2023
Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling
Golan N, Ehrlich D, Bonanno J, O'Brien R, Murillo M, Kauer S, Ravindra N, Van Dijk D, Cafferty W. Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling. Journal Of Neuroscience 2023, 43: 7929-7945. PMID: 37748862, PMCID: PMC10669816, DOI: 10.1523/jneurosci.0811-22.2023.Peer-Reviewed Original ResearchConceptsCorticospinal tract neuronsCorticospinal tractAdult corticospinal tractIrreversible functional deficitsCortical layer 2/3Lumbar spinal cordSpinal cord injuryLayer 5 neuronsClasses of neuronsMolecular heterogeneityAxon collateralizationTract neuronsCord injuryRetrograde labelingMotor pathwaysFemale miceFunctional deficitsLayer 2/3Primary axonsSpinal cordTerminal fieldsNeuron subtypesAdult tractTherapeutic interventionsSingle-cell RNA sequencing
2021
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children
Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children. Immunity 2021, 54: 1083-1095.e7. PMID: 33891889, PMCID: PMC8043654, DOI: 10.1016/j.immuni.2021.04.003.Peer-Reviewed Original ResearchConceptsMIS-C patientsDisease severityInflammatory syndromeTCR repertoireSARS-CoV-2-associated multisystem inflammatory syndromeAsymptomatic SARS-CoV-2 infectionSARS-CoV-2 infectionAdult COVID-19Post-infectious complicationsMultisystem inflammatory syndromeCytotoxicity genesHealthy pediatricImmune dysregulationMemory TActive infectionMyeloid dysfunctionPatientsSingle-cell RNA sequencingFlow cytometrySerum proteomicsRepertoire analysisElevated expressionSeverityAlarminsCOVID-19Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLOS Biology 2021, 19: e3001143. PMID: 33730024, PMCID: PMC8007021, DOI: 10.1371/journal.pbio.3001143.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSARS-CoV-2Human bronchial epithelial cellsInterferon-stimulated genesCell state changesAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionSyndrome coronavirus 2 infectionCell tropismCoronavirus 2 infectionCoronavirus disease 2019Onset of infectionCell-intrinsic expressionCourse of infectionAir-liquid interface culturesHost-viral interactionsBronchial epithelial cellsSingle-cell RNA sequencingCell typesIL-1Disease 2019Human airwaysDevelopment of therapeuticsDrug AdministrationViral replication
2019
Visualizing structure and transitions in high-dimensional biological data
Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, Elzen AVD, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Visualizing structure and transitions in high-dimensional biological data. Nature Biotechnology 2019, 37: 1482-1492. PMID: 31796933, PMCID: PMC7073148, DOI: 10.1038/s41587-019-0336-3.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencing datasetsSingle-cell RNA sequencingUnique biological insightsRNA sequencing datasetsGerm layer differentiationMain developmental branchesHigh-throughput technologiesGut microbiome dataRNA sequencingUndescribed subpopulationsHigh-dimensional biological dataSequencing datasetsBiological insightsDevelopmental branches