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. New England Journal Of Medicine 2023, 388: 1055-1056. PMID: 36920765, PMCID: PMC10134047, DOI: 10.1056/nejmc2211539.Peer-Reviewed Original Research
2024
Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome
Brakta S, Du Q, Chorich L, Hawkins Z, Sullivan M, Ko E, Kim H, Knight J, Taylor H, Friez M, Phillips J, Layman L. Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome. Molecular And Cellular Endocrinology 2024, 589: 112237. PMID: 38599276, DOI: 10.1016/j.mce.2024.112237.Peer-Reviewed Original ResearchCNV regionsDetect intragenic deletionsSingle nucleotide variantsRecurrent deletion regionsC-terminal regionSequencing of familiesGenome sequenceNucleotide variantsProtein expression in vitroLXXLL sequenceMissense variantsDeleted regionChromosome 17q12Exome sequencingGenetic approachesIntragenic deletionsTruncating variantsSanger sequencingSplice variantsMolecular basisHeterozygous variantsStopgain variantsZNHIT3Steroid hormone bindingExpression in vitroAuto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan.
Ryu HY, Jeong DW, Kim SY, Jeoung SW, Zhao D, Knight J, Lam T, Jin JH, Lee HS, Hochstrasser M. Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan. Res Sq 2024 PMID: 38562857, DOI: 10.21203/rs.3.rs-4016606/v1.Peer-Reviewed Original ResearchLow-frequency inherited complement receptor variants are associated with purpura fulminans.
Bendapudi PK, Nazeen S, Ryu J, Söylemez O, Robbins A, Rouaisnel B, O'Neil JK, Pokhriyal R, Yang M, Colling M, Pasko B, Bouzinier M, Tomczak L, Collier L, Barrios D, Ram S, Toth-Petroczy A, Krier J, Fieg E, Dzik WH, Hudspeth JC, Pozdnyakova O, Nardi V, Knight J, Maas R, Sunyaev S, Losman JA. Low-frequency inherited complement receptor variants are associated with purpura fulminans. Blood 2024, 143: 1032-1044. PMID: 38096369, DOI: 10.1182/blood.2023021231.Peer-Reviewed Original ResearchActivated sputum eosinophils associated with exacerbations in children on mepolizumab
Wilson G, Knight J, Liu Q, Shelar A, Stewart E, Wang X, Yan X, Sanders J, Visness C, Gill M, Gruchalla R, Liu A, Kattan M, Khurana Hershey G, Togias A, Becker P, Altman M, Busse W, Jackson D, Montgomery R, Chupp G. Activated sputum eosinophils associated with exacerbations in children on mepolizumab. Journal Of Allergy And Clinical Immunology 2024, 154: 297-307.e13. PMID: 38485057, PMCID: PMC11305967, DOI: 10.1016/j.jaci.2024.01.031.Peer-Reviewed Original ResearchAirway eosinophilsSputum eosinophilsPatients treated with mepolizumabPlacebo-controlled clinical trialAnti-IL-5 treatmentEffect of mepolizumabEosinophil subpopulationsSevere eosinophilic asthmaAnti-interleukin-5Expression of CD62LFrequency of exacerbationsEosinophilic asthmaActivation markersSputum samplesUnsupervised cluster analysisMepolizumabTreatment armsReduce exacerbationsCD62LClinical trialsExacerbationMass cytometryEosinophilsExacerbation riskIntracellular markers
2023
Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas
Youngblood M, Erson-Omay Z, Li C, Najem H, Coșkun S, Tyrtova E, Montejo J, Miyagishima D, Barak T, Nishimura S, Harmancı A, Clark V, Duran D, Huttner A, Avşar T, Bayri Y, Schramm J, Boetto J, Peyre M, Riche M, Goldbrunner R, Amankulor N, Louvi A, Bilgüvar K, Pamir M, Özduman K, Kilic T, Knight J, Simon M, Horbinski C, Kalamarides M, Timmer M, Heimberger A, Mishra-Gorur K, Moliterno J, Yasuno K, Günel M. Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas. Nature Communications 2023, 14: 6279. PMID: 37805627, PMCID: PMC10560290, DOI: 10.1038/s41467-023-41926-y.Peer-Reviewed Original ResearchIntegrated exome sequencing and microarray analyses detected genetic defects and underlying pathways of hepatocellular carcinoma
Chong M, Knight J, Peng G, Ji W, Chai H, Lu Y, Wu S, Li P, Hu Q. Integrated exome sequencing and microarray analyses detected genetic defects and underlying pathways of hepatocellular carcinoma. Cancer Genetics 2023, 276: 30-35. PMID: 37418972, DOI: 10.1016/j.cancergen.2023.06.002.Peer-Reviewed Original ResearchConceptsTumor mutation burdenWhole-exome sequencingGrade IIIHepatocellular carcinomaCNA burdenCase seriesBarcelona Clinic Liver Cancer stageExome sequencingBCLC stage CLiver Cancer stageEdmondson-Steiner gradingLarge case seriesGenetic defectsHigher CNA burdenAdjacent nontumor tissuesΒ-catenin pathwayBetter prognosisClinicopathologic findingsPoor prognosisClinicopathologic classificationCancer stageSurvival statusMutation burdenStage CPrognostic predictionTranscriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection
Agidigbi T, Kwon H, Knight J, Zhao D, Lee F, Oh I. Transcriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection. Frontiers In Cellular And Infection Microbiology 2023, 13: 1198115. PMID: 37434783, PMCID: PMC10332306, DOI: 10.3389/fcimb.2023.1198115.Peer-Reviewed Original ResearchConceptsDiabetic foot ulcersPeripheral blood mononuclear cellsHost immune responseActive infectionImmune responseDiabetic foot ulcer infectionsInfected diabetic foot ulcersFoot ulcer infectionsPatients 8 weeksIntravenous antibiotic therapyBlood mononuclear cellsWound healing statusDFU infectionsPBMC expressionSalvage therapyUlcer infectionDifferent time pointsAntibiotic therapyMajor complicationsSurgical treatmentFoot ulcersMononuclear cellsPotential intervention optionsSpecies-specific infectionTreatment response