2025
Enhanced insights into the genetic architecture of 3D cranial vault shape using pleiotropy-informed GWAS
Goovaerts S, Naqvi S, Hoskens H, Herrick N, Yuan M, Shriver M, Shaffer J, Walsh S, Weinberg S, Wysocka J, Claes P. Enhanced insights into the genetic architecture of 3D cranial vault shape using pleiotropy-informed GWAS. Communications Biology 2025, 8: 439. PMID: 40087503, PMCID: PMC11909261, DOI: 10.1038/s42003-025-07875-6.Peer-Reviewed Original ResearchConceptsCranial vault shapeVault shapeGenomic lociGenetic discovery effortsSNP discoveryCraniofacial developmentGenetic architectureGWAS dataGWAS studiesTranscription factorsGenetic studiesCranial vaultGenetic understandingShape variationSignaling pathwayBrain shapeExperimental biologyBrain shape variationCraniofacial complexFDR methodLociDiscovery effortsFacial shapeWealth of knowledgeGWASOptimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants
Yuan M, Goovaerts S, Lee M, Devine J, Richmond S, Walsh S, Shriver M, Shaffer J, Marazita M, Peeters H, Weinberg S, Claes P. Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants. Briefings In Bioinformatics 2025, 26: bbaf090. PMID: 40062617, PMCID: PMC11891655, DOI: 10.1093/bib/bbaf090.Peer-Reviewed Original ResearchConceptsRare variant association studiesGenome-wide association studiesComplex morphological traitsGenomic lociSNP heritabilityAssociation studiesRare variantsPhenotypic variationMorphological traitsAxes of phenotypic variationContext of genome-wide association studiesVariant association studiesIndividuals of European ancestryGene-based testsLinkage disequilibrium score regressionRare genetic variantsGenomic relatednessOptimal phenotypeUnrelated individualsGenetic variantsRelevant traitsEuropean ancestryScore regressionPhenotype distributionFamily data
2024
23. GENOME-WIDE ASSOCIATION STUDIES OF BINGE-EATING BEHAVIOUR AND ANOREXIA NERVOSA YIELD INSIGHTS INTO THE UNIQUE AND SHARED BIOLOGY OF EATING DISORDER PHENOTYPES
Huckins L, Termorshuizen J, Davies H, Lee S, Johnson J, Munn-Chernoff M, Thornton L, Källberg J, Bulik C, Breen G, Coleman J. 23. GENOME-WIDE ASSOCIATION STUDIES OF BINGE-EATING BEHAVIOUR AND ANOREXIA NERVOSA YIELD INSIGHTS INTO THE UNIQUE AND SHARED BIOLOGY OF EATING DISORDER PHENOTYPES. European Neuropsychopharmacology 2024, 87: 60. DOI: 10.1016/j.euroneuro.2024.08.137.Peer-Reviewed Original ResearchGenome-wide association studiesIdentification of novel lociGenome-wide association study meta-analysisGenetic correlationsEating Disorders Working GroupBinge-eating behaviorNovel lociGenome-wideGenomic lociAssociation studiesLociGenetic componentEating disorder phenotypesPhenotypeEarly onset obesityBE phenotypeSevere early onset obesityDisorder phenotypesTrans-diagnosticAN subtypesAN-BPAN-RAN-R.Eating DisordersBinge-eating/purgingGenetic mapping across autoimmune diseases reveals shared associations and mechanisms
Lincoln M, Connally N, Axisa P, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers I, Padyukov L, Rich S, Graham R, Gaffney P, Langefeld C, Vyse T, Hafler D, Chun S, Sunyaev S, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nature Genetics 2024, 56: 838-845. PMID: 38741015, DOI: 10.1038/s41588-024-01732-8.Peer-Reviewed Original ResearchConceptsGenetic mapResolution of genetic mappingExpression quantitative trait lociFine-mapping resolutionQuantitative trait lociGenomic lociTrait lociPolygenic disorderAllelesRisk allelesLociPathogenic mechanismsImmune systemAutoimmune mechanismsAutoimmune diseasesInflammatory diseasesTraitsMechanismDiseaseSample collectionExpressionGenomic insights into the comorbidity between type 2 diabetes and schizophrenia
Arruda A, Khandaker G, Morris A, Smith G, Huckins L, Zeggini E. Genomic insights into the comorbidity between type 2 diabetes and schizophrenia. Schizophrenia 2024, 10: 22. PMID: 38383672, PMCID: PMC10881980, DOI: 10.1038/s41537-024-00445-5.Peer-Reviewed Original ResearchBody mass indexType 2 diabetesType 2 diabetes riskEffect of body mass indexPutative effector genesN-methyl-D-aspartatePublic health challengeIncreased Body Mass IndexLipid-related pathwaysRisk-increasing effectMulti-omics dataMendelian randomizationPotential causal relationshipGene expression studiesDirection of effectMental healthDrug repurposing opportunitiesAssociation signalsGenomic lociGenomic insightsHealth challengesEffector genesGenetic liabilityMass indexExpression studies
2023
W22. DISENTANGLING THE ROLES OF GENETICS AND BODY MASS INDEX ACROSS PSYCHIATRIC DISORDERS
Signer R, Seah C, Young H, de Pins A, Johnson J, Cote A, Huckins L. W22. DISENTANGLING THE ROLES OF GENETICS AND BODY MASS INDEX ACROSS PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2023, 75: s116. DOI: 10.1016/j.euroneuro.2023.08.213.Peer-Reviewed Original ResearchExpression quantitative trait lociBody mass indexGenome-wide association studiesEffect of body mass indexAssociation studiesAvailability of genome-wide association studyGenetic riskPhenome-wide association studyIndirect effect of body mass indexPsychiatric disordersBody mass index spectrumStatistical fine-mappingQuantitative trait lociGenetic risk modelsCell-type specific mannerTissue enrichmentImpact of body mass indexGWAS lociTranscriptome imputationGenomic lociWhole genomeFine-mappingTrait lociGenomic underpinningsPhenotypic consequencesNucleolar structure connects with global nuclear organization.
Wang C, Ma H, Baserga S, Pederson T, Huang S. Nucleolar structure connects with global nuclear organization. Molecular Biology Of The Cell 2023, 34: ar114. PMID: 37610836, PMCID: PMC10846622, DOI: 10.1091/mbc.e23-02-0062.Peer-Reviewed Original ResearchConceptsNucleolar structureGenomic lociNuclear domainsSpecific genomic lociGlobal nuclear organizationRNA processing factorsRNA polymerase ICajal bodiesNuclear organizationRibosome synthesisNuclear bodiesKnockdown cellsPerinucleolar compartmentPolymerase IIntranuclear locationHeLa cellsNucleolar segregationSpatial organizationNucleoliLociUtp4CellsRPA194SegregationCompositional changesClonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic
Panda A, Suvakov M, Mariani J, Drucker K, Park Y, Jang Y, Kollmeyer T, Sarkar G, Bae T, Kim J, Yoon W, Jenkins R, Vaccarino F, Abyzov A. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. The CRISPR Journal 2023, 6: 176-182. PMID: 37071670, PMCID: PMC10123805, DOI: 10.1089/crispr.2022.0050.Peer-Reviewed Original ResearchConceptsCopy number alterationsSeparate genomic lociSingle nucleotide mutationsApplication of CRISPRCRISPR-Cas editingOff-target editsScreening of clonesGenomic divergenceWhole-genome sequencingGenomic lociSelection of clonesGenome sequencingNucleotide mutationsTarget editsCultured cellsClonal linesNumber alterationsCell cloningClonesMutationsCloningCRISPR
2022
APOBEC3A regulates transcription from interferon-stimulated response elements
Taura M, Frank JA, Takahashi T, Kong Y, Kudo E, Song E, Tokuyama M, Iwasaki A. APOBEC3A regulates transcription from interferon-stimulated response elements. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2011665119. PMID: 35549556, PMCID: PMC9171812, DOI: 10.1073/pnas.2011665119.Peer-Reviewed Original ResearchConceptsGene expressionResponse elementHost genomic lociInterferon-stimulated response elementRNA sequence analysisLong terminal repeatNegative feedback loopGenomic lociHuman genomeLethal mutationsProximal promoterHIV-1 transcriptionUnexpected roleIFN-I treatmentTerminal repeatDependent inductionViral genomeCytidine deaminaseISG15 inductionAntiviral responseA3AGenomeISG15 expressionType I IFNTranscriptionMapping genomic loci implicates genes and synaptic biology in schizophrenia
Trubetskoy V, Pardiñas A, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli T, Bryois J, Chen C, Dennison C, Hall L, Lam M, Watanabe K, Frei O, Ge T, Harwood J, Koopmans F, Magnusson S, Richards A, Sidorenko J, Wu Y, Zeng J, Grove J, Kim M, Li Z, Voloudakis G, Zhang W, Adams M, Agartz I, Atkinson E, Agerbo E, Al Eissa M, Albus M, Alexander M, Alizadeh B, Alptekin K, Als T, Amin F, Arolt V, Arrojo M, Athanasiu L, Azevedo M, Bacanu S, Bass N, Begemann M, Belliveau R, Bene J, Benyamin B, Bergen S, Blasi G, Bobes J, Bonassi S, Braun A, Bressan R, Bromet E, Bruggeman R, Buckley P, Buckner R, Bybjerg-Grauholm J, Cahn W, Cairns M, Calkins M, Carr V, Castle D, Catts S, Chambert K, Chan R, Chaumette B, Cheng W, Cheung E, Chong S, Cohen D, Consoli A, Cordeiro Q, Costas J, Curtis C, Davidson M, Davis K, de Haan L, Degenhardt F, DeLisi L, Demontis D, Dickerson F, Dikeos D, Dinan T, Djurovic S, Duan J, Ducci G, Dudbridge F, Eriksson J, Fañanás L, Faraone S, Fiorentino A, Forstner A, Frank J, Freimer N, Fromer M, Frustaci A, Gadelha A, Genovese G, Gershon E, Giannitelli M, Giegling I, Giusti-Rodríguez P, Godard S, Goldstein J, González Peñas J, González-Pinto A, Gopal S, Gratten J, Green M, Greenwood T, Guillin O, Gülöksüz S, Gur R, Gur R, Gutiérrez B, Hahn E, Hakonarson H, Haroutunian V, Hartmann A, Harvey C, Hayward C, Henskens F, Herms S, Hoffmann P, Howrigan D, Ikeda M, Iyegbe C, Joa I, Julià A, Kähler A, Kam-Thong T, Kamatani Y, Karachanak-Yankova S, Kebir O, Keller M, Kelly B, Khrunin A, Kim S, Klovins J, Kondratiev N, Konte B, Kraft J, Kubo M, Kučinskas V, Kučinskiene Z, Kusumawardhani A, Kuzelova-Ptackova H, Landi S, Lazzeroni L, Lee P, Legge S, Lehrer D, Lencer R, Lerer B, Li M, Lieberman J, Light G, Limborska S, Liu C, Lönnqvist J, Loughland C, Lubinski J, Luykx J, Lynham A, Macek M, Mackinnon A, Magnusson P, Maher B, Maier W, Malaspina D, Mallet J, Marder S, Marsal S, Martin A, Martorell L, Mattheisen M, McCarley R, McDonald C, McGrath J, Medeiros H, Meier S, Melegh B, Melle I, Mesholam-Gately R, Metspalu A, Michie P, Milani L, Milanova V, Mitjans M, Molden E, Molina E, Molto M, Mondelli V, Moreno C, Morley C, Muntané G, Murphy K, Myin-Germeys I, Nenadić I, Nestadt G, Nikitina-Zake L, Noto C, Nuechterlein K, O’Brien N, O’Neill F, Oh S, Olincy A, Ota V, Pantelis C, Papadimitriou G, Parellada M, Paunio T, Pellegrino R, Periyasamy S, Perkins D, Pfuhlmann B, Pietiläinen O, Pimm J, Porteous D, Powell J, Quattrone D, Quested D, Radant A, Rampino A, Rapaport M, Rautanen A, Reichenberg A, Roe C, Roffman J, Roth J, Rothermundt M, Rutten B, Saker-Delye S, Salomaa V, Sanjuan J, Santoro M, Savitz A, Schall U, Scott R, Seidman L, Sharp S, Shi J, Siever L, Sigurdsson E, Sim K, Skarabis N, Slominsky P, So H, Sobell J, Söderman E, Stain H, Steen N, Steixner-Kumar A, Stögmann E, Stone W, Straub R, Streit F, Strengman E, Stroup T, Subramaniam M, Sugar C, Suvisaari J, Svrakic D, Swerdlow N, Szatkiewicz J, Ta T, Takahashi A, Terao C, Thibaut F, Toncheva D, Tooney P, Torretta S, Tosato S, Tura G, Turetsky B, Üçok A, Vaaler A, van Amelsvoort T, van Winkel R, Veijola J, Waddington J, Walter H, Waterreus A, Webb B, Weiser M, Williams N, Witt S, Wormley B, Wu J, Xu Z, Yolken R, Zai C, Zhou W, Zhu F, Zimprich F, Atbaşoğlu E, Ayub M, Benner C, Bertolino A, Black D, Bray N, Breen G, Buccola N, Byerley W, Chen W, Cloninger C, Crespo-Facorro B, Donohoe G, Freedman R, Galletly C, Gandal M, Gennarelli M, Hougaard D, Hwu H, Jablensky A, McCarroll S, Moran J, Mors O, Mortensen P, Müller-Myhsok B, Neil A, Nordentoft M, Pato M, Petryshen T, Pirinen M, Pulver A, Schulze T, Silverman J, Smoller J, Stahl E, Tsuang D, Vilella E, Wang S, Xu S, Adolfsson R, Arango C, Baune B, Belangero S, Børglum A, Braff D, Bramon E, Buxbaum J, Campion D, Cervilla J, Cichon S, Collier D, Corvin A, Curtis D, Forti M, Domenici E, Ehrenreich H, Escott-Price V, Esko T, Fanous A, Gareeva A, Gawlik M, Gejman P, Gill M, Glatt S, Golimbet V, Hong K, Hultman C, Hyman S, Iwata N, Jönsson E, Kahn R, Kennedy J, Khusnutdinova E, Kirov G, Knowles J, Krebs M, Laurent-Levinson C, Lee J, Lencz T, Levinson D, Li Q, Liu J, Malhotra A, Malhotra D, McIntosh A, McQuillin A, Menezes P, Morgan V, Morris D, Mowry B, Murray R, Nimgaonkar V, Nöthen M, Ophoff R, Paciga S, Palotie A, Pato C, Qin S, Rietschel M, Riley B, Rivera M, Rujescu D, Saka M, Sanders A, Schwab S, Serretti A, Sham P, Shi Y, St Clair D, Stefánsson H, Stefansson K, Tsuang M, van Os J, Vawter M, Weinberger D, Werge T, Wildenauer D, Yu X, Yue W, Holmans P, Pocklington A, Roussos P, Vassos E, Verhage M, Visscher P, Yang J, Posthuma D, Andreassen O, Kendler K, Owen M, Wray N, Daly M, Huang H, Neale B, Sullivan P, Ripke S, Walters J, O’Donovan M. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature 2022, 604: 502-508. PMID: 35396580, PMCID: PMC9392466, DOI: 10.1038/s41586-022-04434-5.Peer-Reviewed Original ResearchConceptsGenomic lociTwo-stage genome-wide association studyVariant associationsDistinct genomic lociGenome-wide association studiesTranscription factor Sp4Functional genomics dataCommon variant associationsRare variant associationsCommon risk allelesSynaptic biologyGenomic dataBiological processesAssociation studiesGenesCell typesNeurodevelopmental disordersRegion variationLociFundamental processesNeuronal functionSuch variantsRisk allelesMechanistic studiesVariants
2021
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues
D’Antonio M, Nguyen J, Arthur T, Matsui H, Neale B, Daly M, Ganna A, Stevens C, Pathak G, Andrews S, Kanai M, Cordioli M, Ganna A, Karjalainen J, Pathak G, Polimanti R, Andrews S, Cordioli M, Pirinen M, Kanai M, Harerimana N, Veerapen K, Wolford B, Nguyen H, Solomonson M, Stevens C, Liao R, Chwialkowska K, Trankiem A, Balaconis M, Hayward C, Richmond A, Campbell A, Morris M, Fawns-Ritchie C, Glessner J, Shaw D, Chang X, Polikowski H, Lauren E, Chen H, Wanying Z, Hakonarson H, Porteous D, Below J, North K, McCormick J, Timmers P, Wilson J, Tenesa A, D’Mellow K, Kerr S, Niemi M, Cordioli M, Nkambul L, von Hohenstaufen K, Sobh A, Eltoukhy M, Yassen A, Hegazy M, Okasha K, Eid M, Moahmed H, Shahin D, El-Sherbiny Y, Elhadidy T, Elghafar M, El-Jawhari J, Mohamed A, Elnagdy M, Samir A, Abdel-Aziz M, Khafaga W, El-Lawaty W, Torky M, El-shanshory M, Batini C, Lee P, Shrine N, Williams A, Tobin M, Guyatt A, John C, Packer R, Ali A, Free R, Wang X, Wain L, Hollox E, Venn L, Bee C, Adams E, Niemi M, Niavarani A, Cordioli M, Nkambul L, Sharififard B, Aliannejad R, Amirsavadkouhi A, Naderpour Z, Tadi H, Aleagha A, Ahmadi S, Moghaddam S, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Chamnanphon M, Suttichet T, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Jantarabenjakul W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Hirankarn N, Nilaratanakul V, Sodsai P, Brumpton B, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold B, Abedalthagafi M, Alaamery M, Alqahtani S, Baraka D, Al Harthi F, Alsolm E, Abu Safieh L, Alowayn A, Alqubaishi F, Al Mutairi A, Mangul S, Alshareef A, Sawaji M, Almutairi M, Aljawini N, Albesher N, Arabi Y, Mahmoud E, Khattab A, Halawani R, Alahmadey Z, Albakri J, Felemban W, Suliman B, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, Alrashed M, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Massadeh S, AlMalik A, 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SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Reports 2021, 37: 110020. PMID: 34762851, PMCID: PMC8563343, DOI: 10.1016/j.celrep.2021.110020.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingComputational BiologyCOVID-19Databases, GeneticEthnicityGene ExpressionGene Expression ProfilingGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansOrgan SpecificityPolymorphism, Single NucleotideQuantitative Trait LociSARS-CoV-2Severity of Illness IndexTranscriptomeConceptsExpression quantitative trait lociGenome-wide association study signalsTissue/cell typesQuantitative trait lociGenetic fine mappingGene expression levelsLoci colocalizeGenomic lociGWAS lociTrait lociFine mappingVariety of tissuesCausal SNPsGene expressionSNP setsStudy signalsLociCell typesSARS-CoV-2 susceptibilityGenetic variantsSuggestive associationExpression levelsTissue typesSNPsCredible setsDirect targeting of amplified gene loci for proapoptotic anticancer therapy
Kaushik Tiwari M, Colon-Rios DA, Tumu HCR, Liu Y, Quijano E, Krysztofiak A, Chan C, Song E, Braddock DT, Suh HW, Saltzman WM, Rogers FA. Direct targeting of amplified gene loci for proapoptotic anticancer therapy. Nature Biotechnology 2021, 40: 325-334. PMID: 34711990, PMCID: PMC8930417, DOI: 10.1038/s41587-021-01057-5.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksTriplex-forming oligonucleotidesDNA damage responseDouble-strand breaksDrug resistanceGene amplificationP53-independent apoptosisHER2-positive breastOvarian cancer modelHuman tumor xenograftsInduction of apoptosisGenomic lociNumber of drugsCellular functionsDamage responseGene locusProtein productsHER2-positive cancer cellsDriver genesClinical efficacyCombat drug resistanceDNA damageHER2 amplificationTherapeutic strategiesTumor xenograftsMultiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy
Woodworth M, Ng K, Halpern A, Pease N, Nguyen P, Kueh H, Vaughan J. Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Research 2021, 49: e82-e82. PMID: 34048564, PMCID: PMC8373070, DOI: 10.1093/nar/gkab423.Peer-Reviewed Original ResearchConceptsHistone modificationsGenomic lociChromatin stateNon-repetitive genomic regionsRegulation of genome architectureRNA polymerase II loadingFunction of multicellular organismsMultiple histone modificationsDevelopmentally-regulated genesHistone modification levelsPopulation-averaged measurementsExpansion microscopySingle cellsGenome architectureGenomic regionsHistone marksMulticellular organismsIndividual lociEpigenetic stateHousekeeping genesGene locusLociHistoneModification levelsGenesGenome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology
Mullins N, Forstner AJ, O’Connell K, Coombes B, Coleman JRI, Qiao Z, Als TD, Bigdeli TB, Børte S, Bryois J, Charney AW, Drange OK, Gandal MJ, Hagenaars SP, Ikeda M, Kamitaki N, Kim M, Krebs K, Panagiotaropoulou G, Schilder BM, Sloofman LG, Steinberg S, Trubetskoy V, Winsvold BS, Won HH, Abramova L, Adorjan K, Agerbo E, Al Eissa M, Albani D, Alliey-Rodriguez N, Anjorin A, Antilla V, Antoniou A, Awasthi S, Baek JH, Bækvad-Hansen M, Bass N, Bauer M, Beins EC, Bergen SE, Birner A, Bøcker Pedersen C, Bøen E, Boks MP, Bosch R, Brum M, Brumpton BM, Brunkhorst-Kanaan N, Budde M, Bybjerg-Grauholm J, Byerley W, Cairns M, Casas M, Cervantes P, Clarke TK, Cruceanu C, Cuellar-Barboza A, Cunningham J, Curtis D, Czerski PM, Dale AM, Dalkner N, David FS, Degenhardt F, Djurovic S, Dobbyn AL, Douzenis A, Elvsåshagen T, Escott-Price V, Ferrier IN, Fiorentino A, Foroud TM, Forty L, Frank J, Frei O, Freimer NB, Frisén L, Gade K, Garnham J, Gelernter J, Giørtz Pedersen M, Gizer IR, Gordon SD, Gordon-Smith K, Greenwood TA, Grove J, Guzman-Parra J, Ha K, Haraldsson M, Hautzinger M, Heilbronner U, Hellgren D, Herms S, Hoffmann P, Holmans PA, Huckins L, Jamain S, Johnson JS, Kalman JL, Kamatani Y, Kennedy JL, Kittel-Schneider S, Knowles JA, Kogevinas M, Koromina M, Kranz TM, Kranzler HR, Kubo M, Kupka R, Kushner SA, Lavebratt C, Lawrence J, Leber M, Lee HJ, Lee PH, Levy SE, Lewis C, Liao C, Lucae S, Lundberg M, MacIntyre DJ, Magnusson SH, Maier W, Maihofer A, Malaspina D, Maratou E, Martinsson L, Mattheisen M, McCarroll SA, McGregor NW, McGuffin P, McKay JD, Medeiros H, Medland SE, Millischer V, Montgomery GW, Moran JL, Morris DW, Mühleisen TW, O’Brien N, O’Donovan C, Olde Loohuis LM, Oruc L, Papiol S, Pardiñas AF, Perry A, Pfennig A, Porichi E, Potash JB, Quested D, Raj T, Rapaport MH, DePaulo JR, Regeer EJ, Rice JP, Rivas F, Rivera M, Roth J, Roussos P, Ruderfer DM, Sánchez-Mora C, Schulte EC, Senner F, Sharp S, Shilling PD, Sigurdsson E, Sirignano L, Slaney C, Smeland OB, Smith DJ, Sobell JL, Søholm Hansen C, Soler Artigas M, Spijker AT, Stein DJ, Strauss JS, Świątkowska B, Terao C, Thorgeirsson TE, Toma C, Tooney P, Tsermpini EE, Vawter MP, Vedder H, Walters JTR, Witt SH, Xi S, Xu W, Yang JMK, Young AH, Young H, Zandi PP, Zhou H, Zillich L, Adolfsson R, Agartz I, Alda M, Alfredsson L, Babadjanova G, Backlund L, Baune B, Bellivier F, Bengesser S, Berrettini W, Blackwood D, Boehnke M, Børglum A, Breen G, Carr V, Catts S, Corvin A, Craddock N, Dannlowski U, Dikeos D, Esko T, Etain B, Ferentinos P, Frye M, Fullerton J, Gawlik M, Gershon E, Goes F, Green M, Grigoroiu-Serbanescu M, Hauser J, Henskens F, Hillert J, Hong K, Hougaard D, Hultman C, Hveem K, Iwata N, Jablensky A, Jones I, Jones L, Kahn R, Kelsoe J, Kirov G, Landén M, Leboyer M, Lewis C, Li Q, Lissowska J, Lochner C, Loughland C, Martin N, Mathews C, Mayoral F, McElroy S, McIntosh A, McMahon F, Melle I, Michie P, Milani L, Mitchell P, Morken G, Mors O, Mortensen P, Mowry B, Müller-Myhsok B, Myers R, Neale B, Nievergelt C, Nordentoft M, Nöthen M, O’Donovan M, Oedegaard K, Olsson T, Owen M, Paciga S, Pantelis C, Pato C, Pato M, Patrinos G, Perlis R, Posthuma D, Ramos-Quiroga J, Reif A, Reininghaus E, Ribasés M, Rietschel M, Ripke S, Rouleau G, Saito T, Schall U, Schalling M, Schofield P, Schulze T, Scott L, Scott R, Serretti A, Shannon Weickert C, Smoller J, Stefansson H, Stefansson K, Stordal E, Streit F, Sullivan P, Turecki G, Vaaler A, Vieta E, Vincent J, Waldman I, Weickert T, Werge T, Wray N, Zwart J, Biernacka J, Nurnberger J, Cichon S, Edenberg H, Stahl E, McQuillin A, Di Florio A, Ophoff R, Andreassen O. Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology. Nature Genetics 2021, 53: 817-829. PMID: 34002096, PMCID: PMC8192451, DOI: 10.1038/s41588-021-00857-4.Peer-Reviewed Original ResearchConceptsAssociation studiesQuantitative trait loci dataExpression quantitative trait loci (eQTL) dataGenome-wide association studiesBipolar disorder casesBrain-expressed genesWide association studyHeritable mental illnessSynaptic signaling pathwaysGenomic lociTargets of antipsychoticsLoci dataImperfect genetic correlationGene expressionSignaling pathwaysFunctional followGenesGenetic correlationsDruggable targetsSignal enrichmentEuropean ancestryLociBipolar disorder risk allelesNew insightsTherapeutic leads
2020
ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization
Hu M, Yang B, Cheng Y, Radda JSD, Chen Y, Liu M, Wang S. ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. Scientific Reports 2020, 10: 22031. PMID: 33328483, PMCID: PMC7745008, DOI: 10.1038/s41598-020-76439-x.Peer-Reviewed Original ResearchConceptsSingle-molecule RNA FISHSpecific genomic lociSitu hybridizationNucleome architecturesRNA FISHGenomic lociRNA speciesMultiplexed fluorescenceFISH techniqueFishRecent technological advancesMultiplexed imagingHybridizationMultiplexed mannerLociSpeciesFluorescencePowerful methodNotable exampleProbeProbe designTechnological advancesTumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6
Arnal-Estapé A, Cai WL, Albert AE, Zhao M, Stevens LE, López-Giráldez F, Patel KD, Tyagi S, Schmitt EM, Westbrook TF, Nguyen DX. Tumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6. Oncogene 2020, 39: 3726-3737. PMID: 32157212, PMCID: PMC7190573, DOI: 10.1038/s41388-020-1246-z.Peer-Reviewed Original ResearchConceptsChromatin landscapeTranscription factorsBone morphogenetic protein (BMP) signalingDiverse transcriptional programsAlters chromatin accessibilityMultiple genomic lociMorphogenetic protein signalingDistal enhancer elementsSelective transcription factorsEpithelial cell typesSurfactant protein CChromatin accessibilityGenomic lociTranscriptional programsLung adenocarcinoma progressionTumor progressionEpigenetic mechanismsProtein signalingBiological functionsLUAD progressionLUAD cellsEnhancer elementsLineage dependencyTumor suppressionLung cancer cells
2019
Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue
Wilkins O, Johnson K, Houseman E, King J, Marsit C, Christensen B. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019, 15: 398-418. PMID: 31842685, PMCID: PMC7153548, DOI: 10.1080/15592294.2019.1695332.Peer-Reviewed Original ResearchConceptsGenome-wide characterizationGenome-wide patternsGenome-wide mapsGene regulatory programsActive chromatinGenomic lociGene regulationTranscriptional inactivityRegulatory regionsGene regionMammalian tissuesRegulatory programsCpG lociDNA treatmentImmune cell functionCell functionLociLactate oxidationNormal breast tissueIndependent data setsPre-invasive breast cancerRecent evidenceHeterochromatinChromatinBisulfiteProteomic Detection and Validation of Translated Small Open Reading Frames
Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Current Protocols In Chemical Biology 2019, 11: e77. PMID: 31750990, PMCID: PMC6878975, DOI: 10.1002/cpch.77.Peer-Reviewed Original ResearchConceptsSiRNA-based silencingSmall open reading framesNon-AUG start codonsOpen reading frameStandard proteomic methodsSpecific transcript isoformsCultured human cellsUnique tryptic peptidesGenomic lociShorter proteinTranscript isoformsProtein databaseProteomic methodsNovel regulatorReading frameProteomic detectionStart codonFunctional characterizationMass spectrometry-based detectionComplete annotationSmall proteinsHuman cellsTryptic peptidesProtein extractionSmORFsGenetic Overlap Between Alzheimer’s Disease and Bipolar Disorder Implicates the MARK2 and VAC14 Genes
Drange O, Smeland O, Shadrin A, Finseth P, Witoelar A, Frei O, Group P, Wang Y, Hassani S, Djurovic S, Dale A, Andreassen O, Stahl E, Breen G, Forstner A, McQuillin A, Ripke S, Trubetskoy V, Mattheisen M, Wang Y, Coleman J, Gaspar H, de Leeuw C, Steinberg S, Pavlides J, Trzaskowski M, Pers T, Holmans P, Abbott L, Agerbo E, Akil H, Albani D, Alliey-Rodriguez N, Als T, Anjorin A, Antilla V, Awasthi S, Badner J, Bækvad-Hansen M, Barchas J, Bass N, Bauer M, Belliveau R, Bergen S, Pedersen C, Bøen E, Boks M, Boocock J, Budde M, Bunney W, Burmeister M, Bybjerg-Grauholm J, Byerley W, Casas M, Cerrato F, Cervantes P, Chambert K, Charney A, Chen D, Churchhouse C, Clarke T, Coryell W, Craig D, Cruceanu C, Curtis D, Czerski P, Dale A, de Jong S, Degenhardt F, Del-Favero J, DePaulo J, Djurovic S, Dobbyn A, Dumont A, Elvsåshagen T, Escott-Price V, Fan C, Fischer S, Flickinger M, Foroud T, Forty L, Frank J, Fraser C, Freimer N, Friseìn L, Gade K, Gage D, Garnham J, Giambartolomei C, Pedersen M, Goldstein J, Gordon S, Gordon-Smith K, Green E, Green M, Greenwood T, Grove J, Guan W, Parra J, Hamshere M, Hautzinger M, Heilbronner U, Herms S, Hipolito M, Hoffmann P, Holland D, Huckins L, Jamain S, Johnson J, Jureìus A, Kandaswamy R, Karlsson R, Kennedy J, Kittel-Schneider S, Knott S, Knowles J, Kogevinas M, Koller A, Kupka R, Lavebratt C, Lawrence J, Lawson W, Leber M, Lee P, Levy S, Li J, Liu C, Lucae S, Maaser A, MacIntyre D, Mahon P, Maier W, Martinsson L, McCarroll S, McGuffin P, McInnis M, McKay J, Medeiros H, Medland S, Meng F, Milani L, Montgomery G, Morris D, Mühleisen T, Mullins N, Nguyen H, Nievergelt C, Adolfsson A, Nwulia E, O’Donovan C, Loohuis L, Ori A, Oruc L, Ösby U, Perlis R, Perry A, Pfennig A, Potash J, Purcell S, Regeer E, Reif A, Reinbold C, Rice J, Rivas F, Rivera M, Roussos P, Ruderfer D, Ryu E, Saìnchez-Mora C, Schatzberg A, Scheftner W, Schork N, Weickert C, Shehktman T, Shilling P, Sigurdsson E, Slaney C, Smeland O, Sobell J, Hansen C, Spijker A, St Clair D, Steffens M, Strauss J, Streit F, Strohmaier J, Szelinger S, Thompson R, Thorgeirsson T, Treutlein J, Vedder H, Wang W, Watson S, Weickert T, Witt S, Xi S, Xu W, Young A, Zandi P, Zhang P, Zollner S, Adolfsson R, Agartz I, Alda M, Backlund L, Baune B, Bellivier F, Berrettini W, Biernacka J, Blackwood D, Boehnke M, Børglum A, Corvin A, Craddock N, Daly M, Dannlowski U, Esko T, Etain B, Frye M, Fullerton J, Gershon E, Gill M, Goes F, Grigoroiu-Serbanescu M, Hauser J, Hougaard D, Hultman C, Jones I, Jones L, Kahn R, Kirov G, Landeìn M, Leboyer M, Lewis C, Li Q, Lissowska J, Martin N, Mayoral F, McElroy S, McIntosh A, McMahon F, Melle I, Metspalu A, Mitchell P, Morken G, Mors O, Mortensen P, Müller-Myhsok B, Myers R, Neale B, Nimgaonkar V, Nordentoft M, Nöthen M, O’Donovan M, Oedegaard K, Owen M, Paciga S, Pato C, Pato M, Posthuma D, Ramos-Quiroga J, Ribaseìs M, Rietschel M, Rouleau G, Schalling M, Schofield P, Schulze T, Serretti A, Smoller J, Stefansson H, Stefansson K, Stordal E, Sullivan P, Turecki G, Vaaler A, Vieta E, Vincent J, Werge T, Nurnberger J, Wray N, Di Florio A, Edenberg H, Cichon S, Ophoff R, Scott L, Andreassen O, Kelsoe J, Sklar P. Genetic Overlap Between Alzheimer’s Disease and Bipolar Disorder Implicates the MARK2 and VAC14 Genes. Frontiers In Neuroscience 2019, 13: 220. PMID: 30930738, PMCID: PMC6425305, DOI: 10.3389/fnins.2019.00220.Peer-Reviewed Original ResearchCommon genetic variantsNovel lociGenetic variantsGenetic overlapPolygenic overlapGenome-wide associationNovel genomic lociNumerous common genetic variantsGenomic lociComplex traitsWide associationGenesLociInternational GenomicsGenetic originTraitsAlzheimer's diseaseImplicatingVariantsGenomicsOverlapBipolar disorderDistinct featuresFurther studiesBinding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination
Liang Z, Liang F, Teng Y, Chen X, Liu J, Longerich S, Rao T, Green AM, Collins NB, Xiong Y, Lan L, Sung P, Kupfer GM. Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination. Cell Reports 2019, 26: 564-572.e5. PMID: 30650351, PMCID: PMC6350941, DOI: 10.1016/j.celrep.2018.12.084.Peer-Reviewed Original ResearchConceptsR-loopsCo-transcriptional R-loopsFANCI-FANCD2 complexFanconi anemiaR-loop structuresSeries of RNADNA replicative stressGuanine-rich sequencesFANCD2 monoubiquitinationGenomic lociID2 complexReplicative stressFA cellsRNA transcriptionFA pathwayComplex bindsDNA hybridsCancer predispositionBone marrow failureDNA damageRNAMonoubiquitinationDevelopmental abnormalitiesMarrow failureSsRNA
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