2024
Posttraumatic Stress Disorder, Obesity, and Accelerated Epigenetic Aging Among US Military Veterans
Fischer I, Na P, Nagamatsu S, Jeste D, Cabrera-Mendoza B, Montalvo-Ortiz J, Krystal J, Polimanti R, Gelernter J, Pietrzak R. Posttraumatic Stress Disorder, Obesity, and Accelerated Epigenetic Aging Among US Military Veterans. JAMA Psychiatry 2024, 81 PMID: 39476130, PMCID: PMC11581715, DOI: 10.1001/jamapsychiatry.2024.3403.Peer-Reviewed Original ResearchT7. COVID-19 RELATED STRESSORS ARE ASSOCIATED WITH PSYCHIATRIC DISORDERS AND ACCELERATED EPIGENETIC AGING IN AN ISLAND-BASED PUERTO RICAN POPULATION
Garayua A, Nunez D, Nagamatsu S, Giusti-Rodriguez P, Martinez-Gonzalez K, Montalvo-Ortiz J. T7. COVID-19 RELATED STRESSORS ARE ASSOCIATED WITH PSYCHIATRIC DISORDERS AND ACCELERATED EPIGENETIC AGING IN AN ISLAND-BASED PUERTO RICAN POPULATION. European Neuropsychopharmacology 2024, 87: 159. DOI: 10.1016/j.euroneuro.2024.08.317.Peer-Reviewed Original ResearchPost-traumatic stress disorderMajor depressive disorderCOVID-19 related stressorsCOVID-19 stressorsMajor depressive disorder symptomsPost-traumatic stress disorder symptomsAccelerated epigenetic agingRelated stressorsCombined sex analysesSymptoms of major depressive disorderPsychiatric disorder symptomsCOVID-19-related stressorsSex-stratified analysesSelf-report measuresCOVID-related stressorsAdverse mental health outcomesTargeted mental health interventionsSignificant stressorsAt-risk populationsMental health interventionsMental health outcomesConsequences of stressorsAccelerated biological agingEpigenetic ageAt-riskW69. ALTERNATIVE SPLICING DYNAMICS IN HUMAN PREFRONTAL CORTEX SUBREGIONS
Nunez D, Martinez-Magana J, Nagamatsu S, Andrade-Brito D, Hernandez-Amaya L, Montalvo-Ortiz J. W69. ALTERNATIVE SPLICING DYNAMICS IN HUMAN PREFRONTAL CORTEX SUBREGIONS. European Neuropsychopharmacology 2024, 87: 138-139. DOI: 10.1016/j.euroneuro.2024.08.278.Peer-Reviewed Original ResearchDorsal anterior cingulate cortexPrefrontal cortex subregionsPrefrontal cortexOrbitofrontal cortexDifferential transcript usagePercent-spliced-inSubgenual prefrontal cortexPrefrontal cortex regionsAnterior cingulate cortexDorsolateral prefrontal cortexDSM-IV criteriaAS eventsTranscript usageSynaptic processesExon skippingDSM-IVSCID-1Cingulate cortexIntron retentionMood disordersPsychiatric disordersSplice siteAlternative splicingCognitive functionNon-psychiatric diagnosesONCOGENES AND TUMOR SUPPRESSOR GENES IN CARCINOMA EX PLEOMORPHIC ADENOMA DEVELOPMENT: OLD FACTS AND NEW HYPOTHESES.
SCARINI J, NAGAMATSU S, CARAZZOLLE M, Abu EGAL É, ALTEMANI A, CASTILHO R, MARIANO F. ONCOGENES AND TUMOR SUPPRESSOR GENES IN CARCINOMA EX PLEOMORPHIC ADENOMA DEVELOPMENT: OLD FACTS AND NEW HYPOTHESES. Oral Surgery Oral Medicine Oral Pathology And Oral Radiology 2024, 137: e303. DOI: 10.1016/j.oooo.2023.12.719.Peer-Reviewed Original ResearchTumor suppressor geneWhole-exome sequencingSingle nucleotide variantsGenetic alterationsAllele frequenciesSuppressor geneHg38 reference genomeDisease allele frequencyReference genomeSequence readsNucleotide variantsExome sequencingDNA samplesMYBOncogenic activityPublic databasesPleomorphic adenomaGenesOncogenePre-existing pleomorphic adenomaPotential involvementSequenceTP53Background CarcinomaRare tumorThe Prefrontal Cortex Transcriptomic Landscape of the Comorbidity Between Post-Traumatic Stress Disorder and Opioid Misuse
Martinez-Magaña J, Nagamatsu S, Nunez-Rios D, Krystal J, Girgenti M, Group T, Montalvo-Ortiz J. The Prefrontal Cortex Transcriptomic Landscape of the Comorbidity Between Post-Traumatic Stress Disorder and Opioid Misuse. Biological Psychiatry 2024, 95: s69. DOI: 10.1016/j.biopsych.2024.02.169.Peer-Reviewed Original ResearchMulti-Omics Mapping in Human Cortical Neurons Reveals Well-Known and Novel Loci of Post-Traumatic Stress Disorder
Nunez-Rios D, Hurd Y, Rompala G, Nagamatsu S, Martinez-Magaña J, Krystal J, Group T, Montalvo-Ortiz J. Multi-Omics Mapping in Human Cortical Neurons Reveals Well-Known and Novel Loci of Post-Traumatic Stress Disorder. Biological Psychiatry 2024, 95: s34. DOI: 10.1016/j.biopsych.2024.02.087.Peer-Reviewed Original ResearchNeuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder
Andrade-Brito D, Núñez-Ríos D, Martínez-Magaña J, Nagamatsu S, Rompala G, Zillich L, Witt S, Clark S, Lattig M, Montalvo-Ortiz J, Alvarez V, Benedek D, Che A, Cruz D, Davis D, Girgenti M, Hoffman E, Holtzheimer P, Huber B, Kaye A, Keane T, Krystal J, Labadorf A, Logue M, Marx B, Mash D, McKee A, Miller M, Montalvo-Ortiz J, Noller C, Schnurr P, Scott W, Stein T, Ursano R, Williamson D, Wolf E, Young K. Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder. Frontiers In Genetics 2024, 15: 1345410. PMID: 38633406, PMCID: PMC11021708, DOI: 10.3389/fgene.2024.1345410.Peer-Reviewed Original ResearchAssociated with alcohol use disorderAlcohol use disorderOrbitofrontal cortexEpigenome-wide association studiesUse disorderStudy of alcohol use disorderHuman orbitofrontal cortexAlcohol-related traitsHuman brainPostmortem brain samplesHuman postmortem brain samplesEnrichment analysisDifferential CpG sitesPostmortem brain tissueGenome-wide levelOxidative bisulfite sequencingAssessed 5Functional enrichment analysisBrain tissueFalse discovery rateBisulfite sequencingAssociation studiesDifferential methylationIdentified genesDNA methylationCorrection: Psychosocial moderators of polygenic risk scores of inflammatory biomarkers in relation to GrimAge
Tamman A, Koller D, Nagamatsu S, Cabrera-Mendoza B, Abdallah C, Krystal J, Gelernter J, Montalvo-Ortiz J, Polimanti R, Pietrzak R. Correction: Psychosocial moderators of polygenic risk scores of inflammatory biomarkers in relation to GrimAge. Neuropsychopharmacology 2024, 49: 764-764. PMID: 38182778, PMCID: PMC10876612, DOI: 10.1038/s41386-023-01786-y.Peer-Reviewed Original Research
2023
Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives
Horácio E, de Carvalho L, Pereira G, Abrahim M, Coelho M, De Jesus D, García G, de Melo-Minardi R, Nagamatsu S. Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives. PLOS Computational Biology 2023, 19: e1011679. PMID: 38127831, PMCID: PMC10735175, DOI: 10.1371/journal.pcbi.1011679.Peer-Reviewed Original ResearchPsychosocial moderators of polygenic risk scores of inflammatory biomarkers in relation to GrimAge
Tamman A, Koller D, Nagamatsu S, Cabrera-Mendoza B, Abdallah C, Krystal J, Gelernter J, Montalvo-Ortiz J, Polimanti R, Pietrzak R. Psychosocial moderators of polygenic risk scores of inflammatory biomarkers in relation to GrimAge. Neuropsychopharmacology 2023, 49: 699-708. PMID: 37848731, PMCID: PMC10876568, DOI: 10.1038/s41386-023-01747-5.Peer-Reviewed Original ResearchPolygenic risk scoresRisk scoreGenetic predispositionModifiable psychosocial variablesAge-related morbidityGamma-glutamyl transferaseInflammatory biomarkersSystemic inflammationNational HealthApolipoprotein BMale veteransPsychosocial factorsVeterans StudySaliva samplesPsychosocial moderatorsPsychosocial variablesAntihistamine drugsMilitary veteransGrimAgeGrimAge accelerationInflammationUK BiobankDrugsRepresentative samplePredispositionProfiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex
Rompala G, Nagamatsu S, Martínez-Magaña J, Nuñez-Ríos D, Wang J, Girgenti M, Krystal J, Gelernter J, Hurd Y, Montalvo-Ortiz J. Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex. Nature Communications 2023, 14: 4544. PMID: 37507366, PMCID: PMC10382503, DOI: 10.1038/s41467-023-40285-y.Peer-Reviewed Original ResearchConceptsOpioid use disorderMulti-omics findingsGene expression patternsCo-methylation analysisGene expression profilesMulti-omics profilingGene networksDNA methylationNeuronal methylomesDNA hydroxymethylationMethylomic analysisExpression patternsExpression profilesEpigenetic disturbancesUse disordersPsychiatric traitsOrbitofrontal cortexOpioid-related drugsPostmortem orbitofrontal cortexEnvironmental factorsDrug interaction analysisOUD treatmentHuman orbitofrontal cortexOpioid signalingInteraction analysisCpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder
Nagamatsu S, Rompala G, Hurd Y, Núñez-Rios D, Montalvo-Ortiz J, Group T, Alvarez V, Benedek D, Che A, Cruz D, Davis D, Girgenti M, Hoffman E, Holtzheimer P, Huber B, Kaye A, Krystal J, Labadorf A, Keane T, Logue M, McKee A, Marx B, Mash D, Miller M, Noller C, JM-O, Scott W, Schnurr P, Stein T, Ursano R, Williamson D, Wolf E, Young K. CpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder. Frontiers In Psychiatry 2023, 13: 1078894. PMID: 36745154, PMCID: PMC9892724, DOI: 10.3389/fpsyt.2022.1078894.Peer-Reviewed Original ResearchOpioid use disorderOrbital frontal cortexDNA methylationKEGG enrichment analysisUse disordersMCPH lociTreatment of OUDGene OntologyEnrichment analysisOpioid-related drugsCpG sitesDrug targetsOxidative bisulfite sequencingImportant biological pathwaysDrug interaction analysisDrug-gene interaction databaseNervous system developmentSmoking statusBrain BankCortical neuronsFrontal cortexNeuronal nucleiHuman studiesGene regulationMethylome analysis
2022
Dissecting the epigenomic differences between smoking and nicotine dependence in a veteran cohort
Nagamatsu S, Pietrzak R, Xu K, Krystal J, Gelernter J, Montalvo‐Ortiz J. Dissecting the epigenomic differences between smoking and nicotine dependence in a veteran cohort. Addiction Biology 2022, 28: e13259. PMID: 36577721, DOI: 10.1111/adb.13259.Peer-Reviewed Original ResearchConceptsSmoking statusNicotine dependenceVeteran cohortNon-current smokersSerious public health issueNovel treatment strategiesPublic health issueUS military veteransEpigenome-wide association studiesCurrent smokersTreatment strategiesFagerström TestNicotine addictionSmokingHealth issuesRole of epigeneticsMilitary veteransMethylationEPIC BeadChip arraySmokersContinuous variablesF2RL3 geneCohortBiomarkersBeadChip arrayPrevious findingsPsychosocial Factors Associated With Accelerated GrimAge in Male U.S. Military Veterans
Tamman AJF, Nagamatsu S, Krystal JH, Gelernter J, Montalvo-Ortiz JL, Pietrzak RH. Psychosocial Factors Associated With Accelerated GrimAge in Male U.S. Military Veterans. American Journal Of Geriatric Psychiatry 2022, 31: 97-109. PMID: 36210262, DOI: 10.1016/j.jagp.2022.09.002.Peer-Reviewed Original ResearchConceptsRisk factorsPremature mortalityU.S. veteransPsychosocial variablesNovel epigenetic clockLifetime substance use disorderRisk stratification modelMale U.S. veteransCross-sectional studyU.S. veteran populationWeekly physical exerciseSubstance use disordersMale U.S. military veteransBiological agingU.S. military veteransHealth morbidityModifiable correlatesMortality riskSleep qualityHigh riskGreater oddsUse disordersPhysical exercisePsychosocial factorsVeteran populationAssociation of Symptoms of Posttraumatic Stress Disorder and GrimAge, an Epigenetic Marker of Mortality Risk, in US Military Veterans.
Na PJ, Montalvo-Ortiz JL, Nagamatsu ST, Southwick SM, Krystal JH, Gelernter J, Pietrzak RH. Association of Symptoms of Posttraumatic Stress Disorder and GrimAge, an Epigenetic Marker of Mortality Risk, in US Military Veterans. The Journal Of Clinical Psychiatry 2022, 83 PMID: 35802930, PMCID: PMC10859885, DOI: 10.4088/jcp.21br14309.Peer-Reviewed Original ResearchRational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw
de Mello FDSB, Maneira C, Suarez FUL, Nagamatsu S, Vargas B, Vieira C, Secches T, Coradini ALV, de Carvalho Silvello M, Goldbeck R, Pereira GAG, Teixeira GS. Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw. Journal Of Genetic Engineering And Biotechnology 2022, 20: 80. PMID: 35612634, PMCID: PMC9133290, DOI: 10.1186/s43141-022-00359-8.Peer-Reviewed Original ResearchXylose reductaseS. cerevisiaeBrazilian bioethanol industryIndustrial S. cerevisiaeMajor yeastGenomic integrationNucleotide sequenceCRISPR editingGenetic engineeringInhibitor toleranceXylitol productionIndustrial strainsRobust chassisHigh economic valueNADPH availabilityNADPH cofactorAvailable cofactorsRational engineeringRedox environmentGenetic backgroundXylitol titerHemicellulosic materialLaboratory strainsFermentation performanceCerevisiaeGenetic variation in symbiotic islands of natural variant strains of soybean Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens differing in competitiveness and in the efficiency of nitrogen fixation
Bender FR, Nagamatsu ST, Delamuta JRM, Ribeiro RA, Nogueira MA, Hungria M. Genetic variation in symbiotic islands of natural variant strains of soybean Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens differing in competitiveness and in the efficiency of nitrogen fixation. Microbial Genomics 2022, 8: 000795. PMID: 35438622, PMCID: PMC9453064, DOI: 10.1099/mgen.0.000795.Peer-Reviewed Original ResearchConceptsGenetic variationSymbiotic islandSymbiotic phenotypeNatural variantsCPAC 15Single nucleotide polymorphismsCPAC 7LysR family transcriptional regulatorFamily transcriptional regulatorBiological nitrogen fixation processDephospho-CoA kinaseHexosamine biosynthetic pathwayPotential genetic variationNitrogen fixation processNif proteinsNodulation genesBradyrhizobium diazoefficiensTranscriptional regulatorsInternode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids
Yanagui K, Camargo ELO, Abreu LGF, Nagamatsu ST, Fiamenghi MB, Silva NV, Carazzolle MF, Nascimento LC, Franco SF, Bressiani JA, Mieczkowski PA, Grassi MCB, Pereira GAG. Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids. Gene 2022, 828: 146476. PMID: 35413393, DOI: 10.1016/j.gene.2022.146476.Peer-Reviewed Original ResearchConceptsInternode elongationSaccharum hybridsSecondary cell wall formationDetailed transcriptome analysisCell wall formationDevelopment of plantsMolecular regulatory mechanismsEnergy caneRNA-seq analysisGrowth-related genesDifferent biological processesGene expression analysisCell wall characterizationDivision zoneTranscriptional regulationUnique genesCellulose synthesisTranscriptome analysisHigh biomass productionKey genesCell divisionWall formationBreeding programsBiomass biosynthesisExpression analysis
2021
DNA methylation changes in African American women with a history of preterm birth from the InterGEN study
Barcelona V, Montalvo-Ortiz JL, Wright ML, Nagamatsu ST, Dreisbach C, Crusto CA, Sun YV, Taylor JY. DNA methylation changes in African American women with a history of preterm birth from the InterGEN study. BMC Genomic Data 2021, 22: 30. PMID: 34482817, PMCID: PMC8418749, DOI: 10.1186/s12863-021-00988-x.Peer-Reviewed Original ResearchConceptsPreterm birthHealth disordersFull-term birthCentral nervous systemEpigenome-wide association studiesAfrican American womenInterGEN StudyBackgroundPreterm birthMaternal moodWomen 3Cardiovascular diseaseIndependent cohortPhysiologic mechanismsNervous systemAfrican American mothersSignificant CpG sitesEWAS approachWomenBirthSensory processingDNA methylationLong-term epigenetic effectsAmerican womenCommon outcomeFurther studiesLiga Brasileira de Bioinformática: Desafios para estimular a formação de estudantes de Bioinformática e Biologia Computacional
Nagamatsu S, Costa M, dos Santos R, de Carvalho L, Fonseca Júnior N, da Silva V, de Jesus D, Aburjaile F, García G, Pereira G, Câmara A, Neves M, Coelho M, Horácio E. Liga Brasileira de Bioinformática: Desafios para estimular a formação de estudantes de Bioinformática e Biologia Computacional. 2021 DOI: 10.51780/978-6-599-275326-18.Peer-Reviewed Original Research