Yoshiaki Yasumizu, MD, PhD
Associate Research ScientistCards
About
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
2025
Alternative Splicing Alterations in Patients With Amyotrophic Lateral Sclerosis: Link to the Disruption of TAR DNA‐Binding Protein 43 kDa Functions
Miwa T, Takeuchi E, Ogawa K, Abdelhamid R, Morita J, Hiraki Y, Yasumizu Y, Nakamura Y, Ohkura N, Saito Y, Murayama S, Nagai Y, Mochizuki H, Nagano S. Alternative Splicing Alterations in Patients With Amyotrophic Lateral Sclerosis: Link to the Disruption of TAR DNA‐Binding Protein 43 kDa Functions. Neurology And Clinical Neuroscience 2025 DOI: 10.1111/ncn3.12880.Peer-Reviewed Original ResearchAlternative splicing alterationsAlternative splicingTDP-43Splicing changesSplicing alterationsAmyotrophic lateral sclerosis pathologyAmyotrophic lateral sclerosisDNA-binding proteinsDysregulation of alternative splicingTAR DNA-binding proteinAberrant alternative splicingTAR DNA-binding protein 43 kDaSH-SY5Y cellsRNA metabolismDNA-binding protein 43 kDaNovel genesSplicing patternsNeurons of patientsRNA sequencingSplicingLateral sclerosisMotor neuronsTreatment of amyotrophic lateral sclerosisPolymerase chain reaction analysisMotor neurons of patients
2024
A Newly Identified Gene Ahed Plays Essential Roles in Murine Hematopoiesis through RNA Splicing
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 Hematopoiesis through RNA Splicing. Blood 2024, 144: 5614-5614. DOI: 10.1182/blood-2024-209978.Peer-Reviewed Original ResearchGene trap vectorUncharacterized genesRNA splicingDatabase of protein-protein interactionsConditional knockoutRegulation of RNA splicingHomozygous mutant clonesEmbryonic stem cellsDNA sequencing technologiesHematopoietic cellsFetal liverMutant embryonic stem cellsProtein-protein interactionsBloom's syndrome geneHematopoietic systemGene expression databaseDevelopment of hematopoietic cellsMouse ESC linesGenetic abnormalitiesMRNAs of genesEssential genesSequencing technologiesInterchromosomal recombinationTrap vectorUncharacterized functionAuthor 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 regionsPathologyCells