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 heterogeneityA local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer
Wu Y, Biswas D, Usaite I, Angelova M, Boeing S, Karasaki T, Veeriah S, Czyzewska-Khan J, Morton C, Joseph M, Hessey S, Reading J, Georgiou A, Al-Bakir M, McGranahan N, Jamal-Hanjani M, Hackshaw A, Quezada S, Hayday A, Swanton C. A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer. Nature Cancer 2022, 3: 696-709. PMID: 35637401, PMCID: PMC9236901, DOI: 10.1038/s43018-022-00376-z.Peer-Reviewed Original ResearchConceptsT cell populationsT cellsLung tissueLung cancerCD8+ T cellsNonsmall-cell lung cancerNonsmall cell lung cancerEffector memory phenotypeT cell compartmentCell lung cancerAssociated with survivalNonmalignant lung tissuesStem-like featuresNontumor lung tissuesT cell biologyHuman lung tissueImmunotherapeutic strategiesMemory phenotypeNatural killerLung tumorsTissue-residentPost-surgeryResident memoryMurine tissuesTumorThe future of liquid biopsy
Biswas D, Ganeshalingam J, Wan J. The future of liquid biopsy. The Lancet Oncology 2020, 21: e550. PMID: 33271107, DOI: 10.1016/s1470-2045(20)30687-2.Peer-Reviewed Original Research
2024
Artificial intelligence methods for improved detection of undiagnosed heart failure with preserved ejection fraction
Wu J, Biswas D, Ryan M, Bernstein B, Rizvi M, Fairhurst N, Kaye G, Baral R, Searle T, Melikian N, Sado D, Lüscher T, Grocott‐Mason R, Carr‐White G, Teo J, Dobson R, Bromage D, McDonagh T, Shah A, O'Gallagher K. Artificial intelligence methods for improved detection of undiagnosed heart failure with preserved ejection fraction. European Journal Of Heart Failure 2024, 26: 302-310. PMID: 38152863, DOI: 10.1002/ejhf.3115.Peer-Reviewed Original ResearchConceptsLeft ventricular ejection fractionDiagnosis of HFpEFEuropean Society of CardiologyHeart failureNatural language processingElectronic health recordsEuropean Society of Cardiology criteriaClinical diagnosis of HFEuropean Society of Cardiology diagnostic criteriaDiagnostic criteriaVentricular ejection fractionRetrospective cohort studyDiagnosis of HFSociety of CardiologyClinician-assigned diagnosisConsecutive patientsHFpEF patientsEjection fractionElectronic health record dataAcute cardiovascular eventsExpert clinical reviewNatural language processing methodsNatural language processing pipelineHFpEFCardiovascular eventsPD-1 defines a distinct, functional, tissue-adapted state in Vδ1+ T cells with implications for cancer immunotherapy
Davies D, Kamdar S, Woolf R, Zlatareva I, Iannitto M, Morton C, Haque Y, Martin H, Biswas D, Ndagire S, Munonyara M, Gillett C, O’Neill O, Nussbaumer O, Hayday A, Wu Y. PD-1 defines a distinct, functional, tissue-adapted state in Vδ1+ T cells with implications for cancer immunotherapy. Nature Cancer 2024, 5: 420-432. PMID: 38172341, PMCID: PMC10965442, DOI: 10.1038/s43018-023-00690-0.Peer-Reviewed Original ResearchConceptsCheckpoint inhibitionPD-1T cellsProgrammed cell death protein 1Cell death protein 1PD-1 expressionResponse to TCR signalingPD-1 engagementT cell recognitionCancer immunotherapyTCR signalingTranscriptomic programsProtein 1CancerFunctional relevanceCellsImmunotherapyNeoantigensMelanomaPatientsOncology
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-analysesTherapyTracking early lung cancer metastatic dissemination in TRACERx using ctDNA
Abbosh C, Frankell A, Harrison T, Kisistok J, Garnett A, Johnson L, Veeriah S, Moreau M, Chesh A, Chaunzwa T, Weiss J, Schroeder M, Ward S, Grigoriadis K, Shahpurwalla A, Litchfield K, Puttick C, Biswas D, Karasaki T, Black J, Martínez-Ruiz C, Bakir M, Pich O, Watkins T, Lim E, Huebner A, Moore D, Godin-Heymann N, L’Hernault A, Bye H, Odell A, Roberts P, Gomes F, Patel A, Manzano E, Hiley C, Carey N, Riley J, Cook D, Hodgson D, Stetson D, Barrett J, Kortlever R, Evan G, Hackshaw A, Daber R, Shaw J, Aerts H, Licon A, Stahl J, Jamal-Hanjani M, Birkbak N, McGranahan N, Swanton C. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 2023, 616: 553-562. PMID: 37055640, PMCID: PMC7614605, DOI: 10.1038/s41586-023-05776-4.Peer-Reviewed Original ResearchConceptsCirculating tumor DNANon-small-cell lung cancerMetastatic disseminationClinical outcomesPlasma samplesEarly-stage non-small-cell lung cancerCirculating tumor DNA levelsCirculating tumor DNA detectionCytotoxic adjuvant therapyPreoperative ctDNA detectionResidual tumor cellsLongitudinal plasma samplesCancer cell fractionBiomarker of relapseProcess of metastatic disseminationAnalysis of plasma samplesClinical relapseDisease relapseAdjuvant therapyTumor DNAPreoperative plasmaRadiological surveillanceCtDNA detectionPatient cohortTumor cellsEvolutionary characterization of lung adenocarcinoma morphology in TRACERx
Karasaki T, Moore D, Veeriah S, Naceur-Lombardelli C, Toncheva A, Magno N, Ward S, Bakir M, Watkins T, Grigoriadis K, Huebner A, Hill M, Frankell A, Abbosh C, Puttick C, Zhai H, Gimeno-Valiente F, Saghafinia S, Kanu N, Dietzen M, Pich O, Lim E, Martínez-Ruiz C, Black J, Biswas D, Campbell B, Lee C, Colliver E, Enfield K, Hessey S, Hiley C, Zaccaria S, Litchfield K, Birkbak N, Cadieux E, Demeulemeester J, Van Loo P, Adusumilli P, Tan K, Cheema W, Sanchez-Vega F, Jones D, Rekhtman N, Travis W, Hackshaw A, Marafioti T, Salgado R, Le Quesne J, Nicholson A, McGranahan N, Swanton C, Jamal-Hanjani M. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nature Medicine 2023, 29: 833-845. PMID: 37045996, PMCID: PMC7614478, DOI: 10.1038/s41591-023-02230-w.Peer-Reviewed Original ResearchConceptsPrimary tumor regionLung adenocarcinomaPresence of micropapillary patternLoss of chromosome 3pSolid pattern tumorsHigh-grade patternsClonal evolution analysisSomatic copy number alterationsTumor regionLoss of heterozygosityWhole-exome sequencing dataCopy number alterationsAdenocarcinoma morphologyIntrathoracic recurrenceLepidic tumorsRNA sequencing dataMicropapillary patternRelapse riskGene alterationsMetastatic samplesHistological spectrumMicropapillary tumorsChromosome 3pHigh-gradeHistopathological analysisThe evolution of lung cancer and impact of subclonal selection in TRACERx
Frankell A, Dietzen M, Al Bakir M, Lim E, Karasaki T, Ward S, Veeriah S, Colliver E, Huebner A, Bunkum A, Hill M, Grigoriadis K, Moore D, Black J, Liu W, Thol K, Pich O, Watkins T, Naceur-Lombardelli C, Cook D, Salgado R, Wilson G, Bailey C, Angelova M, Bentham R, Martínez-Ruiz C, Abbosh C, Nicholson A, Le Quesne J, Biswas D, Rosenthal R, Puttick C, Hessey S, Lee C, Prymas P, Toncheva A, Smith J, Xing W, Nicod J, Price G, Kerr K, Naidu B, Middleton G, Blyth K, Fennell D, Forster M, Lee S, Falzon M, Hewish M, Shackcloth M, Lim E, Benafif S, Russell P, Boleti E, Krebs M, Lester J, Papadatos-Pastos D, Ahmad T, Thakrar R, Lawrence D, Navani N, Janes S, Dive C, Blackhall F, Summers Y, Cave J, Marafioti T, Herrero J, Quezada S, Peggs K, Schwarz R, Van Loo P, Miedema D, Birkbak N, Hiley C, Hackshaw A, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 2023, 616: 525-533. PMID: 37046096, PMCID: PMC10115649, DOI: 10.1038/s41586-023-05783-5.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerDisease-free survivalCell lung cancerWhole-genome doublingLung cancerLung adenocarcinomaAssociated with shorter disease-free survivalShorter disease-free survivalEvolution of lung cancerPattern of relapseSubclonal selectionPrimary study endpointHistory of smokingSubclonal expansionsCopy number instabilityEGFR mutationsCancer-associated mortalityCopy number heterogeneityClinical outcomesStudy endpointIntratumour heterogeneityNever-smokersClonal expansionFollow-upOncogenic isoform
2022
RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma
East P, Kelly G, Biswas D, Marani M, Hancock D, Creasy T, Sachsenmeier K, Swanton C, Downward J, de Carné Trécesson S. RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma. Nature Communications 2022, 13: 5632. PMID: 36163168, PMCID: PMC9512813, DOI: 10.1038/s41467-022-33290-0.Peer-Reviewed Original ResearchConceptsResponse to chemotherapyLung adenocarcinomaRas oncogene activationOncogenic activityKRAS wild-type tumorsReduced response to chemotherapyWild-type tumorsKRAS mutant tumorsResistance to therapyCohort of patientsAdverse clinical outcomesResponse to treatmentRAS pathway activationActive patient groupAggressive diseaseMutant tumorsKRAS mutationsClinical outcomesPreclinical studiesActivating mutationsClinical decision-makingGenetic alterationsPatient stratificationPatient groupKRAS
2021
Impact of cancer evolution on immune surveillance and checkpoint inhibitor response
Wu Y, Biswas D, Swanton C. Impact of cancer evolution on immune surveillance and checkpoint inhibitor response. Seminars In Cancer Biology 2021, 84: 89-102. PMID: 33631295, PMCID: PMC9253787, DOI: 10.1016/j.semcancer.2021.02.013.Peer-Reviewed Original ResearchConceptsImmune checkpoint inhibitorsCheckpoint inhibitor therapyCheckpoint inhibitorsIntratumour heterogeneityImmune surveillancePatient's response to immune checkpoint inhibitorsResponse to immune checkpoint inhibitorsCheckpoint inhibitor responseProportion of patientsStandard of carePredictive biomarkersStratify patientsImmune evasionDiagnostic accuracyInhibitor responseImmune systemMechanisms of genetic instabilityPatientsGenetic instabilityCancer evolutionTherapyCancerSurveillanceInhibitorsIntratumourMeta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Litchfield K, Reading J, Puttick C, Thakkar K, Abbosh C, Bentham R, Watkins T, Rosenthal R, Biswas D, Rowan A, Lim E, Al Bakir M, Turati V, Guerra-Assunção J, Conde L, Furness A, Saini S, Hadrup S, Herrero J, Lee S, Van Loo P, Enver T, Larkin J, Hellmann M, Turajlic S, Quezada S, McGranahan N, Swanton C. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition. Cell 2021, 184: 596-614.e14. PMID: 33508232, PMCID: PMC7933824, DOI: 10.1016/j.cell.2021.01.002.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorCD8 AntigensChemokine CXCL13Chromosomes, Human, Pair 9Cohort StudiesCyclin D1DNA Copy Number VariationsExomeGene AmplificationHumansImmune Checkpoint InhibitorsImmune EvasionMultivariate AnalysisMutationNeoplasmsPolymorphism, Single NucleotideReceptors, CCR5T-LymphocytesTumor BurdenConceptsTumor mutational burdenTumor-infiltrating lymphocytesHistocompatibility leukocyte antigenCheckpoint inhibitorsCD8 tumor-infiltrating lymphocytesCPI-treated patientsTumor cell-intrinsicClinical outcome criteriaCopy-number analysisCXCL9 expressionCCND1 amplificationMutational burdenLeukocyte antigenTumor typesMultivariate predictorsSingle-cell RNA sequencingAdaptive immunityAssociated with resistanceWhole exomeMicroenvironmental featuresOutcome criteriaCopy-numberFunctional evidenceRNA-seqTumor
2020
Metastasis and Immune Evasion from Extracellular cGAMP HydrolysisENPP1, a Therapeutic Target in Chromosomally Unstable Tumors
Li J, Duran M, Dhanota N, Chatila W, Bettigole S, Kwon J, Sriram R, Humphries M, Salto-Tellez M, James J, Hanna M, Melms J, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li H, Martin M, Dorsaint P, Cavallo J, Li P, Pauli C, Gottesdiener L, DiPardo B, Hollmann T, Merghoub T, Wen H, Reis-Filho J, Riaz N, Su S, Kalbasi A, Vasan N, Powell S, Wolchok J, Elemento O, Swanton C, Shoushtari A, Parkes E, Izar B, Bakhoum S. Metastasis and Immune Evasion from Extracellular cGAMP HydrolysisENPP1, a Therapeutic Target in Chromosomally Unstable Tumors. Cancer Discovery 2020, 11: 1212-1227. PMID: 33372007, PMCID: PMC8102348, DOI: 10.1158/2159-8290.cd-20-0387.Peer-Reviewed Original ResearchConceptsChromosomally unstable tumorsAnti-PD-1/PD-L1 treatmentResponse to immune checkpoint blockadeReduced immune cell infiltrationUnstable tumorsGeneration of extracellular adenosineCancer cells to immune cellsImmune-suppressive pathwaysImmune checkpoint blockadeResistance to immunotherapyTumor immune infiltrationImmune cell infiltrationEvading immune surveillanceMetastatic cancer cellsCGAS-STING innate immune pathwayExtracellular cGAMPCheckpoint blockadeInnate immune pathwaysTumor inflammationImmune surveillanceExtracellular adenosineImmune infiltrationIncreased metastasisImmune cellsCell infiltrationClinical 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 eventsPandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers
Houlihan C, Vora N, Byrne T, Lewer D, Kelly G, Heaney J, Gandhi S, Spyer M, Beale R, Cherepanov P, Moore D, Gilson R, Gamblin S, Kassiotis G, McCoy L, Swanton C, Consortium C, Hayward A, Nastouli E, Investigators S, 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, 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, D'Avola A, Dearing V, Debaisieux S, Diaz-Romero M, Dibbs A, Diring J, Driscoll P, Earl C, Edwards A, Ekin C, Evangelopoulos D, Faraway R, Fearns A, Ferron A, Fidanis E, Fitz D, Fleming J, Frederico B, Gaiba A, Gait A, Gamblin S, Gandhi S, 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, Healy L, Heaney J, Herbst S, Hewitt G, Higgins T, Hindmarsh S, Hirani R, Hope J, Horton E, Hoskins B, Houlihan C, 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, 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 H, 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, Nastouli E, 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, Suarez P, O'Reilly N, Osborne N, Pabari A, Pajak A, Papayannopoulos V, 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, Punatar R, Puvirajasinghe C, Queval C, Ramachandran V, Ramaprasad A, Ratcliffe P, Reed L, Reis e Sousa C, Richardson K, Ridewood S, Roberts R, Rodgers A, Clavijo P, Rosa A, Rossi A, Roustan C, Rowan A, Sahai E, Sait A, Sala K, Sanderson T, Santucci P, Sardar F, Sateriale A, Saunders J, Sawyer C, Schlott A, Schweighoffer E, Segura-Bayona S, Shaw J, Shin G, Dos Santos M, Silvestre M, Singer M, Snell D, Song O, Spyer M, Steel L, Strange A, Sullivan A, Swanton C, 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, Wiliams L, Williams M, Wong W, Wright J, Wu M, Wynne L, Xiang Z, Yap M, Zagalak J, Zecchin D, Zillwood R, Matthews R, Severn A, Adam S, Enfield L, McBride A, Gärtner K, Edwards S, Lorencatto F, Michie S, Manley E, Shahmanesh M, Lukha H, Prymas P, McBain H, Shortman R, Wood L, Davies C, Williams B, Ng K, Cornish G, Faulkner N, Riddell A, Hobson P, Agua-Doce A, Bartolovic K, Russell E, Carr L, Sanchez E, Frampton D, Byott M, Paraskevopoulou S, Crayton E, Meyer C, Vora N, Gkouleli T, Stoltenberg A, Ranieri V, Byrne T, Lewer D, Hayward A, Gilson R, Kelly G, Roberts F, Hatipoglu E. Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers. The Lancet 2020, 396: e6-e7. PMID: 32653078, PMCID: PMC7347344, DOI: 10.1016/s0140-6736(20)31484-7.Peer-Reviewed Original ResearchScalable and robust SARS-CoV-2 testing in an academic center
Aitken J, Ambrose K, Barrell S, Beale R, Bineva-Todd G, Biswas D, Byrne R, Caidan S, Cherepanov P, Churchward L, Clark G, Crawford M, Cubitt L, Dearing V, Earl C, Edwards A, Ekin C, Fidanis E, Gaiba A, Gamblin S, Gandhi S, Goldman J, Goldstone R, Grant P, Greco M, Heaney J, Hindmarsh S, Houlihan C, Howell M, Hubank M, Hughes D, Instrell R, Jackson D, Jamal-Hanjani M, Jiang M, Johnson M, Jones L, Kanu N, Kassiotis G, Kirk S, Kjaer S, Levett A, Levett L, Levi M, Lu W, MacRae J, Matthews J, McCoy L, Moore C, Moore D, Nastouli E, Nicod J, Nightingale L, Olsen J, O’Reilly N, Pabari A, Papayannopoulos V, Patel N, Peat N, Pollitt M, Ratcliffe P, Reis e Sousa C, Rosa A, Rosenthal R, Roustan C, Rowan A, Shin G, Snell D, Song O, Spyer M, Strange A, Swanton C, Turner J, Turner M, Wack A, Walker P, Ward S, Wong W, Wright J, Wu M. Scalable and robust SARS-CoV-2 testing in an academic center. Nature Biotechnology 2020, 38: 927-931. PMID: 32555528, DOI: 10.1038/s41587-020-0588-y.Peer-Reviewed Original ResearchThe T cell differentiation landscape is shaped by tumour mutations in lung cancer
Ghorani E, Reading J, Henry J, Massy M, Rosenthal R, Turati V, Joshi K, Furness A, Ben Aissa A, Saini S, Ramskov S, Georgiou A, Sunderland M, Wong Y, Mucha M, Day W, Galvez-Cancino F, Becker P, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak N, Wilson G, Litchfield K, Conde L, Guerra-Assunção J, Blighe K, Biswas D, Salgado R, Lund T, Bakir M, Moore D, Hiley C, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup S, Hackshaw A, Peggs K, McGranahan N, Chain B, Swanton C, Quezada S. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nature Cancer 2020, 1: 546-561. PMID: 32803172, PMCID: PMC7115931, DOI: 10.1038/s43018-020-0066-y.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerTumor mutational burdenT cellsUntreated non-small cell lung cancerLung cancerCD8 T cell differentiationHigh-dimensional flow cytometryAssociated with poor survivalPersistent antigen exposureCD8 T cellsCD4 T cellsCell lung cancerT cell functionT cell differentiationImmunotherapy outcomesTumor neoantigensUntreated tumorsMutational burdenAntigen exposureTumor mutationsPoor survivalCancer cohortGene signatureTherapeutic manipulationFlow cytometry
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