Featured Publications
A clonal expression biomarker associates with lung cancer mortality
Biswas D, Birkbak N, Rosenthal R, Hiley C, Lim E, Papp K, Boeing S, Krzystanek M, Djureinovic D, La Fleur L, Greco M, Döme B, Fillinger J, Brunnström H, Wu Y, Moore D, Skrzypski M, Abbosh C, Litchfield K, Al Bakir M, Watkins T, Veeriah S, Wilson G, Jamal-Hanjani M, Moldvay J, Botling J, Chinnaiyan A, Micke P, Hackshaw A, Bartek J, Csabai I, Szallasi Z, Herrero J, McGranahan N, Swanton C. A clonal expression biomarker associates with lung cancer mortality. Nature Medicine 2019, 25: 1540-1548. PMID: 31591602, PMCID: PMC6984959, DOI: 10.1038/s41591-019-0595-z.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerClinicopathological risk factorsCell lung cancerLung cancer mortalityPrognostic gene expression signaturesCancer cell proliferationGene expression signaturesCancer mortalityLung cancerRisk factorsExpression-based biomarkersCopy number gainsDisease subtypesClinical descriptorsTranscriptomic biomarkersIndividual tumorsCancer typesDiagnostic precisionMolecular biomarkersExpression signaturesCell proliferationDNA copy number gainsBiomarkersPatientsIntratumor heterogeneity
2023
Quantifying the impact of immunotherapy on RNA dynamics in cancer
Usaite I, Biswas D, Dijkstra K, Watkins T, Pich O, Puttick C, Angelova M, Thakkar K, Hiley C, Birkbak N, Kok M, Zaccaria S, Wu Y, Litchfield K, Swanton C, Kanu N. Quantifying the impact of immunotherapy on RNA dynamics in cancer. Journal For ImmunoTherapy Of Cancer 2023, 11: e007870. PMID: 37914385, PMCID: PMC10626770, DOI: 10.1136/jitc-2023-007870.Peer-Reviewed Original ResearchConceptsCheckpoint inhibitorsCheckpoint inhibitor treatmentBreast cancerOn-therapyImmune microenvironmentPre-therapyCancer typesPatients treated with checkpoint inhibitorsCheckpoint inhibitor therapyImpact of immunotherapyCancer immune microenvironmentSolid tumor typesMechanism of sensitizationClinical responseCombination therapyTumor typesIO targetsResponse ratePatientsBreastCancerImmunotherapyMelanomaMeta-analysesTherapy
2020
Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy
Balestrini S, Koepp M, Gandhi S, Rickman H, Shin G, Houlihan C, Anders-Cannon J, Silvennoinen K, Xiao F, Zagaglia S, Hudgell K, Ziomek M, Haimes P, Sampson A, Parker A, Cross J, Pardington R, Nastouli E, Swanton C, Consortium C, Aitken J, Allen Z, Ambler R, Ambrose K, Ashton E, Avola A, Balakrishnan S, Barns-Jenkins C, Barr G, Barrell S, Basu S, Beale R, Beesley C, Bhardwaj N, Bibi S, Bineva-Todd G, Biswas D, Blackman M, Bonnet D, Bowker F, Broncel M, Brooks C, Buck M, Buckton A, Budd T, Burrell A, Busby L, Bussi C, Butterworth S, Byott M, Byrne F, Byrne R, Caidan S, Campbell J, Canton J, Cardoso A, Carter N, Carvalho L, Carzaniga R, Chandler N, Chen Q, Cherepanov P, Churchward L, Clark G, Clayton B, Gigli C, Collins Z, Cottrell S, Crawford M, Cubitt L, Cullup T, Davies H, Davis P, Davison D, Dearing V, Debaisieux S, Diaz-Romero M, Dibbs A, Diring J, Driscoll P, D'Avola A, Earl C, Edwards A, Ekin C, Evangelopoulos D, Faraway R, Fearns A, Ferron A, Fidanis E, Fitz D, Fleming J, Frampton D, Frederico B, Gaiba A, Gait A, Gamblin S, Gärtner K, Gaul L, Golding H, Goldman J, Goldstone R, Dominguez B, Gong H, Grant P, Greco M, Grobler M, Guedan A, Gutierrez M, Hackett F, Hall R, Halldorsson S, Harris S, Hashim S, Hatipoglu E, Healy L, Heaney J, Herbst S, Hewitt G, Higgins T, Hindmarsh S, Hirani R, Hope J, Horton E, Hoskins B, Howell M, Howitt L, Hoyle J, Htun M, Hubank M, Encabo H, Hughes D, Hughes J, Huseynova A, Hwang M, Instrell R, Jackson D, Jamal-Hanjani M, Jenkins L, Jiang M, Johnson M, Jones L, Kanu N, Kassiotis G, Kelly G, Kiely L, Teixeira A, Kirk S, Kjaer S, Knuepfer E, Komarov N, Kotzampaltiris P, Kousis K, Krylova T, Kucharska A, Labrum R, Lambe C, Lappin M, Lee S, Levett A, Levett L, Levi M, Liu, Loughlin S, Lu W, MacRae J, Madoo A, Marczak J, Martensson M, Martinez T, Marzook B, Matthews J, Matz J, McCall S, McCoy L, McKay F, McNamara E, Minutti C, Mistry G, Molina-Arcas M, Montaner B, Montgomery K, Moore C, Moore D, Moraiti A, Moreira-Teixeira L, Mukherjee J, Naceur-Lombardelli C, Nelson A, Nicod J, Nightingale L, Nofal S, Nurse P, Nutan S, Oedekoven C, O'Garra A, O'Leary J, Olsen J, O'Neill O, O'Reilly N, Suarez P, Osborne N, Pabari A, Pajak A, Papayannopoulos V, Paraskevopoulou S, Patel N, Patel Y, Paun O, Peat N, Castano L, Caballero A, Perez-Lloret J, Perrault M, Perrin A, Poh R, Poirier E, Polke J, Pollitt M, Prieto-Godino L, Proust A, Puvirajasinghe C, Queval C, Ramachandran V, Ramaprasad A, Ratcliffe P, Reed L, Reis e Sousa C, Richardson K, Ridewood S, Roberts F, Roberts R, Rodgers A, Clavijo P, Rosa A, Rossi A, Roustan C, Rowan A, Sahai E, Sait A, Sala K, Sanchez E, Sanderson T, Santucci P, Sardar F, Sateriale A, Saunders J, Sawyer C, Schlott A, Schweighoffer E, Segura-Bayona S, Punatar R, Shahmanesh M, Shaw J, Dos Santos M, Silvestre M, Singer M, Snell D, Song O, Spyer M, Steel L, Strange A, Sullivan A, Tan M, Tautz-Davis Z, Taylor E, Taylor G, Taylor H, Taylor-Beadling A, Subtil F, Torras B, Toolan-Kerr P, Torelli F, Toteva T, Treeck M, Trojer H, Tsai M, Turner J, Turner M, Ule J, Ulferts R, Vanloo S, Veeriah S, Venkatesan S, Vousden K, Wack A, Walder C, Walker P, Wang Y, Ward S, Wenman C, Williams L, Williams M, Wong W, Wright J, Wu M, Wynne L, Xiang Z, Yap M, Zagalak J, Zecchin D, Zillwood R, Sander J, Sisodiya S, Consortium: C, Carthiyaniamma S, DeTisi J, Dick J, Hill A, Kipper K, Kullar B, Norris S, Rugg-Gunn F, Salvatierra R, Shaya G, Sloan A, Singh P, Varley J, Whatley B. Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy. Epilepsy & Behavior 2020, 115: 107602. PMID: 33279440, PMCID: PMC7643621, DOI: 10.1016/j.yebeh.2020.107602.Peer-Reviewed Original ResearchConceptsLong-term care facilitiesCare facilitiesChalfont Centre for EpilepsyResident-to-residentCo-morbiditiesCOVID-19 residentsPreventive measuresMeasured infection ratesCaregiver's levelOne-off testMultiple co-morbiditiesVulnerable peopleCaregiversEpilepsy-related factorsHospital admissionCohort studySymptomatic casesInfection preventionAsymptomatic peopleCOVID-19Clinical outcomes of COVID-19Rates of morbidityAsymptomatic individualsYoung adultsOutcomes of COVID-19Pervasive chromosomal instability and karyotype order in tumour evolution
Watkins T, Lim E, Petkovic M, Elizalde S, Birkbak N, Wilson G, Moore D, Grönroos E, Rowan A, Dewhurst S, Demeulemeester J, Dentro S, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir M, Xu H, Litchfield K, Lu W, Mourikis T, Dietzen M, Spain L, Cresswell G, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates L, Caramia F, Jaulin F, Vicier C, Tomlinson I, Brastianos P, Cho R, Bastian B, Dyrskjøt L, Jönsson G, Savas P, Loi S, Campbell P, Andre F, Luscombe N, Steeghs N, Tjan-Heijnen V, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum S, Schwarz R, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020, 587: 126-132. PMID: 32879494, PMCID: PMC7611706, DOI: 10.1038/s41586-020-2698-6.Peer-Reviewed Original ResearchConceptsSomatic copy number alterationsWhole-genome doublingChromosomal instabilityHuman leukocyte antigenChromosomal instability resultsSomatic copy number alteration analysisLoss of chromosome 8pFocal somatic copy number alterationsLoss of heterozygosityCopy number alterationsMetastatic samplesTumor evolutionKaryotype remodelingChromosome 8q24.1Clear cell renal cellChromosome 1q21Evolutionary eventsHER2+ breast cancerChromosome 8pChromosome 11q13.3Focal amplificationHaploid copiesRecurrent lossSubclonal frequenciesClonal events
2019
An innate-like Vδ1+ γδ T cell compartment in the human breast is associated with remission in triple-negative breast cancer
Wu Y, Kyle-Cezar F, Woolf R, Naceur-Lombardelli C, Owen J, Biswas D, Lorenc A, Vantourout P, Gazinska P, Grigoriadis A, Tutt A, Hayday A. An innate-like Vδ1+ γδ T cell compartment in the human breast is associated with remission in triple-negative breast cancer. Science Translational Medicine 2019, 11 PMID: 31597756, PMCID: PMC6877350, DOI: 10.1126/scitranslmed.aax9364.Peer-Reviewed Original ResearchConceptsT cell compartmentT cell receptorTriple-negative breast cancerInnate-like responsesT cellsBreast cancerExpress T cell receptorsIFN-g productionProgression-free survivalHuman breastAntigen-specific responsesAssociated with remissionHuman breast tumorsT cell receptor signalingMaximal patient benefitProgression-freeNKG2D receptorOverall survivalPeripheral bloodTissue-residentBreast tumorsIFN-gIL-17Paired tumorInflammatory pathologyPulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse
Chemi F, Rothwell D, McGranahan N, Gulati S, Abbosh C, Pearce S, Zhou C, Wilson G, Jamal-Hanjani M, Birkbak N, Pierce J, Kim C, Ferdous S, Burt D, Slane-Tan D, Gomes F, Moore D, Shah R, Al Bakir M, Hiley C, Veeriah S, Summers Y, Crosbie P, Ward S, Mesquita B, Dynowski M, Biswas D, Tugwood J, Blackhall F, Miller C, Hackshaw A, Brady G, Swanton C, Dive C. Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse. Nature Medicine 2019, 25: 1534-1539. PMID: 31591595, PMCID: PMC6986897, DOI: 10.1038/s41591-019-0593-1.Peer-Reviewed Original ResearchConceptsNon-small-cell lung cancerEarly-stage non-small-cell lung cancerDisease relapseGenomic profilingHigh risk of recurrenceDetection of circulating tumor cellsRisk of recurrenceTumor cell disseminationTime of surgeryPredictors of relapsePotential clinical utilityCurative intentPrimary tumorSurgical resectionTumor resectionTumor stagePredicting relapseCell disseminationTumor cellsLung cancerMutational overlapRelapseMultivariate analysisSurgeryHigh risk