Yoshiaki Yasumizu, MD, PhD
Associate Research ScientistCards
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Research
Publications
Featured Publications
Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases
Yasumizu Y, Takeuchi D, Morimoto R, Takeshima Y, Okuno T, Kinoshita M, Morita T, Kato Y, Wang M, Motooka D, Okuzaki D, Nakamura Y, Mikami N, Arai M, Zhang X, Kumanogoh A, Mochizuki H, Ohkura N, Sakaguchi S. Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases. Cell Genomics 2024, 4: 100473. PMID: 38359792, PMCID: PMC10879034, DOI: 10.1016/j.xgen.2023.100473.Peer-Reviewed Original ResearchConceptsGene programSingle-cell transcriptomic landscapeSingle-cell datasetsCell subpopulationsTranscriptional programsTranscriptomic characterizationCD4<sup>+</sup> T-cell subpopulationsCD4<sup>+</sup> T cellsCellular heterogeneityT cell subpopulationsAutoimmune diseasesCell heterogeneityT cellsPeripheral CD4<sup>+</sup> T cellsCell populationsCD4+ T cell populationCanonical clustersCellsT cell populationsQualitative alterationsT cell heterogeneityGenesSubpopulationsClinical statusCell frequencyMyasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma
Yasumizu Y, Ohkura N, Murata H, Kinoshita M, Funaki S, Nojima S, Kido K, Kohara M, Motooka D, Okuzaki D, Suganami S, Takeuchi E, Nakamura Y, Takeshima Y, Arai M, Tada S, Okumura M, Morii E, Shintani Y, Sakaguchi S, Okuno T, Mochizuki H. Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma. Nature Communications 2022, 13: 4230. PMID: 35869073, PMCID: PMC9305039, DOI: 10.1038/s41467-022-31951-8.Peer-Reviewed Original ResearchConceptsMedullary thymic epithelial cellsEctopic expressionCellular composition estimationSingle-cell RNA sequencingThymic epithelial cellsSubpopulation of medullary thymic epithelial cellsEpithelial cellsMG-thymomaRNA sequencingGene expressionCell-cell interaction analysisCell migrationComprehensive atlasEctopic germinal center formationInteraction analysisDendritic cell migrationGerminal center formationMyasthenia gravisCellsTranscriptomeCXCL12-CXCR4Cell accumulationT/B cellsVIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data
Yasumizu Y, Hara A, Sakaguchi S, Ohkura N. VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data. Bioinformatics 2020, 37: 1465-1467. PMID: 33017003, PMCID: PMC7745649, DOI: 10.1093/bioinformatics/btaa859.Peer-Reviewed Original ResearchConceptsConventional RNA-seq dataRNA-seq dataSequence dataSupplementary dataRNA transcriptsBioinformatics methodsVirus copy numberRNA sequencingCopy numberVirus RNAHuman cellsExpression profilesBioinformaticsMultiple virusesInfected cellsClinical samplesTranscriptionRNACellsVirusVirus analysisSARS-CoV-2SequenceMRNAHerpesvirusRegulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases
Ohkura N, Yasumizu Y, Kitagawa Y, Tanaka A, Nakamura Y, Motooka D, Nakamura S, Okada Y, Sakaguchi S. Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases. Immunity 2020, 52: 1119-1132.e4. PMID: 32362325, DOI: 10.1016/j.immuni.2020.04.006.Peer-Reviewed Original ResearchMeSH KeywordsAutoimmune DiseasesBiomarkersCell DifferentiationComputational BiologyCpG IslandsDNA MethylationEpigenesis, GeneticEpigenomicsGene Expression ProfilingGenetic Predisposition to DiseaseGenetic VariationHumansImmunophenotypingPolymorphism, Single NucleotideT-Lymphocyte SubsetsT-Lymphocytes, RegulatoryTranscriptomeConceptsCommon autoimmune diseasesSingle-nucleotide polymorphismsSusceptibility to common autoimmune diseasesCell-specific gene transcriptionGenome-wide epigenetic profilingAssociated with common autoimmune diseasesAssociated with transcriptionPolygenic autoimmune diseasesTreg cellsDemethylated regionCpG hypomethylationSuper-enhancersAutoimmune diseasesDeterminants of susceptibilityEpigenetic modificationsEpigenetic profilesGene transcriptionEpigenetic changesTreg-cell-specific demethylated regionNaive Treg cellsNatural Treg cellsRegional variantsTranscriptionActive stateCellsGenome-Wide Natural Selection Signatures Are Linked to Genetic Risk of Modern Phenotypes in the Japanese Population
Yasumizu Y, Sakaue S, Konuma T, Suzuki K, Matsuda K, Murakami Y, Kubo M, Palamara P, Kamatani Y, Okada Y. Genome-Wide Natural Selection Signatures Are Linked to Genetic Risk of Modern Phenotypes in the Japanese Population. Molecular Biology And Evolution 2020, 37: 1306-1316. PMID: 31957793, PMCID: PMC7182208, DOI: 10.1093/molbev/msaa005.Peer-Reviewed Original ResearchConceptsSelection signaturesNatural selection signaturesTrait-associated variantsGenome-wide scanGenome-wide significanceAlcohol dehydrogenaseNatural selection studyPopulation-specific featuresAlcohol-related phenotypesAdaptive evolutionFine-mappingGenetic lociCluster locusUK Biobank ResourcePhenotypic dataHuman phenotypesSelection pressureJapanese populationEnrichment analysisPopulation-specific evidencePhenotypic spectrumPhenotypeBiobank ResourceGenetic riskImmune-related diseases
2024
Author Correction: A newly identified gene Ahed plays essential roles in murine haematopoiesis
Nakai R, Yokota T, Tokunaga M, Takaishi M, Yokomizo T, Sudo T, Shi H, Yasumizu Y, Okuzaki D, Kokubu C, Tanaka S, Takaoka K, Yamanishi A, Yoshida J, Watanabe H, Kondoh G, Horie K, Hosen N, Sano S, Takeda J. Author Correction: A newly identified gene Ahed plays essential roles in murine haematopoiesis. Nature Communications 2024, 15: 9134. PMID: 39443487, PMCID: PMC11500082, DOI: 10.1038/s41467-024-53499-5.Peer-Reviewed Original ResearchNeoself-antigens are the primary target for autoreactive T cells in human lupus
Mori S, Kohyama M, Yasumizu Y, Tada A, Tanzawa K, Shishido T, Kishida K, Jin H, Nishide M, Kawada S, Motooka D, Okuzaki D, Naito R, Nakai W, Kanda T, Murata T, Terao C, Ohmura K, Arase N, Kurosaki T, Fujimoto M, Suenaga T, Kumanogoh A, Sakaguchi S, Ogawa Y, Arase H. Neoself-antigens are the primary target for autoreactive T cells in human lupus. Cell 2024, 187: 6071-6087.e20. PMID: 39276775, DOI: 10.1016/j.cell.2024.08.025.Peer-Reviewed Original ResearchSystemic lupus erythematosusAutoreactive T cellsT cellsMHC-IISelf-antigensDevelopment of lupus-like diseaseCD4<sup>+</sup> T cellsEpstein-Barr virus reactivationPathogenesis of systemic lupus erythematosusRisk factorsSystemic lupus erythematosus patientsMajor histocompatibility complex class IIHistocompatibility complex class IILupus-like diseaseLupus T cellsHuman lupusGenetic risk factorsVirus reactivationLupus erythematosusAdult micePrimary targetTrigger autoimmunityClass IIPeptide presentationInvariant chainSpatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma
Yasumizu Y, Kinoshita M, Zhang M, Motooka D, Suzuki K, Nojima S, Koizumi N, Okuzaki D, Funaki S, Shintani Y, Ohkura N, Morii E, Okuno T, Mochizuki H. Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma. Cell Reports 2024, 43: 114677. PMID: 39180749, DOI: 10.1016/j.celrep.2024.114677.Peer-Reviewed Original ResearchMyasthenia gravisMedullary thymic epithelial cellsGerminal center responseRegulatory T cellsImmune cell compositionMigratory dendritic cellsThymic epithelial cellsCortico-medullary junctionImmune microenvironmentDendritic cellsT cellsChemokine patternsThymus abnormalitiesHyperplasia samplesThymomaSpatial transcriptomic analysisEpithelial cellsMG pathologyMedullary regionCenter responseMedullaCell compositionCortical regionsPathologyCellsA newly identified gene Ahed plays essential roles in murine haematopoiesis
Nakai R, Yokota T, Tokunaga M, Takaishi M, Yokomizo T, Sudo T, Shi H, Yasumizu Y, Okuzaki D, Kokubu C, Tanaka S, Takaoka K, Yamanishi A, Yoshida J, Watanabe H, Kondoh G, Horie K, Hosen N, Sano S, Takeda J. A newly identified gene Ahed plays essential roles in murine haematopoiesis. Nature Communications 2024, 15: 5090. PMID: 38918373, PMCID: PMC11199565, DOI: 10.1038/s41467-024-49252-7.Peer-Reviewed Original ResearchConceptsMutant embryonic stem cellsConditional knockoutUncharacterised genesHaematopoietic cellsNuclear proteinsFunctional genesHaematopoiesis in vivoAssociated with malignancyBiological functionsGenesSomatic mutationsEmbryonic stem cellsHaematopoietic developmentTransplantation experimentsHaematological malignanciesDeletionAdult miceCancer patientsCoordinated actionEmbryonic dayStem cellsHaematopoiesisMurine haematopoiesisCellsMalignancyNeural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis
Yasumizu Y, Hagiwara M, Umezu Y, Fuji H, Iwaisako K, Asagiri M, Uemoto S, Nakamura Y, Thul S, Ueyama A, Yokoi K, Tanemura A, Nose Y, Saito T, Wada H, Kakuda M, Kohara M, Nojima S, Morii E, Doki Y, Sakaguchi S, Ohkura N. Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis. NAR Cancer 2024, 6: zcae022. PMID: 38751935, PMCID: PMC11094754, DOI: 10.1093/narcan/zcae022.Peer-Reviewed Original ResearchCell deconvolutionDNA methylation dataCancer prognosisTumor-infiltrating immune cellsFormalin-fixed paraffin-embedded sectionsImmune cell profilesAssociated with cancer prognosisImmune cell statusCell-free DNADNA methylationMethylation dataParaffin-embedded sectionsPeripheral bloodImmune cellsIntrahepatic cholangiocarcinoma samplesCell profilesFlow cytometryCell populationsClinical practiceClinical settingCholangiocarcinoma samplesCellular identityEpigenetic modificationsTumorPrognosis