2025
Effect of Dietary Salt Excess on DNA Methylation and Transcriptional Regulation of Human Angiotensinogen Gene Expression
Perla S, Garcia-Milan R, Mopidevi B, Jain S, Kumar A. Effect of Dietary Salt Excess on DNA Methylation and Transcriptional Regulation of Human Angiotensinogen Gene Expression. American Journal Of Hypertension 2025, hpaf150. PMID: 40808626, DOI: 10.1093/ajh/hpaf150.Peer-Reviewed Original ResearchGenome-wide association studiesDNA methylation patternsHap-IITranscriptional regulationHap-IHuman AGTMethylation patternsBinding of transcription factorsGene expressionHuman AGT genePotential gene targetsHigh-salt dietRNA-seqAssociation studiesIntron IDNA demethylationDNA methylationCpG sitesTranscriptional analysisExpressed genesTranscription factorsRisk haplotypeRNA sequencingCanonical pathwaysGene targeting
2024
Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample
Cinciripini P, Wetter D, Wang J, Yu R, Kypriotakis G, Kumar T, Robinson J, Cui Y, Green C, Bergen A, Kosten T, Scherer S, Shete S. Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Scientific Reports 2024, 14: 6385. PMID: 38493193, PMCID: PMC10944542, DOI: 10.1038/s41598-024-56750-7.Peer-Reviewed Original ResearchConceptsIdentification of novel lociSequencing of candidate genesRare variant associationsMapped to genesReceptor Signaling PathwayNovel lociGenes associated with regulationVariant associationsCandidate genesProtective lociDeep sequencingRegulation of bodyweightGenetic studiesCanonical pathwaysSignaling pathwayRare variantsGenetic profileTarget of pharmacotherapyTumor suppressionAssociated with cancerGenesPublic health tollRandomized Controlled TrialsSubstance use disordersEthnically diverse sample
2020
Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry
Franzen AD, Lam TT, Williams KR, Nairn AC, Duman RS, Sathyanesan M, Kumar V, Carpenter LL, Newton SS. Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry. BMC Psychiatry 2020, 20: 481. PMID: 32998701, PMCID: PMC7528485, DOI: 10.1186/s12888-020-02874-9.Peer-Reviewed Original ResearchConceptsPR domain zinc finger protein 1Bioinformatics analysisZinc finger protein 1Quantitative mass spectrometryFinger protein 1Potential biological functionsMajor canonical pathwaysPeroxisome proliferator-activated receptor gamma coactivatorProliferator-activated receptor gamma coactivatorCellular functionsCellular movementCellular compromiseCell signalingCellular developmentOrganismal injuryBiological functionsReceptor gamma coactivatorCanonical pathwaysSignal transducerUpstream regulatorTranscription 3Protein profilesDifferential expressionProtein synthesisProteomics softwareAnalysis of the Transcriptome: Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds
Shan N, Minden A, Furmanski P, Bak M, Cai L, Wernyj R, Sargsyan D, Cheng D, Wu R, Kuo H, Li S, Fang M, Maehr H, Kong A, Suh N. Analysis of the Transcriptome: Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds. Cancer Prevention Research 2020, 13: 673-686. PMID: 32467291, PMCID: PMC7415686, DOI: 10.1158/1940-6207.capr-19-0566.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingCell Line, TumorCell ProliferationDatasets as TopicDisease ProgressionDNA MethylationDown-RegulationEpithelial-Mesenchymal TransitionFemaleGene Expression Regulation, NeoplasticHumansNeoplasm InvasivenessNeoplastic Stem CellsRNA-SeqSignal TransductionUp-RegulationVitamin DConceptsCancer stem-like cellsStem-like cellsInvasive ductal carcinomaVitamin D compoundsNext-generation RNA sequencingCancer stem cell-like populationsGlobal transcriptomic analysisStem cell-like populationIngenuity Pathway AnalysisDuctal carcinomaCell-like populationD compoundsTranscriptomic analysisVitamin DGene methylation statusRNA sequencingEpithelial-mesenchymal transitionGlobal profilingPathway genesBreast cancer stem-like cellsCanonical pathwaysNegative regulatorUpstream regulatorPathway analysisNew breast cancer diagnoses
2019
De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette’s Disorder and Autism
Cappi C, Oliphant ME, Péter Z, Zai G, Conceição do Rosário M, Sullivan CAW, Gupta AR, Hoffman EJ, Virdee M, Olfson E, Abdallah SB, Willsey AJ, Shavitt RG, Miguel EC, Kennedy JL, Richter MA, Fernandez TV. De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette’s Disorder and Autism. Biological Psychiatry 2019, 87: 1035-1044. PMID: 31771860, PMCID: PMC7160031, DOI: 10.1016/j.biopsych.2019.09.029.Peer-Reviewed Original ResearchSA72 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS
Spindola L, Santoro M, Pan P, Talarico F, Xavier G, Carvalho C, Gadelha A, Salum G, Miguel E, Rohde L, Zanardo E, Kulikowski L, Bressan R, Ota V, Belangero S. SA72 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2019, 29: s861. DOI: 10.1016/j.euroneuro.2017.08.144.Peer-Reviewed Original ResearchHigh-risk cohortPsychiatric disordersHealthy controlsGene expression profilingChild Behavior ChecklistEarly-onset psychiatric disordersBlood of adolescentsPrevious psychiatric disorderBlood gene expression profilingCross-sectional studyOnset psychiatric disordersWell-Being AssessmentAttention deficit hyperactivity disorderMost psychiatric disordersCanonical pathwaysSchool-based studyLarge public healthExpression profilingDeficit hyperactivity disorderRisk cohortPrevalent diagnosisPD groupMajor depressionHC groupMultiple comparison correctionSU73 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS
Spindola L, Santoro M, Pan P, Talarico F, Xavier G, Carvalho C, Gadelha A, Salum G, Miguel E, Rohde L, Zanardo E, Kulikowski L, Bressan R, Ota V, Belangero S. SU73 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2019, 29: s927-s928. DOI: 10.1016/j.euroneuro.2017.08.262.Peer-Reviewed Original ResearchHigh-risk cohortPsychiatric disordersHealthy controlsGene expression profilingChild Behavior ChecklistEarly-onset psychiatric disordersBlood of adolescentsPrevious psychiatric disorderBlood gene expression profilingCross-sectional studyOnset psychiatric disordersWell-Being AssessmentAttention deficit hyperactivity disorderMost psychiatric disordersCanonical pathwaysSchool-based studyLarge public healthExpression profilingDeficit hyperactivity disorderRisk cohortPrevalent diagnosisPD groupMajor depressionHC groupMultiple comparison correction
2018
Systematic reconstruction of autism biology from massive genetic mutation profiles
Luo W, Zhang C, Jiang YH, Brouwer CR. Systematic reconstruction of autism biology from massive genetic mutation profiles. Science Advances 2018, 4: e1701799. PMID: 29651456, PMCID: PMC5895441, DOI: 10.1126/sciadv.1701799.Peer-Reviewed Original ResearchConceptsComplex genetic diseasesWhole-exome studiesHundreds of variantsGene functionNovel genesSubpathway levelGene groupsSame geneCanonical pathwaysPathway levelAutism-related mutationsSecond messenger systemsGenesGenetic diseasesASD biologyCAMP second messenger systemBiologyGenetic associationMutationsMultiple independent analysesMost variantsPathwayVariant levelsSynaptic functionGenetic mutation profilesExercise and weight loss interventions and miRNA expression in women with breast cancer
Adams BD, Arem H, Hubal MJ, Cartmel B, Li F, Harrigan M, Sanft T, Cheng CJ, Pusztai L, Irwin ML. Exercise and weight loss interventions and miRNA expression in women with breast cancer. Breast Cancer Research And Treatment 2018, 170: 55-67. PMID: 29511965, PMCID: PMC6444907, DOI: 10.1007/s10549-018-4738-6.Peer-Reviewed Original ResearchConceptsBaseline body mass indexBC survivorsTumor recurrenceWeight gainWeight lossBreast cancer survivorsSerum miRNA expressionWeight loss interventionBody mass indexWeight loss trialCancer-related deathIndependent clinical trialsMiRNA expressionSix-month interventionCanonical pathwaysTop canonical pathwaysPhysical exercise trialsIngenuity Pathway AnalysisIngenuity Pathway Analysis softwareSporadic BCDevelopment of cancerLoss interventionMass indexCancer survivorsExercise trials
2017
Proteomics data on MAP Kinase Kinase 3 knock out bone marrow derived macrophages exposed to cigarette smoke extract
Srivastava R, Mannam P, Rauniyar N, Lam TT, Luo R, Lee PJ, Srivastava A. Proteomics data on MAP Kinase Kinase 3 knock out bone marrow derived macrophages exposed to cigarette smoke extract. Data In Brief 2017, 13: 320-325. PMID: 28653025, PMCID: PMC5476452, DOI: 10.1016/j.dib.2017.05.049.Peer-Reviewed Original ResearchMAP kinase kinase 3Yale Protein Expression DatabaseKinase 3Protein Expression DatabaseAbsolute quantitation (iTRAQ) reagentsIngenuity Pathway Analysis softwarePathway Analysis softwareTotal proteomeCellular proteinsIsobaric tagsProteomic dataMAP kinaseCanonical pathwaysMolecular networksCigarette smoke extractProteome DiscovererMass spectrometry dataBone marrowExpression databaseLC-MS/MSSpectrometry dataPathwaySmoke extractPhosphoproteomeProteomeHER3-EGFR score to predict clinical outcomes in triple-negative breast cancer.
Ogden A, Bhattarai S, Green A, Aleskandarany M, Rakha E, Ellis I, Li X, Krishnamurti U, Janssen E, Jonsdottir K, Reid M, Rida P, Aneja R. HER3-EGFR score to predict clinical outcomes in triple-negative breast cancer. Journal Of Clinical Oncology 2017, 35: 11612-11612. DOI: 10.1200/jco.2017.35.15_suppl.11612.Peer-Reviewed Original ResearchTNBC patientsDistant metastasisPrognostic valueBreast cancerCox proportional hazards regressionTriple-negative breast cancerProportional hazards regressionHigher immunohistochemical expressionTop upstream regulatorsMulti-institutional studyMann-Whitney U testCanonical pathwaysTop canonical pathwaysErbB family membersHER3 levelsPreclinical evidenceClinical outcomesHazards regressionHepatic fibrosisImmunohistochemical biomarkersImmunohistochemical expressionLuminal cytokeratinsMultivariable modelEGFR levelsFibrotic process
2015
Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine
Carrillo J, He Y, Luo J, Menendez K, Tablante N, Zhao K, Paulson J, Li B, Song J. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine. PLOS ONE 2015, 10: e0100476. PMID: 26107953, PMCID: PMC4481310, DOI: 10.1371/journal.pone.0100476.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChickensCpG IslandsDNA MethylationEukaryotic Initiation Factor-2Gene Regulatory NetworksGenomeHerpesvirus 1, GallidImmune System DiseasesInflammationRibosomal Protein S6 Kinases, 70-kDaRNA Processing, Post-TranscriptionalSignal TransductionTOR Serine-Threonine KinasesTranscription Initiation SiteVaccinesConceptsTranscription start siteMethyl-CpG binding domain protein-enriched genome sequencingDNA methylationProtein-enriched genome sequencingRNA post-transcriptional modificationsIdentified canonical pathwaysRegulation of eIF4Post-transcriptional modificationsDifferentially expressed genesAxonal guidance signalingGlobal DNA methylationHypermethylated DMRsP70S6K signalingGenome sequenceStart siteMethylome analysisCpG islandsGene networksMethyl-CpGEIF2 signalingCanonical pathwaysK signalingGenesMTOR signalingInfectious laryngotracheitis
2014
Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data
Tang H, Wei P, Duell EJ, Risch HA, Olson SH, Bueno-de-Mesquita HB, Gallinger S, Holly EA, Petersen G, Bracci PM, McWilliams RR, Jenab M, Riboli E, Tjønneland A, Boutron-Ruault MC, Kaaks R, Trichopoulos D, Panico S, Sund M, Peeters PH, Khaw KT, Amos CI, Li D. Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data. Carcinogenesis 2014, 35: 1039-1045. PMID: 24419231, PMCID: PMC4004205, DOI: 10.1093/carcin/bgu010.Peer-Reviewed Original ResearchConceptsIngenuity Pathway AnalysisKEGG pathwaysSingle nucleotide polymorphism (SNP) levelAxonal guidanceGenome-wide levelGene ontology pathwaysSalivary secretion pathwaysSlit/RoboGenes/SNPsOntology pathwaysPolymorphism levelSecretion pathwayGWAS dataGene setsPancreatic Cancer Case-Control ConsortiumCanonical pathwaysPathway analysisAxon guidanceGenesSNPsRegion SNPsPathwayIPA analysisPancreatic cancerDiscovery studies
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