2023
Objective Analysis and Clinical Significance of the Spatial Tumor-Infiltrating Lymphocyte Patterns in Non-Small Cell Lung Cancer.
Lopez De Rodas M, Wang Y, Peng G, Gu J, Mino-Kenudson M, Riess J, Velcheti V, Hellmann M, Gainor J, Zhao H, Schalper K. Objective Analysis and Clinical Significance of the Spatial Tumor-Infiltrating Lymphocyte Patterns in Non-Small Cell Lung Cancer. Clinical Cancer Research 2023, 30: 998-1008. PMID: 38127300, PMCID: PMC10922461, DOI: 10.1158/1078-0432.ccr-23-2457.Peer-Reviewed Original ResearchNon-small cell lung cancerTIL subsetsCell lung cancerImmune evasion mechanismsSubset of casesLymphocyte infiltration patternsPathology-based approachStrong biomarker potentialTIL markersNSCLC patientsImmunotherapy outcomesLymphocyte patternsLung cancerTumor bedWorse outcomesClinical significanceMost tumorsEvasion mechanismsStromal tissueTumor samplesMultiplexed immunofluorescenceBiomarker potentialTumorsInfiltration patternsImmunotherapyProfilin1 is required to prevent mitotic catastrophe in murine and human glomerular diseases
Tian X, Pedigo C, Li K, Ma X, Bunda P, Pell J, Lek A, Gu J, Zhang Y, Rangel P, Li W, Schwartze E, Nagata S, Lerner G, Perincheri S, Priyadarshini A, Zhao H, Lek M, Menon M, Fu R, Ishibe S. Profilin1 is required to prevent mitotic catastrophe in murine and human glomerular diseases. Journal Of Clinical Investigation 2023, 133: e171237. PMID: 37847555, PMCID: PMC10721156, DOI: 10.1172/jci171237.Peer-Reviewed Original ResearchConceptsProteinuric kidney diseaseKidney diseasePodocyte lossHuman glomerular diseasesMitotic catastrophePodocyte cell cycleSevere proteinuriaCell cycle reentryKidney failureGlomerular diseaseCell cycleKidney tissueG1/S checkpointUnsuccessful repairCyclin D1Glomerular integrityIrregular nucleiTissue-specific lossMouse podocytesPodocytesAltered expressionDiseaseCyclin B1Ribosome affinity purificationMultinucleated cellsHBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol
Cheng Z, Li L, Zhang Y, Ren Y, Gu J, Wang X, Zhao H, Lu H. HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol. Briefings In Bioinformatics 2023, 24: bbac601. PMID: 36736372, DOI: 10.1093/bib/bbac601.Peer-Reviewed Original ResearchConceptsHepatocellular carcinomaClinical stageImmune microenvironmentTumor sizeHepatitis B virus infectionLow alpha-fetoprotein levelsMetabolism-related proteinsRelevant subgroupsB virus infectionSevere liver dysfunctionGood liver functionHigh AFP levelsAlpha-fetoprotein levelsPrimary liver malignancySmaller tumor sizeLarger tumor sizeLower clinical stageHigher clinical stageCancer-related deathProliferation activityPrevention of HBVNear-normal levelsLow proliferation activityLiver dysfunctionHigh proliferation activity
2022
Cell Cycle and Senescence Regulation by Podocyte Histone Deacetylase 1 and 2
Rangel P, Cross E, Liu C, Pedigo C, Tian X, Gutiérrez-Calabrés E, Nagata S, Priyadarshini A, Lerner G, Bunda P, Perincheri S, Gu J, Zhao H, Wang Y, Inoue K, Ishibe S. Cell Cycle and Senescence Regulation by Podocyte Histone Deacetylase 1 and 2. Journal Of The American Society Of Nephrology 2022, 34: 433-450. PMID: 36414418, PMCID: PMC10103311, DOI: 10.1681/asn.2022050598.Peer-Reviewed Original ResearchConceptsCell cycle entryDNA damageSenescence-associated β-galactosidase activityDouble knockout miceRole of HDACsNormal glomerular filtration barrierAssociated phenotypesP21-mediated cell cycle arrestOpen chromatin conformationGlomerular filtration barrierSevere proteinuriaKidney failureProinflammatory cytokinesCell cycle regulationHistone deacetylase 1Cell cycle arrestKi67 expressionSustained DNA damagePodocyte lossIntact expressionMice leadsPodocyte-specific lossMatrix metalloproteinasesPodocyte detachmentProteinuriaMIF is a common genetic determinant of COVID-19 symptomatic infection and severity
Shin JJ, Fan W, Par-Young J, Piecychna M, Leng L, Israni-Winger K, Qing H, Gu J, Zhao H, Schulz WL, Unlu S, Kuster J, Young G, Liu J, Ko AI, Garcia A, Sauler M, Wisnewski AV, Young L, Orduña A, Wang A, Klementina O, Garcia AB, Hegyi P, Armstrong ME, Mitchell P, Ordiz DB, Garami A, Kang I, Bucala R. MIF is a common genetic determinant of COVID-19 symptomatic infection and severity. QJM 2022, 116: 205-212. PMID: 36222594, PMCID: PMC9620729, DOI: 10.1093/qjmed/hcac234.Peer-Reviewed Original ResearchConceptsMacrophage migration inhibitory factorLow-expression MIF alleleCOVID-19 infectionMIF allelesCATT7 alleleHealthy controlsCOVID-19Serum macrophage migration inhibitory factorSymptomatic SARS-CoV-2 infectionHigher serum MIF levelsHigh-expression MIF allelesRetrospective case-control studySARS-CoV-2 infectionFunctional polymorphismsAvailable clinical characteristicsMultinational retrospective studySerum MIF levelsUninfected healthy controlsSymptomatic COVID-19Tertiary medical centerHealthy control subjectsCase-control studyMigration inhibitory factorCoronavirus disease 2019Common functional polymorphismsTET3 epigenetically controls feeding and stress response behaviors via AGRP neurons
Xie D, Stutz B, Li F, Chen F, Lv H, Sestan-Pesa M, Catarino J, Gu J, Zhao H, Stoddard CE, Carmichael GG, Shanabrough M, Taylor HS, Liu ZW, Gao XB, Horvath TL, Huang Y. TET3 epigenetically controls feeding and stress response behaviors via AGRP neurons. Journal Of Clinical Investigation 2022, 132: e162365. PMID: 36189793, PMCID: PMC9525119, DOI: 10.1172/jci162365.Peer-Reviewed Original ResearchConceptsAgRP neuronsNeuropeptide YExpression of AgRPControl of feedingHypothalamic agoutiAnxiolytic effectsNeurotransmitter GABAMouse modelLeptin signalingStress-like behaviorsGenetic ablationNeuronsAgRPCritical central regulatorsEnergy expenditureGABAEnergy metabolismAppetiteFeedingCentral regulatorMetabolismCentral controlHuman cellsTET3ObesityShort-Term Effects of Ambient Air Pollutants on Outpatient Visits for Childhood Allergic Diseases in Shanghai, China
Hu Y, Gu J, Wu D, Wang X, Lü H, Yu G. Short-Term Effects of Ambient Air Pollutants on Outpatient Visits for Childhood Allergic Diseases in Shanghai, China. Journal Of Shanghai Jiaotong University (Science) 2022, 29: 979-994. DOI: 10.1007/s12204-022-2454-1.Peer-Reviewed Original ResearchChildhood allergic diseasesAmbient air pollutantsAllergic diseasesOutpatient visitsShort-term exposureTotal outpatient visitsAtopic dermatitisLag non-linear modelAge stratificationShort-term effectsDiseaseVisitsPositive associationTerm effectsAir pollutantsDisease classificationExposureAsthmaDermatitisHemodynamic differences between women and men with elevated blood pressure in China: A non-invasive assessment of 45,082 adults using impedance cardiography
Caraballo C, Mahajan S, Gu J, Lu Y, Spatz ES, Dreyer RP, Zhang M, Sun N, Ren Y, Zheng X, Zhao H, Lu H, J. Z, Krumholz HM. Hemodynamic differences between women and men with elevated blood pressure in China: A non-invasive assessment of 45,082 adults using impedance cardiography. PLOS ONE 2022, 17: e0269777. PMID: 35700163, PMCID: PMC9197037, DOI: 10.1371/journal.pone.0269777.Peer-Reviewed Original ResearchConceptsElevated blood pressureSystemic vascular resistance indexVascular resistance indexBlood pressureCardiac indexResistance indexHigh systemic vascular resistance indexLower systemic vascular resistance indexHigher mean systolic blood pressureMean diastolic blood pressureMean systolic blood pressureImpedance cardiographyLow cardiac indexHigher cardiac indexDiastolic blood pressureSystolic blood pressureBody mass indexYear old womanPersonalization of treatmentSame age groupNon-invasive assessmentSex differencesHemodynamic profileMass indexHemodynamic differencesComprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective
Gu J, Dai J, Lu H, Zhao H. Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective. Genomics Proteomics & Bioinformatics 2022, 21: 164-176. PMID: 35569803, PMCID: PMC10373092, DOI: 10.1016/j.gpb.2021.08.017.Peer-Reviewed Original ResearchConceptsGlobal expression patternsHuman transcriptomeExpression patternsHuman genesTemporal gene expression patternsVaried expression patternsGene expression patternsInternal reference genesHuman genomeTranscriptomeRegulatory codeGene clusteringMolecular mechanismsReference genesStable expressionIslet beta cellsHuman diseasesGenesExpression measurementsBeta cellsUbiquitouslyPhysiological conditionsValuable resourceComprehensive characterizationExtensive collection
2021
Effectiveness of an impedance cardiography guided treatment strategy to improve blood pressure control in a real-world setting: results from a pragmatic clinical trial
Wang L, Lu Y, Wang H, Gu J, J Z, Lian Z, Zhang Z, Krumholz H, Sun N. Effectiveness of an impedance cardiography guided treatment strategy to improve blood pressure control in a real-world setting: results from a pragmatic clinical trial. Open Heart 2021, 8: e001719. PMID: 34580169, PMCID: PMC8477318, DOI: 10.1136/openhrt-2021-001719.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overAntihypertensive AgentsBlood PressureCardiography, ImpedanceChinaClinical Decision-MakingFemaleFollow-Up StudiesHumansHypertensionIncidenceMaleMiddle AgedPractice Guidelines as TopicRetrospective StudiesTherapy, Computer-AssistedTime FactorsTreatment OutcomeYoung AdultConceptsBody mass indexPeking University People's HospitalStandard care groupBlood pressure controlSystolic BPHaemodynamic groupsTreatment strategiesImpedance cardiographyBaseline BPBP goalHypertension clinicHaemodynamic profileBP levelsCare groupPeople's HospitalMean baseline systolic BPPressure controlReal-world clinical practiceBaseline systolic BPMean systolic BPDiastolic BP levelsProportion of patientsPragmatic clinical trialsReal-world populationBaseline DBPToll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function
Huang J, Peng J, Pearson JA, Efthimiou G, Hu Y, Tai N, Xing Y, Zhang L, Gu J, Jiang J, Zhao H, Zhou Z, Wong FS, Wen L. Toll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function. Cellular & Molecular Immunology 2021, 18: 328-338. PMID: 33432061, PMCID: PMC8027372, DOI: 10.1038/s41423-020-00590-8.Peer-Reviewed Original ResearchConceptsType 1 diabetes developmentToll-like receptorsType 1 diabetesDiabetes developmentB cellsTLR7 deficiencyNOD miceB cell differentiationT cellsClassical MHC class I moleculesHuman type 1 diabetesImmunodeficient NOD miceNOD B cellsDiabetogenic T cellsAntigen-presenting functionNonobese diabetic (NOD) miceT cell responsesB cell functionMHC class I moleculesPattern recognition receptorsT cell activationPathogen molecular patternsClass I moleculesDiabetogenic CD4Cytotoxic CD8
2020
The role of the gut microbiome in cancer-related fatigue: pilot study on epigenetic mechanisms
Xiao C, Fedirko V, Beitler J, Bai J, Peng G, Zhou C, Gu J, Zhao H, Lin IH, Chico CE, Jeon S, Knobf TM, Conneely KN, Higgins K, Shin DM, Saba N, Miller A, Bruner D. The role of the gut microbiome in cancer-related fatigue: pilot study on epigenetic mechanisms. Supportive Care In Cancer 2020, 29: 3173-3182. PMID: 33078326, PMCID: PMC8055716, DOI: 10.1007/s00520-020-05820-3.Peer-Reviewed Original ResearchConceptsCancer-related fatigueGut microbiomePilot studyHigh-fatigue groupLow-fatigue groupsGut-brain axisMultidimensional Fatigue InventoryGut microbiota patternBrain healthCancer patientsFatigue InventoryNeck cancerPurposeRecent evidenceStool samplesImmune responseMicrobiota patternsGut microbiotaInflammationOne monthBrain functionPatientsConclusionsOur resultsFatty acid synthesisEPIC BeadChipDNA methylation changesGut Microbiome Associated with the Psychoneurological Symptom Cluster in Patients with Head and Neck Cancers
Bai J, Bruner DW, Fedirko V, Beitler JJ, Zhou C, Gu J, Zhao H, Lin IH, Chico CE, Higgins KA, Shin DM, Saba NF, Miller AH, Xiao C. Gut Microbiome Associated with the Psychoneurological Symptom Cluster in Patients with Head and Neck Cancers. Cancers 2020, 12: 2531. PMID: 32899975, PMCID: PMC7563252, DOI: 10.3390/cancers12092531.Peer-Reviewed Original ResearchPsychoneurological symptomsCancer patientsGut microbiomeNeck cancerPost-radiation therapyPsychoneurological symptom clusterCommon Terminology CriteriaPatient gut microbiomeGut Microbiome AssociatedFunctional pathway analysisTerminology CriteriaAdverse eventsOutcomes versionDiscriminant analysis effect sizeLinear discriminant analysis effect sizeStool specimensPatientsSymptom clustersCancer treatmentPilot studyGreater decreaseVitamin metabolismPotential rolePreliminary dataSignificant differencesImproving the Diagnosis of Phenylketonuria by Using a Machine Learning–Based Screening Model of Neonatal MRM Data
Zhu Z, Gu J, Genchev G, Cai X, Wang Y, Guo J, Tian G, Lu H. Improving the Diagnosis of Phenylketonuria by Using a Machine Learning–Based Screening Model of Neonatal MRM Data. Frontiers In Molecular Biosciences 2020, 7: 115. PMID: 32733913, PMCID: PMC7358370, DOI: 10.3389/fmolb.2020.00115.Peer-Reviewed Original ResearchNerve developmentCommon genetic metabolic disorderShanghai Children's HospitalMetabolic patternsLogistic regression analysis modelNewborn Screening CenterPositive predictive valueGenetic metabolic disordersPediatric patientsChildren's HospitalPatient recallMetabolic disordersScreening centerHealth providersPredictive valueDiagnosis of phenylketonuriaScreening methodDevelopmental delayFalse positive rateRegression analysis modelHigh false positive ratePhenylketonuriaPatientsHospitalScreening dataElevated serum interleukin-8 is associated with enhanced intratumor neutrophils and reduced clinical benefit of immune-checkpoint inhibitors
Schalper KA, Carleton M, Zhou M, Chen T, Feng Y, Huang SP, Walsh AM, Baxi V, Pandya D, Baradet T, Locke D, Wu Q, Reilly TP, Phillips P, Nagineni V, Gianino N, Gu J, Zhao H, Perez-Gracia JL, Sanmamed MF, Melero I. Elevated serum interleukin-8 is associated with enhanced intratumor neutrophils and reduced clinical benefit of immune-checkpoint inhibitors. Nature Medicine 2020, 26: 688-692. PMID: 32405062, PMCID: PMC8127102, DOI: 10.1038/s41591-020-0856-x.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, MonoclonalAntineoplastic Agents, ImmunologicalBiomarkers, PharmacologicalBiomarkers, TumorCell Cycle CheckpointsCohort StudiesFemaleHumansInterleukin-8MaleNeoplasmsNeutrophil InfiltrationNeutrophilsPrognosisProtein Kinase InhibitorsRetrospective StudiesSurvival AnalysisTreatment FailureTumor MicroenvironmentUp-RegulationConceptsSerum IL-8 levelsImmune checkpoint inhibitorsIL-8 levelsAdvanced cancerSerum interleukin-8 levelsPhase 3 clinical trialsSerum interleukin-8Interleukin-8 levelsLarge-scale retrospective analysisNeutrophil infiltrationWorse prognosisClinical benefitPoor outcomeIndependent biomarkerTumor immunobiologyClinical trialsInterleukin-8Retrospective analysisPatientsCancerInhibitorsIpilimumabNivolumabEverolimusPrognosisRelationship of Age With the Hemodynamic Parameters in Individuals With Elevated Blood Pressure
Mahajan S, Gu J, Caraballo C, Lu Y, Spatz ES, Zhao H, Zhang M, Sun N, Zheng X, Lu H, Yuan H, J. Z, Krumholz HM. Relationship of Age With the Hemodynamic Parameters in Individuals With Elevated Blood Pressure. Journal Of The American Geriatrics Society 2020, 68: 1520-1528. PMID: 32212398, DOI: 10.1111/jgs.16411.Peer-Reviewed Original ResearchConceptsElevated blood pressureBlood pressureCardiac indexHemodynamic profileHemodynamic parametersHealth checkup centerFinal study populationPathophysiology of hypertensionSelection of therapyCross-sectional studyMin/Relationship of ageDifferent age groupsHemodynamic assessmentMean ageStudy populationMAIN OUTCOMEAge strataAge groupsLarger studyImpedance cardiographyAgeSVRIWomenMen
2019
Genomic analysis of a spinal muscular atrophy (SMA) discordant family identifies a novel mutation in TLL2, an activator of growth differentiation factor 8 (myostatin): a case report
Jiang J, Huang J, Gu J, Cai X, Zhao H, Lu H. Genomic analysis of a spinal muscular atrophy (SMA) discordant family identifies a novel mutation in TLL2, an activator of growth differentiation factor 8 (myostatin): a case report. BMC Medical Genomics 2019, 20: 204. PMID: 31888525, PMCID: PMC6938020, DOI: 10.1186/s12881-019-0935-3.Peer-Reviewed Original ResearchConceptsSMA casesHeterozygous mutationsInternational SMA ConsortiumBackgroundSpinal muscular atrophyDifferent clinical typesRare neuromuscular disorderCopies of SMN2Compound heterozygous mutationsWhole-exome sequencingSeverity of SMAGenomic analysisFemale patientsMale patientsClinical typesCase reportAccurate counselingRare caseMouse modelDiagnostic criteriaMuscular functionPatientsGrowth differentiation factor 8Neuromuscular disordersSMA patientsMuscular atrophyHemodynamic Phenotypes of Hypertension Based on Cardiac Output and Systemic Vascular Resistance
Mahajan S, Gu J, Lu Y, Khera R, Spatz ES, Zhang M, Sun N, Zheng X, Zhao H, Lu H, Ma ZJ, Krumholz HM. Hemodynamic Phenotypes of Hypertension Based on Cardiac Output and Systemic Vascular Resistance. The American Journal Of Medicine 2019, 133: e127-e139. PMID: 31525336, DOI: 10.1016/j.amjmed.2019.08.042.Peer-Reviewed Original ResearchConceptsSystemic vascular resistance indexVascular resistance indexSystemic vascular resistanceCardiac indexBlood pressure categoriesResistance index ratioResistance indexVascular resistanceCardiac outputBlood pressureHemodynamic phenotypesPressure categoriesHigh systemic vascular resistance indexNormal systemic vascular resistance indexSystolic blood pressure 140Systolic blood pressure categoriesBlood pressure 140Health checkup centerNormal cardiac indexLow cardiac indexStroke volume indexHigher cardiac indexSystolic blood pressureBody mass indexSubtypes of hypertensionExpression of the type 3 InsP3 receptor is a final common event in the development of hepatocellular carcinoma
Guerra MT, Florentino RM, Franca A, Lima Filho AC, Dos Santos ML, Fonseca RC, Lemos FO, Fonseca MC, Kruglov E, Mennone A, Njei B, Gibson J, Guan F, Cheng YC, Ananthanarayanan M, Gu J, Jiang J, Zhao H, Lima CX, Vidigal PT, Oliveira AG, Nathanson MH, Leite MF. Expression of the type 3 InsP3 receptor is a final common event in the development of hepatocellular carcinoma. Gut 2019, 68: 1676. PMID: 31315892, PMCID: PMC7087395, DOI: 10.1136/gutjnl-2018-317811.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsApoptosisCalcium SignalingCarcinogenesisCarcinoma, HepatocellularCell ProliferationCells, CulturedDNA MethylationFemaleGene Expression Regulation, NeoplasticHepatocytesHumansInositol 1,4,5-Trisphosphate ReceptorsLiverLiver NeoplasmsLiver RegenerationMaleMice, KnockoutMiddle AgedSurvival AnalysisConceptsChronic liver diseaseITPR3 expressionLiver cancer cellsLiver diseaseMouse modelFinal common eventCancer cellsSpecimens of patientsIndependent patient cohortsControl liver specimensHuman HCC cellsType 3 InsP3 receptorHuman liver samplesIncreased expression levelCancer deathPatient cohortCommon molecular eventPoor survivalHepatocellular carcinomaLiver specimensNormal liverHCC cellsAbstractTextHCCType 3 isoformVCF‐Server: A web‐based visualization tool for high‐throughput variant data mining and management
Jiang J, Gu J, Zhao T, Lu H. VCF‐Server: A web‐based visualization tool for high‐throughput variant data mining and management. Molecular Genetics & Genomic Medicine 2019, 7: e00641. PMID: 31127704, PMCID: PMC6625089, DOI: 10.1002/mgg3.641.Peer-Reviewed Original ResearchConceptsWeb-based visualization toolGraphical interfaceCentralized wayVisualization toolsVCF filesVariant call format filesInteractive graphical interfaceUse graphical interfaceLittle bioinformatics backgroundVariant dataData miningWeb-based analysisFile systemGenetic variant dataProgramming skillsFiltering rulesBioinformatics backgroundFormat fileLocal deploymentProgramming codeInteractive analysisUsersVariant informationFilesVariant annotation