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
2024
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. 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
2023
IL‐27 produced during acute malaria infection regulates Plasmodium‐specific memory CD4+ T cells
Macalinao M, Inoue S, Tsogtsaikhan S, Matsumoto H, Bayarsaikhan G, Jian J, Kimura K, Yasumizu Y, Inoue T, Yoshida H, Hafalla J, Kimura D, Yui K. IL‐27 produced during acute malaria infection regulates Plasmodium‐specific memory CD4+ T cells. EMBO Molecular Medicine 2023, 15: e17713. PMID: 37855243, PMCID: PMC10701605, DOI: 10.15252/emmm.202317713.Peer-Reviewed Original ResearchConceptsCD4<sup>+</sup> T cellsT cellsIL-27Malaria infectionCD4<sup>+</sup> T cell responsesCD4<sup>+</sup> T cell subsetsMemory CD4+ T cellsImmune responseCD4+ T cellsNeutralization of IL-27T cell responsesT cell subsetsPathogenic immune responsesHumoral immune responseSingle-cell RNA-seq analysisPlasmodium chabaudiDevelopment of vaccinesAcute infectionCytokine productionEffector responsesChronic phaseActive infectionProliferative capacityAcute phaseInfectionS254: A NEW GENE AHED PLAYS ESSENTIAL ROLES IN HEMATOPOIESIS THROUGH RNA‐SPLICING
Nakai R, Yokota T, Tokunaga M, Takaishi M, 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. S254: A NEW GENE AHED PLAYS ESSENTIAL ROLES IN HEMATOPOIESIS THROUGH RNA‐SPLICING. HemaSphere 2023, 7: e1226943. PMCID: PMC10428432, DOI: 10.1097/01.hs9.0000967928.12269.43.Peer-Reviewed Original ResearchIncreased anti‐oxidative action compensates for collagen tissue degeneration in vitiligo dermis
Yokoi K, Yasumizu Y, Ohkura N, Shinzawa K, Okuzaki D, Shimoda N, Ando H, Yamada N, Fujimoto M, Tanemura A. Increased anti‐oxidative action compensates for collagen tissue degeneration in vitiligo dermis. Pigment Cell & Melanoma Research 2023, 36: 355-364. PMID: 37230937, DOI: 10.1111/pcmr.13094.Peer-Reviewed Original ResearchConceptsCollagen-related genesUninvolved perilesional skinOxidative stressSignaling pathway activationCollagen homeostasisVitiligo lesionsPathway activationPerilesional skinExpression levelsAnti-oxidant enzymesAnti-oxidative actionDegraded collagen fibersNrf2 signaling pathway activationDefense systemProduction of oxidative stress