2023
Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs
Klämbt V, Buerger F, Wang C, Naert T, Richter K, Nauth T, Weiss A, Sieckmann T, Lai E, Connaughton D, Seltzsam S, Mann N, Majmundar A, Wu C, Onuchic-Whitford A, Shril S, Schneider S, Schierbaum L, Dai R, Bekheirnia M, Joosten M, Shlomovitz O, Vivante A, Banne E, Mane S, Lifton R, Kirschner K, Kispert A, Rosenberger G, Fischer K, Lienkamp S, Zegers M, Hildebrandt F. Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs. Journal Of The American Society Of Nephrology 2023, 34: 273-290. PMID: 36414417, PMCID: PMC10103091, DOI: 10.1681/asn.2022010050.Peer-Reviewed Original ResearchConceptsIntegrin-linked kinaseFocal adhesion proteinsThree-dimensional (3D) MadinCdc42/Rac1Genetic variantsRac1/Cdc42Loss of interactionFrog modelPolarity defectsExchange factorNovel genesFocal adhesionsLamellipodia formationARHGEF6Adhesion proteinsDisease genesDeleterious variantsCell spreadingLumen formationCell migrationGenesProteinHemizygous variantKidney cellsExome sequencing
2020
Whole-Exome Sequencing in 97 Families with Renal Ciliopathies Reveals a Causative Mutation in a Known Kidney Disease Gene in 62% and Identifies Potential Novel Causative Genes
Deutsch K, Klambt V, Kitzler T, Jobst-Schwan T, Shril S, Mane S, Hildebrandt F. Whole-Exome Sequencing in 97 Families with Renal Ciliopathies Reveals a Causative Mutation in a Known Kidney Disease Gene in 62% and Identifies Potential Novel Causative Genes. Journal Of The American Society Of Nephrology 2020, 31: 487-487. DOI: 10.1681/asn.20203110s1487b.Peer-Reviewed Original Research
2018
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw C, Pardiñas AF, Hu M, Jin F, Li Y, Owen M, O’Donovan M, Walters J, Posthuma D, Reimers M, Levitt P, Weinberger D, Hyde T, Kleinman J, Geschwind D, Hawrylycz M, State M, Sanders S, Sullivan P, Gerstein M, Lein E, Knowles J, Sestan N, Willsey A, Oldre A, Szafer A, Camarena A, Cherskov A, Charney A, Abyzov A, Kozlenkov A, Safi A, Jones A, Ashley-Koch A, Ebbert A, Price A, Sekijima A, Kefi A, Bernard A, Amiri A, Sboner A, Clark A, Jaffe A, Tebbenkamp A, Sodt A, Guillozet-Bongaarts A, Nairn A, Carey A, Huttner A, Chervenak A, Szekely A, Shieh A, Harmanci A, Lipska B, Carlyle B, Gregor B, Kassim B, Sheppard B, Bichsel C, Hahn C, Lee C, Chen C, Kuan C, Dang C, Lau C, Cuhaciyan C, Armoskus C, Mason C, Liu C, Slaughterbeck C, Bennet C, Pinto D, Polioudakis D, Franjic D, Miller D, Bertagnolli D, Lewis D, Feng D, Sandman D, Clarke D, Williams D, DelValle D, Fitzgerald D, Shen E, Flatow E, Zharovsky E, Burke E, Olson E, Fulfs E, Mattei E, Hadjimichael E, Deelman E, Navarro F, Wu F, Lee F, Cheng F, Goes F, Vaccarino F, Liu F, Hoffman G, Gürsoy G, Gee G, Mehta G, Coppola G, Giase G, Sedmak G, Johnson G, Wray G, Crawford G, Gu G, van Bakel H, Witt H, Yoon H, Pratt H, Zhao H, Glass I, Huey J, Arnold J, Noonan J, Bendl J, Jochim J, Goldy J, Herstein J, Wiseman J, Miller J, Mariani J, Stoll J, Moore J, Szatkiewicz J, Leng J, Zhang J, Parente J, Rozowsky J, Fullard J, Hohmann J, Morris J, Phillips J, Warrell J, Shin J, An J, Belmont J, Nyhus J, Pendergraft J, Bryois J, Roll K, Grennan K, Aiona K, White K, Aldinger K, Smith K, Girdhar K, Brouner K, Mangravite L, Brown L, Collado-Torres L, Cheng L, Gourley L, Song L, Ubieta L, Habegger L, Ng L, Hauberg M, Onorati M, Webster M, Kundakovic M, Skarica M, Reimers M, Johnson M, Chen M, Garrett M, Sarreal M, Reding M, Gu M, Peters M, Fisher M, Gandal M, Purcaro M, Smith M, Brown M, Shibata M, Brown M, Xu M, Yang M, Ray M, Shapovalova N, Francoeur N, Sjoquist N, Mastan N, Kaur N, Parikshak N, Mosqueda N, Ngo N, Dee N, Ivanov N, Devillers O, Roussos P, Parker P, Manser P, Wohnoutka P, Farnham P, Zandi P, Emani P, Dalley R, Mayani R, Tao R, Gittin R, Straub R, Lifton R, Jacobov R, Howard R, Park R, Dai R, Abramowicz S, Akbarian S, Schreiner S, Ma S, Parry S, Shapouri S, Weissman S, Caldejon S, Mane S, Ding S, Scuderi S, Dracheva S, Butler S, Lisgo S, Rhie S, Lindsay S, Datta S, Souaiaia T, Roychowdhury T, Gomez T, Naluai-Cecchini T, Beach T, Goodman T, Gao T, Dolbeare T, Fliss T, Reddy T, Chen T, Hyde T, Brunetti T, Lemon T, Desta T, Borrman T, Haroutunian V, Spitsyna V, Swarup V, Shi X, Jiang Y, Xia Y, Chen Y, Jiang Y, Wang Y, Chae Y, Yang Y, Kim Y, Riley Z, Krsnik Z, Deng Z, Weng Z, Lin Z, Li Z. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 2018, 362 PMID: 30545854, PMCID: PMC6413317, DOI: 10.1126/science.aat7615.Peer-Reviewed Original ResearchConceptsIntegrative functional genomic analysisFunctional genomic analysisCell typesGene coexpression modulesDistinct cell typesCell type-specific dynamicsGenomic basisEpigenomic reorganizationEpigenomic landscapeEpigenomic regulationGenomic analysisCoexpression modulesIntegrative analysisHuman brain developmentFetal transitionHuman neurodevelopmentGenetic associationCellular compositionNeuropsychiatric riskBrain developmentNeurodevelopmental processesGenesTraitsPostnatal developmentNeuropsychiatric disordersMutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Ashraf S, Kudo H, Rao J, Kikuchi A, Widmeier E, Lawson JA, Tan W, Hermle T, Warejko JK, Shril S, Airik M, Jobst-Schwan T, Lovric S, Braun DA, Gee HY, Schapiro D, Majmundar AJ, Sadowski CE, Pabst WL, Daga A, van der Ven AT, Schmidt JM, Low BC, Gupta AB, Tripathi BK, Wong J, Campbell K, Metcalfe K, Schanze D, Niihori T, Kaito H, Nozu K, Tsukaguchi H, Tanaka R, Hamahira K, Kobayashi Y, Takizawa T, Funayama R, Nakayama K, Aoki Y, Kumagai N, Iijima K, Fehrenbach H, Kari JA, El Desoky S, Jalalah S, Bogdanovic R, Stajić N, Zappel H, Rakhmetova A, Wassmer SR, Jungraithmayr T, Strehlau J, Kumar AS, Bagga A, Soliman NA, Mane SM, Kaufman L, Lowy DR, Jairajpuri MA, Lifton RP, Pei Y, Zenker M, Kure S, Hildebrandt F. Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment. Nature Communications 2018, 9: 1960. PMID: 29773874, PMCID: PMC5958119, DOI: 10.1038/s41467-018-04193-w.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsChildChild, PreschoolDisease Models, AnimalDNA Mutational AnalysisDrug ResistanceExome SequencingFemaleGene Knockdown TechniquesGlucocorticoidsHEK293 CellsHigh-Throughput Nucleotide SequencingHumansInfantMaleMiceMice, Inbred C57BLMice, KnockoutMiddle AgedMutationNephrotic SyndromePedigreePodocytesProtein Interaction MapsRhoA GTP-Binding ProteinRNA, Small InterferingTreatment OutcomeConceptsKnockdown of DLC1Small GTPase activityExchange factorNephrotic syndromeRhoA regulationGTPase activityDifferent genesDLC1GenesNS phenotypePotential therapeutic targetChronic kidney diseaseMutationsCultured podocytesKnockdownTherapeutic targetMigration rateSteroid treatmentKidney diseaseKnockout micePathogenic pathwaysFrequent causeITSN1Cdc42ITSN2A homozygous missense variant in VWA2, encoding an interactor of the Fraser-complex, in a patient with vesicoureteral reflux
van der Ven AT, Kobbe B, Kohl S, Shril S, Pogoda HM, Imhof T, Ityel H, Vivante A, Chen J, Hwang DY, Connaughton DM, Mann N, Widmeier E, Taglienti M, Schmidt JM, Nakayama M, Senguttuvan P, Kumar S, Tasic V, Kehinde EO, Mane SM, Lifton RP, Soliman N, Lu W, Bauer SB, Hammerschmidt M, Wagener R, Hildebrandt F. A homozygous missense variant in VWA2, encoding an interactor of the Fraser-complex, in a patient with vesicoureteral reflux. PLOS ONE 2018, 13: e0191224. PMID: 29351342, PMCID: PMC5774751, DOI: 10.1371/journal.pone.0191224.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acid SubstitutionAnimalsAnimals, NewbornBiomarkers, TumorCalcium-Binding ProteinsChildConsanguinityConserved SequenceExonsExtracellular Matrix ProteinsFraser SyndromeGene Expression Regulation, DevelopmentalHomozygoteHumansMaleMiceModels, AnimalModels, MolecularMutation, MissensePedigreeSequence Homology, Amino AcidUrogenital AbnormalitiesUrogenital SystemVesico-Ureteral RefluxConceptsMetanephric mesenchymeUreteric budWhole-exome sequencingHomozygosity mappingIntermolecular disulfide bond formationDisulfide bond formationDirect interactorsNeomorphic effectMonogenic causesCysteine residuesHomozygous missense mutationComplex subunit 1Unpaired cysteine residueNovel CAKUTSubunit 1Homozygous missense variantFraser ComplexMissense mutationsGenesProteinInteractorsMissense variantsMutationsExome sequencingNephrogenic zone
2017
De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis
Timberlake AT, Furey CG, Choi J, Nelson-Williams C, Loring E, Galm A, Kahle K, Steinbacher D, Larysz D, Persing J, Lifton R, Bilguvar K, Mane S, Tikhonova I, Castaldi C, Knight J. De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e7341-e7347. PMID: 28808027, PMCID: PMC5584457, DOI: 10.1073/pnas.1709255114.Peer-Reviewed Original ResearchConceptsBone morphogenetic proteinRas/ERKDe novo mutationsNovo mutationsRas/ERK pathwayDamaging de novo mutationsHigh locus heterogeneityRare syndromic diseaseCommon risk variantsInhibitor of WntSyndromic craniosynostosesNew genesParent-offspring triosSyndromic diseaseMorphogenetic proteinsNegative regulatorERK pathwayMore cranial suturesGenesMidline craniosynostosisRisk variantsWntLocus heterogeneityMutationsExome sequencing
2003
Constitutive expression of cytotoxic proteases and down-regulation of protease inhibitors in LGL leukemia.
Kothapalli R, Bailey R, Kusmartseva I, Mane S, Epling-Burnette P, Loughran T. Constitutive expression of cytotoxic proteases and down-regulation of protease inhibitors in LGL leukemia. International Journal Of Oncology 2003, 22: 33-9. PMID: 12469182, DOI: 10.3892/ijo.22.1.33.Peer-Reviewed Original ResearchConceptsRNase protection assaysGene expressionPeripheral blood mononuclear cellsGroup of genesDifferential gene expressionNormal peripheral blood mononuclear cellsBlood mononuclear cellsNorthern blot analysisLGL leukemiaSmall subunitCaspase-8Protein perforinConstitutive expressionMicroarray technologyMononuclear cellsCytotoxic proteasesGenesProtection assaysCysteine proteinasesLarge granular lymphocyte leukemiaBlot analysisLGL leukemia patientsGranular lymphocyte leukemiaAlpha-1 antitrypsinExpression
2001
Defining a molecular fingerprint of STAT3-regulated genes associated with oncogenesis using microarray technology and novel statistical methods
Sinibaldi D, Garcia R, Bloom G, Mane S, Geiser P, Minton S, Muro-Cacho C, Lazaridis E, Jove R. Defining a molecular fingerprint of STAT3-regulated genes associated with oncogenesis using microarray technology and novel statistical methods. Nature Genetics 2001, 27: 86-86. DOI: 10.1038/87296.Peer-Reviewed Original Research