2023
A large-scale retrospective study enabled deep-learning based pathological assessment of frozen procurement kidney biopsies to predict graft loss and guide organ utilization
Yi Z, Xi C, Menon M, Cravedi P, Tedla F, Soto A, Sun Z, Liu K, Zhang J, Wei C, Chen M, Wang W, Veremis B, Garcia-Barros M, Kumar A, Haakinson D, Brody R, Azeloglu E, Gallon L, O'Connell P, Naesens M, Shapiro R, Colvin R, Ward S, Salem F, Zhang W. A large-scale retrospective study enabled deep-learning based pathological assessment of frozen procurement kidney biopsies to predict graft loss and guide organ utilization. Kidney International 2023, 105: 281-292. PMID: 37923131, PMCID: PMC10892475, DOI: 10.1016/j.kint.2023.09.031.Peer-Reviewed Original ResearchArterial intimal fibrosisGraft lossOrgan utilizationIntimal fibrosisSclerotic glomeruliLarge-scale retrospective studyGlomerular filtration rateDeceased donor kidneysPathologist scoresTransplant outcomesBiopsy findingsSurvival prediction modelWedge biopsyRisk stratificationRetrospective studyFiltration ratePathological assessmentDonor biopsiesNeedle biopsySimilar survivalHistological scoringUnnecessary organsDiscovery setKidneyLesion scoresMultiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival
Sun Z, Zhang Z, Banu K, Gibson I, Colvin R, Yi Z, Zhang W, De Kumar B, Reghuvaran A, Pell J, Manes T, Djamali A, Gallon L, O'Connell P, He J, Pober J, Heeger P, Menon M. Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival. Journal Of Clinical Investigation 2023, 133: e170420. PMID: 37676733, PMCID: PMC10617779, DOI: 10.1172/jci170420.Peer-Reviewed Original ResearchConceptsDeath-censored graft lossHuman leukocyte antigenExpression quantitative trait lociT cellsTGF-β1TGF-β1/Smad pathwayDonor-recipient differencesKidney allograft lossChronic allograft rejectionKidney transplant survivalDonor-recipient mismatchActive TGF-β1Allograft lossGraft lossAllograft rejectionTransplant cohortPeripheral bloodLeukocyte antigenClinical trialsImmune cellsHaplotype mismatchGenome-wide scaleTransplant survivalQuantitative trait lociSingle nucleotide polymorphism data
2021
Recipient APOL1 risk alleles associate with death-censored renal allograft survival and rejection episodes
Zhang Z, Sun Z, Fu J, Lin Q, Banu K, Chauhan K, Planoutene M, Wei C, Salem F, Yi Z, Liu R, Cravedi P, Cheng H, Hao K, O’Connell P, Ishibe S, Zhang W, Coca SG, Gibson IW, Colvin RB, He J, Heeger PS, Murphy B, Menon MC. Recipient APOL1 risk alleles associate with death-censored renal allograft survival and rejection episodes. Journal Of Clinical Investigation 2021, 131 PMID: 34499625, PMCID: PMC8592534, DOI: 10.1172/jci146643.Peer-Reviewed Original ResearchConceptsDeath-censored allograft lossAPOL1 risk allelesRisk allelesTransplant outcomesDeath-censored renal allograft survivalRenal allograft survivalChronic allograft rejectionKidney transplant waitlistKidney transplant cohortRisk allele carriersAllograft lossAllograft survivalGraft lossRejection episodesTransplant cohortAllograft rejectionDonor kidneysNative kidneysNK cellsImmunomodulatory roleTransplant waitlistAPOL1 genotypeClinical trialsHealthy controlsHispanic recipientsDeep learning identified pathological abnormalities predictive of graft loss in kidney transplant biopsies
Yi Z, Salem F, Menon MC, Keung K, Xi C, Hultin S, Haroon Al Rasheed MR, Li L, Su F, Sun Z, Wei C, Huang W, Fredericks S, Lin Q, Banu K, Wong G, Rogers NM, Farouk S, Cravedi P, Shingde M, Smith RN, Rosales IA, O'Connell PJ, Colvin RB, Murphy B, Zhang W. Deep learning identified pathological abnormalities predictive of graft loss in kidney transplant biopsies. Kidney International 2021, 101: 288-298. PMID: 34757124, PMCID: PMC10285669, DOI: 10.1016/j.kint.2021.09.028.Peer-Reviewed Original ResearchConceptsGraft lossTransplant biopsiesDamage scoreBanff scoresPathological lesionsOne-year graft lossPost-transplant graft lossGlomerular filtration rate declineIntermediate-risk groupKidney allograft failurePost-transplant biopsiesKidney transplant biopsiesMononuclear leukocyte infiltrationTissue compartmentsMononuclear leukocyte infiltrateProtocol biopsiesAllograft failureTransplant recipientsClinical predictorsTubular atrophyGraft damageRisk stratificationInterstitial fibrosisLeukocyte infiltrationLeukocyte infiltrate
2019
A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection
Zhang W, Yi Z, Keung KL, Shang H, Wei C, Cravedi P, Sun Z, Xi C, Woytovich C, Farouk S, Huang W, Banu K, Gallon L, Magee CN, Najafian N, Samaniego M, Djamali A, Alexander SI, Rosales IA, Smith RN, Xiang J, Lerut E, Kuypers D, Naesens M, O'Connell PJ, Colvin R, Menon MC, Murphy B. A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection. Journal Of The American Society Of Nephrology 2019, 30: 1481-1494. PMID: 31278196, PMCID: PMC6683710, DOI: 10.1681/asn.2018111098.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBiomarkersBiopsyFemaleGene Expression ProfilingGenomicsGraft RejectionGraft SurvivalHumansImmunosuppressive AgentsInflammationKaplan-Meier EstimateKidney Failure, ChronicKidney TransplantationMaleMiddle AgedOligonucleotide Array Sequence AnalysisProspective StudiesRisk FactorsSequence Analysis, RNAConceptsSubclinical acute rejectionKidney transplant recipientsAcute cellular rejectionAcute rejectionTransplant recipientsSurveillance biopsiesACR 3Graft functionHigh riskIndependent cohortPeripheral blood gene expression signaturesClinical acute rejectionFuture graft lossOngoing acute rejectionStable graft functionBlood gene expression signaturesCellular rejectionGraft lossGraft outcomeGraft survivalBorderline changesGene expression signaturesCox analysisHistologic featuresPeripheral blood