HIV-1 through virus-host protein interaction networks
van Dijk D, Ertaylan G, Boucher CA, Sloot PM. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Systems Biology 2010, 4: 96. PMID: 20633292, PMCID: PMC2913931, DOI: 10.1186/1752-0509-4-96.Peer-Reviewed Original ResearchConceptsProtein interaction networksHuman protein interaction networkHuman proteinsInteraction networksCellular processesRNA polymerase II transcriptionVirus-host protein interaction networksPolymerase II transcriptionHuman Protein Interaction DatabaseSet of proteinsNetwork motifsPotential survival strategiesVirus-host dynamicsProtein interaction databasesCentral human proteinsVirus-host systemsTranscriptional machineryProteasomal proteinsMotif analysisImportant proteinsNetwork motif analysisInteraction databasesViral strategiesProteinSurvival strategies