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
Hypoxia-induced Wnt5a-secreting fibroblasts promote colon cancer progression
Harada A, Yasumizu Y, Harada T, Fumoto K, Sato A, Maehara N, Sada R, Matsumoto S, Nishina T, Takeda K, Morii E, Kayama H, Kikuchi A. Hypoxia-induced Wnt5a-secreting fibroblasts promote colon cancer progression. Nature Communications 2025, 16: 3653. PMID: 40246836, PMCID: PMC12006413, DOI: 10.1038/s41467-025-58748-9.Peer-Reviewed Original ResearchConceptsColon cancer progressionSingle-cell RNA-seq dataCancer progressionEndothelial cellsRNA-seq dataColon cancer aggressivenessSuppression of angiogenesisColon cancer growthColon cancer formationCancer aggressivenessInflammatory fibroblastsVEGF receptor1Cancer growthPromote tumorigenesisCancer formationWnt5aMeta-analysisWnt ligandsLuminal sideFibroblast subtypesColonHypoxic environmentFibroblastsCellsTranscriptomic profiling after B-cell depletion reveals central and peripheral immune cell changes in multiple sclerosis
Wei J, Moon J, Yasumizu Y, Zhang L, Raddassi K, Buitrago-Pocasangre N, Deerhake M, Strauli N, Chen C, Herman A, Pedotti R, Raposo C, Yim I, Pappalardo J, Longbrake E, Sumida T, Axisa P, Hafler D. Transcriptomic profiling after B-cell depletion reveals central and peripheral immune cell changes in multiple sclerosis. Journal Of Clinical Investigation 2025, 135: e182790. PMID: 40067358, PMCID: PMC12126227, DOI: 10.1172/jci182790.Peer-Reviewed Original ResearchConceptsB-cell depletionImmune landscapeMultiple sclerosisAnti-CD20-mediated B-cell depletionPeripheral CD4+ T cell populationsEffect of B cell depletionB cell depletion treatmentCD4+ T cell populationB cell depletion therapyCerebrospinal fluidCD4+ T cellsTreatment of early diseaseCD16+ monocytesImmune cell changesImmune cell subsetsT cell populationsPeripheral blood monocytesFlow cytometry-based methodTNF-a mRNACell type-specific changesCell subsetsT cellsImmunological changesAutoimmune activityB cellsTranscriptome signature in the blood of neuromyelitis optica spectrum disorder under steroid tapering
Yamamura R, Kinoshita M, Yasumizu Y, Yata T, Kihara K, Motooka D, Shiraishi N, Sugiyama Y, Beppu S, Murata H, Koizumi N, Sano I, Koda T, Okuno T, Mochizuki H. Transcriptome signature in the blood of neuromyelitis optica spectrum disorder under steroid tapering. Frontiers In Immunology 2025, 16: 1508977. PMID: 39963140, PMCID: PMC11830620, DOI: 10.3389/fimmu.2025.1508977.Peer-Reviewed Original ResearchConceptsNeuromyelitis optica spectrum disorderPeripheral blood mononuclear cellsNeuromyelitis optica spectrum disorder patientsSteroid taperIL-10Steroid dosagePeripheral blood transcriptomic signatureDecreased expressionInterferon signalingTransform treatment strategiesIndicator of disease activityNon-relapsing patientsAnti-AQP4 antibodyDisease activity biomarkersTranscriptomic signaturesBlood mononuclear cellsAdvent of biologicsBlood transcriptomic signaturesAnti-inflammatory pathwayIL-10 signalingRelapsed patientsImmune signaturesSteroid reductionDisease activityActivation biomarkersAlternative 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, 13: 187-194. 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 patientsElucidating the role of autoreactive T cells and B cells in autoimmune hepatitis
Yasumizu Y, Hafler D. Elucidating the role of autoreactive T cells and B cells in autoimmune hepatitis. Journal Of Clinical Investigation 2025, 135: e188538. PMID: 39817449, PMCID: PMC11735092, DOI: 10.1172/jci188538.Peer-Reviewed Original Research