James Knight, PhD
Research Scientist in GeneticsCards
About
Research
Publications
Featured Publications
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing
Knight JR, Dunne EM, Mulholland EK, Saha S, Satzke C, Tothpal A, Weinberger DM. Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing. Microbial Genomics 2020, 7: mgen000494. PMID: 33355528, PMCID: PMC8115901, DOI: 10.1099/mgen.0.000494.Peer-Reviewed Original ResearchIntegrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
Farshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nature Communications 2022, 13: 898. PMID: 35197475, PMCID: PMC8866401, DOI: 10.1038/s41467-022-28566-4.Peer-Reviewed Original ResearchConceptsAcral melanomaMelanoma subtypesClinical profilingCommon melanoma subtypeImmune checkpoint blockadeCheckpoint blockadeInferior survivalMelanoma cell linesKey molecular driversPoor prognosisTherapeutic targetAnchorage-independent growthImmunomodulatory genesNon-white individualsHotspot mutationsMolecular driversCandidate oncogeneMelanomaApoptotic cell deathLZTR1Focal amplificationTumor promoterCell linesMetastasisTumor suppressorUnexplained Female Infertility Associated with Genetic Disease Variants
Dougherty M, Poch A, Chorich L, Hawkins Z, Xu H, Roman R, Liu H, Brakta S, Taylor H, Knight J, Kim H, Diamond M, Layman L. Unexplained Female Infertility Associated with Genetic Disease Variants. The New England Journal Of Medicine 2023, 388: 1055-1056. PMID: 36920765, PMCID: PMC10134047, DOI: 10.1056/nejmc2211539.Commentaries, Editorials and Letters
2026
Impaired glycosylation promotes rapid transition to hepatocellular carcinoma in model of diet induced steatotic liver disease
Singh A, Chaube B, Citrin K, Fowler J, Lee S, Catarino J, Knight J, Lowery S, Shree S, Mahoney K, Boutagy N, Ruz-Maldonado I, Harry K, Shanabrough M, Ross T, Malaker S, Suárez Y, Fernández-Hernando C, Grabińska K, Sessa W. Impaired glycosylation promotes rapid transition to hepatocellular carcinoma in model of diet induced steatotic liver disease. Journal Of Clinical Investigation 2026, 136: e197719. PMID: 41805633, PMCID: PMC13132402, DOI: 10.1172/jci197719.Peer-Reviewed Original ResearchSteatotic liver diseaseLiver-specific knockoutHepatocellular carcinomaPharmacological inhibitionLiver diseaseHepatic TAG accumulationCis-prenyltransferaseKnock-in modelTAG accumulationHigh-fat diet conditionsTransition to hepatocellular carcinomaTriacylglycerol synthesisTranscriptome atlasImpaired glycosylationChronic liver diseaseHepatocellular carcinoma burdenMolecular analysisMolecular mechanismsHepatocellular carcinoma developmentDGAT2 inhibitionER/oxidative stressHepatocellular carcinoma formationNgBRLipid uptakeVery-low-densityOptimizing next-generation sequencing for genetic diagnosis in autosomal dominant polycystic kidney disease
Ma D, Cho S, Meng X, Gulati A, Knight J, Goralsky L, Peng G, Shaw M, Widomski A, Popa A, Zhao C, Dykas D, Tikhonova I, Bale A, Somlo S, Zhang H, Besse W. Optimizing next-generation sequencing for genetic diagnosis in autosomal dominant polycystic kidney disease. Genetics In Medicine 2026, 28: 102529. PMID: 41653026, DOI: 10.1016/j.gim.2026.102529.Peer-Reviewed Original ResearchNext-generation sequencingGenome sequenceExome sequencingAutosomal dominant polycystic kidney diseaseDisease genesPathogenic variantsLong-range polymerase chain reactionPrimary disease geneDominant polycystic kidney diseasePolycystic kidney diseaseGC contentRadiologic imaging studiesPKD1 pathogenic variantsPolypyrimidine tractPKD2 variantsVariant detectionSanger sequencingPKD1Genetic diagnosisClinical geneticistsPseudogenesKidney diseaseSequenceAutosomal dominant polycystic kidney disease patientsCapture reagent
2025
Pathogenic variants in medically actionable genes among women with Mayer-Rokitansky-Küster-Hauser syndrome
Theisen J, Chorich L, Hawkins Z, Xu H, Knight J, Kim H, Taylor H, Layman L. Pathogenic variants in medically actionable genes among women with Mayer-Rokitansky-Küster-Hauser syndrome. BMJ Connections Clinical Genetics And Genomics 2025, 2: e000004. DOI: 10.1136/bmjccgg-2024-000004.Peer-Reviewed Original ResearchMayer-Rokitansky-Kuster-HauserP/LP variantsUK BiobankAmerican CollegeElectronic medical recordsActionable genesMayer-Rokitansky-Kuster-Hauser syndromeExome sequencingGenetic counselingPrevalence of variantsMedical recordsMedical surveillanceSecondary findingsEmergency databaseStudy aimCongenital absenceUnexplained infertilityPathogenic variantsPrevalenceWomenBiobankSanger sequencingVariant prevalenceControl databaseAuditory anomaliesLZTR1 is a melanoma oncogene that promotes invasion and suppresses apoptosis
Bacchiocchi A, Mak M, Khan Z, Gong X, Sznol M, Na Z, Su H, Chan L, Yan Q, Zhao D, Mortlock R, Knight J, Slavoff S, Halaban R. LZTR1 is a melanoma oncogene that promotes invasion and suppresses apoptosis. Oncogene 2025, 44: 3974-3984. PMID: 40885854, PMCID: PMC12500468, DOI: 10.1038/s41388-025-03538-2.Peer-Reviewed Original ResearchDegradation of ubiquitinated proteinsActin-related proteinsActin cytoskeleton organizationUbiquitin-proteasome systemSrc tyrosine kinaseAnchorage-independent growthNormal cell survivalCargo adapterActin organizationProximity biotinylationCytoskeleton organizationLC-MS/MS proteomicsLeucine zipperProteasome systemUbiquitinated proteinsCo-ImmunoprecipitationTargeting Pyk2Cell spreadingMelanoma cellsEnvironmental stressGrowth advantageMolecular characterizationCell migrationCell survivalLZTR1Activation of Pvt1b isoform contributes to local Pvt1 abundance to repress Myc during stress
Li Q, Olivero C, Floyd E, Ding J, Dangelmaier E, Knight J, Dimitrova N. Activation of Pvt1b isoform contributes to local Pvt1 abundance to repress Myc during stress. PLOS Genetics 2025, 21: e1011790. PMID: 40743223, PMCID: PMC12312954, DOI: 10.1371/journal.pgen.1011790.Peer-Reviewed Original ResearchConceptsTranscription start siteSequence elementsOncogenic stressLong-read sequencingP53-induced increaseIsoform-specific activitiesMYC proto-oncogeneLncRNA lociStart siteMYC regulationMyc repressionLong noncoding RNAsStress responseMYCTumor suppressionNoncoding RNAsProto-oncogeneIsoformsTranscriptionAbundanceIn vivoIn vitro modelLociPVT1RepressionCopy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients: Reevaluation Following Current Guidelines and Reanalysis by Genome Sequencing
Li W, Xie X, Chai H, DiAdamo A, Bistline E, Li P, Dai Y, Knight J, Avni-Singer A, Burger J, Ment L, Spencer-Manzon M, Zhang H, Wen J. Copy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients: Reevaluation Following Current Guidelines and Reanalysis by Genome Sequencing. Genes 2025, 16: 874. PMID: 40869922, PMCID: PMC12385847, DOI: 10.3390/genes16080874.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingChromosomal microarray analysisCopy number variantsGenome sequenceMicroarray analysisCausative genetic variantsDiagnostic valueClinical cytogenetics laboratoryPediatric casesConsecutive pediatric casesConsecutive pediatric patientsPathogenic CNVsGenetic variantsBenign CNVsGenetic counselorsClinical geneticistsRate of reclassificationLaboratory reevaluationCytogenetic laboratoriesPediatric patientsChromosomeClinical impactSequenceVariantsCopyAuto-sumoylation of the yeast Ubc9 E2 SUMO-conjugating enzyme extends cellular lifespan
Jeong D, Lee D, Kim S, Jeoung S, Zhao D, Knight J, Lam T, Jin J, Lee H, Hochstrasser M, Ryu H. Auto-sumoylation of the yeast Ubc9 E2 SUMO-conjugating enzyme extends cellular lifespan. Nature Communications 2025, 16: 3735. PMID: 40254622, PMCID: PMC12009981, DOI: 10.1038/s41467-025-58925-w.Peer-Reviewed Original ResearchConceptsE2 SUMO-conjugating enzymeSUMO-conjugating enzymeSUMO-specific proteasesPost-translational levelIn vitro evolutionSevere cellular stressCalorie restrictionRegulation of multiple targetsGene expression profilesIncreased mitochondrial activityCellular lifespanLifespan extensionReplicative lifespanCellular stressMitochondrial activityYeastCR-mediated lifespan extensionEnhanced growth rateEnzyme resultsDiverse processesExpression profilesLifespan effectsReplication abilityEnergy metabolismAged cells