2024
Histologic and Genomic Analysis of Conjunctival SCC in African and American Cohorts Reveal UV Light and HPV Signatures and High Tumor Mutation Burden
Gleber-Netto F, Nagarajan P, Sagiv O, Pickering C, Gross N, Ning J, Yeshi M, Mitku Y, Tetzlaff M, Esmaeli B. Histologic and Genomic Analysis of Conjunctival SCC in African and American Cohorts Reveal UV Light and HPV Signatures and High Tumor Mutation Burden. Investigative Ophthalmology & Visual Science 2024, 65: 24. PMID: 38597722, PMCID: PMC11008748, DOI: 10.1167/iovs.65.4.24.Peer-Reviewed Original ResearchConceptsHigh-risk human papillomavirusTumor mutational burdenMutational burdenHistological featuresHigh risk human papillomavirus statusConjunctival squamous cell carcinomaHigh tumor mutational burdenDensity of CD8+PD-L1 expressionTumor-infiltrating lymphocytesCD3+ cellsTumors of patientsSquamous cell carcinomaWhole-exome sequencingPotential treatment strategySCC subtypeThicker tumorsPD-L1CD8+Cell carcinomaHuman papillomavirusCutaneous SCCGenomic alterationsCancer Genome AtlasTreatment strategies
2018
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Network T, Caesar-Johnson S, Demchok J, Felau I, Kasapi M, Ferguson M, Hutter C, Sofia H, Tarnuzzer R, Wang Z, Yang L, Zenklusen J, Zhang J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Cho J, DeFreitas T, Frazer S, Gehlenborg N, Getz G, Heiman D, Kim J, Lawrence M, Lin P, Meier S, Noble M, Saksena G, Voet D, Zhang H, Bernard B, Chambwe N, Dhankani V, Knijnenburg T, Kramer R, Leinonen K, Liu Y, Miller M, Reynolds S, Shmulevich I, Thorsson V, Zhang W, Akbani R, Broom B, Hegde A, Ju Z, Kanchi R, Korkut A, Li J, Liang H, Ling S, Liu W, Lu Y, Mills G, Ng K, Rao A, Ryan M, Wang J, Weinstein J, Zhang J, Abeshouse A, Armenia J, Chakravarty D, Chatila W, de Bruijn I, Gao J, Gross B, Heins Z, Kundra R, La K, Ladanyi M, Luna A, Nissan M, Ochoa A, Phillips S, Reznik E, Sanchez-Vega F, Sander C, Schultz N, Sheridan R, Sumer S, Sun Y, Taylor B, Wang J, Zhang H, Anur P, Peto M, Spellman P, Benz C, Stuart J, Wong C, Yau C, Hayes D, Parker J, Wilkerson M, Ally A, Balasundaram M, Bowlby R, Brooks D, Carlsen R, Chuah E, Dhalla N, Holt R, Jones S, Kasaian K, Lee D, Ma Y, Marra M, Mayo M, Moore R, Mungall A, Mungall K, Robertson A, Sadeghi S, Schein J, Sipahimalani P, Tam A, Thiessen N, Tse K, Wong T, Berger A, Beroukhim R, Cherniack A, Cibulskis C, Gabriel S, Gao G, Ha G, Meyerson M, Schumacher S, Shih J, Kucherlapati M, Kucherlapati R, Baylin S, Cope L, Danilova L, Bootwalla M, Lai P, Maglinte D, Van Den Berg D, Weisenberger D, Auman J, Balu S, Bodenheimer T, Fan C, Hoadley K, Hoyle A, Jefferys S, Jones C, Meng S, Mieczkowski P, Mose L, Perou A, Perou C, Roach J, Shi Y, Simons J, Skelly T, Soloway M, Tan D, Veluvolu U, Fan H, Hinoue T, Laird P, Shen H, Zhou W, Bellair M, Chang K, Covington K, Creighton C, Dinh H, Doddapaneni H, Donehower L, Drummond J, Gibbs R, Glenn R, Hale W, Han Y, Hu J, Korchina V, Lee S, Lewis L, Li W, Liu X, Morgan M, Morton D, Muzny D, Santibanez J, Sheth M, Shinbrot E, Wang L, Wang M, Wheeler D, Xi L, Zhao F, Hess J, Appelbaum E, Bailey M, Cordes M, Ding L, Fronick C, Fulton L, Fulton R, Kandoth C, Mardis E, McLellan M, Miller C, Schmidt H, Wilson R, Crain D, Curley E, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Thompson E, Yena P, Bowen J, Gastier-Foster J, Gerken M, Leraas K, Lichtenberg T, Ramirez N, Wise L, Zmuda E, Corcoran N, Costello T, Hovens C, Carvalho A, de Carvalho A, Fregnani J, Longatto-Filho A, Reis R, Scapulatempo-Neto C, Silveira H, Vidal D, Burnette A, Eschbacher J, Hermes B, Noss A, Singh R, Anderson M, Castro P, Ittmann M, Huntsman D, Kohl B, Le X, Thorp R, Andry C, Duffy E, Lyadov V, Paklina O, Setdikova G, Shabunin A, Tavobilov M, McPherson C, Warnick R, Berkowitz R, Cramer D, Feltmate C, Horowitz N, Kibel A, Muto M, Raut C, Malykh A, Barnholtz-Sloan J, Barrett W, Devine K, Fulop J, Ostrom Q, Shimmel K, Wolinsky Y, Sloan A, De Rose A, Giuliante F, Goodman M, Karlan B, Hagedorn C, Eckman J, Harr J, Myers J, Tucker K, Zach L, Deyarmin B, Hu H, Kvecher L, Larson C, Mural R, Somiari S, Vicha A, Zelinka T, Bennett J, Iacocca M, Rabeno B, Swanson P, Latour M, Lacombe L, Têtu B, Bergeron A, McGraw M, Staugaitis S, Chabot J, Hibshoosh H, Sepulveda A, Su T, Wang T, Potapova O, Voronina O, Desjardins L, Mariani O, Roman-Roman S, Sastre X, Stern M, Cheng F, Signoretti S, Berchuck A, Bigner D, Lipp E, Marks J, McCall S, McLendon R, Secord A, Sharp A, Behera M, Brat D, Chen A, Delman K, Force S, Khuri F, Magliocca K, Maithel S, Olson J, Owonikoko T, Pickens A, Ramalingam S, Shin D, Sica G, Van Meir E, Zhang H, Eijckenboom W, Gillis A, Korpershoek E, Looijenga L, Oosterhuis W, Stoop H, van Kessel K, Zwarthoff E, Calatozzolo C, Cuppini L, Cuzzubbo S, DiMeco F, Finocchiaro G, Mattei L, Perin A, Pollo B, Chen C, Houck J, Lohavanichbutr P, Hartmann A, Stoehr C, Stoehr R, Taubert H, Wach S, Wullich B, Kycler W, Murawa D, Wiznerowicz M, Chung K, Edenfield W, Martin J, Baudin E, Bubley G, Bueno R, De Rienzo A, Richards W, Kalkanis S, Mikkelsen T, Noushmehr H, Scarpace L, Girard N, Aymerich M, Campo E, Giné E, Guillermo A, Van Bang N, Hanh P, Phu B, Tang Y, Colman H, Evason K, Dottino P, Martignetti J, Gabra H, Juhl H, Akeredolu T, Stepa S, Hoon D, Ahn K, Kang K, Beuschlein F, Breggia A, Birrer M, Bell D, Borad M, Bryce A, Castle E, Chandan V, Cheville J, Copland J, Farnell M, Flotte T, Giama N, Ho T, Kendrick M, Kocher J, Kopp K, Moser C, Nagorney D, O’Brien D, O’Neill B, Patel T, Petersen G, Que F, Rivera M, Roberts L, Smallridge R, Smyrk T, Stanton M, Thompson R, Torbenson M, Yang J, Zhang L, Brimo F, Ajani J, Gonzalez A, Behrens C, Bondaruk J, Broaddus R, Czerniak B, Esmaeli B, Fujimoto J, Gershenwald J, Guo C, Lazar A, Logothetis C, Meric-Bernstam F, Moran C, Ramondetta L, Rice D, Sood A, Tamboli P, Thompson T, Troncoso P, Tsao A, Wistuba I, Carter C, Haydu L, Hersey P, Jakrot V, Kakavand H, Kefford R, Lee K, Long G, Mann G, Quinn M, Saw R, Scolyer R, Shannon K, Spillane A, Stretch O, Synott M, Thompson J, Wilmott J, Al-Ahmadie H, Chan T, Ghossein R, Gopalan A, Levine D, Reuter V, Singer S, Singh B, Tien N, Broudy T, Mirsaidi C, Nair P, Drwiega P, Miller J, Smith J, Zaren H, Park J, Hung N, Kebebew E, Linehan W, Metwalli A, Pacak K, Pinto P, Schiffman M, Schmidt L, Vocke C, Wentzensen N, Worrell R, Yang H, Moncrieff M, Goparaju C, Melamed J, Pass H, Botnariuc N, Caraman I, Cernat M, Chemencedji I, Clipca A, Doruc S, Gorincioi G, Mura S, Pirtac M, Stancul I, Tcaciuc D, Albert M, Alexopoulou I, Arnaout A, Bartlett J, Engel J, Gilbert S, Parfitt J, Sekhon H, Thomas G, Rassl D, Rintoul R, Bifulco C, Tamakawa R, Urba W, Hayward N, Timmers H, Antenucci A, Facciolo F, Grazi G, Marino M, Merola R, de Krijger R, Gimenez-Roqueplo A, Piché A, Chevalier S, McKercher G, Birsoy K, Barnett G, Brewer C, Farver C, Naska T, Pennell N, Raymond D, Schilero C, Smolenski K, Williams F, Morrison C, Borgia J, Liptay M, Pool M, Seder C, Junker K, Omberg L, Dinkin M, Manikhas G, Alvaro D, Bragazzi M, Cardinale V, Carpino G, Gaudio E, Chesla D, Cottingham S, Dubina M, Moiseenko F, Dhanasekaran R, Becker K, Janssen K, Slotta-Huspenina J, Abdel-Rahman M, Aziz D, Bell S, Cebulla C, Davis A, Duell R, Elder J, Hilty J, Kumar B, Lang J, Lehman N, Mandt R, Nguyen P, Pilarski R, Rai K, Schoenfield L, Senecal K, Wakely P, Hansen P, Lechan R, Powers J, Tischler A, Grizzle W, Sexton K, Kastl A, Henderson J, Porten S, Waldmann J, Fassnacht M, L. S, Schadendorf D, Couce M, Graefen M, Huland H, Sauter G, Schlomm T, Simon R, Tennstedt P, Olabode O, Nelson M, Bathe O, Carroll P, Chan J, Disaia P, Glenn P, Kelley R, Landen C, Phillips J, Prados M, Simko J, Smith-McCune K, VandenBerg S, Roggin K, Fehrenbach A, Kendler A, Sifri S, Steele R, Jimeno A, Carey F, Forgie I, Mannelli M, Carney M, Hernandez B, Campos B, Herold-Mende C, Jungk C, Unterberg A, von Deimling A, Bossler A, Galbraith J, Jacobus L, Knudson M, Knutson T, Ma D, Milhem M, Sigmund R, Godwin A, Madan R, Rosenthal H, Adebamowo C, Adebamowo S, Boussioutas A, Beer D, Giordano T, Mes-Masson A, Saad F, Bocklage T, Landrum L, Mannel R, Moore K, Moxley K, Postier R, Walker J, Zuna R, Feldman M, Valdivieso F, Dhir R, Luketich J, Pinero E, Quintero-Aguilo M, Carlotti C, Dos Santos J, Kemp R, Sankarankuty A, Tirapelli D, Catto J, Agnew K, Swisher E, Creaney J, Robinson B, Shelley C, Godwin E, Kendall S, Shipman C, Bradford C, Carey T, Haddad A, Moyer J, Peterson L, Prince M, Rozek L, Wolf G, Bowman R, Fong K, Yang I, Korst R, Rathmell W, Fantacone-Campbell J, Hooke J, Kovatich A, Shriver C, DiPersio J, Drake B, Govindan R, Heath S, Ley T, Van Tine B, Westervelt P, Rubin M, Lee J, Aredes N, Mariamidze A, Stuart J, Laird P, Hoadley K, Weinstein J, Peto M, Pickering C, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports 2018, 23: 194-212.e6. PMID: 29617660, PMCID: PMC6002769, DOI: 10.1016/j.celrep.2018.03.063.Peer-Reviewed Original ResearchConceptsChromosomal copy number alterationsSquamous cell carcinomaRAS-MAPK pathwayChromatin modifiersGenomic integrityCopy number alterationsAlternative promotersHuman papillomavirusDNA mutationsPathway networkAberrant methylationCell stemnessHarbor mutationsOxidative damageAtlas studyMesenchymal differentiationCell signatureMutationsMolecular featuresImmune checkpointsImmune therapySquamous carcinomaCell carcinomaImmunoregulatory moleculesTherapeutic approachesThe Integrated Genomic Landscape of Thymic Epithelial Tumors
Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Network T, Ally A, Appelbaum E, Auman J, Balasundaram M, Balu S, Behera M, Beroukhim R, Berrios M, Blandino G, Bodenheimer T, Bootwalla M, Bowen J, Brooks D, Carcano F, Carlsen R, Carvalho A, Castro P, Chalabreysse L, Chin L, Cho J, Choe G, Chuah E, Chudamani S, Cibulskis C, Cope L, Cordes M, Crain D, Curley E, Defreitas T, Demchok J, Detterbeck F, Dhalla N, Dienemann H, Edenfield W, Facciolo F, Ferguson M, Frazer S, Fronick C, Fulton L, Fulton R, Gabriel S, Gardner J, Gastier-Foster J, Gehlenborg N, Gerken M, Getz G, Heiman D, Hobensack S, Holbrook A, Holt R, Hoyle A, Hutter C, Ittmann M, Jefferys S, Jones C, Jones S, Kasaian K, Kim J, Kimes P, Lai P, Laird P, Lawrence M, Lin P, Liu J, Lolla L, Lu Y, Ma Y, Maglinte D, Mallery D, Mardis E, Marra M, Martin J, Mayo M, Meier S, Meister M, Meng S, Meyerson M, Mieczkowski P, Miller C, Mills G, Moore R, Morris S, Mose L, Muley T, Mungall A, Mungall K, Naresh R, Newton Y, Noble M, Owonikoko T, Parker J, Paulaskis J, Penny R, Perou C, Perrin C, Pihl T, Radenbaugh A, Ramalingam S, Ramirez N, Rieker R, Roach J, Sadeghi S, Saksena G, Schein J, Schmidt H, Schumacher S, Shelton C, Shelton T, Shi Y, Shih J, Sica G, Silveira H, Simons J, Sipahimalani P, Skelly T, Sofia H, Soloway M, Stuart J, Sun Q, Tam A, Tan D, Tarnuzzer R, Thiessen N, Van Den Berg D, Vasef M, Veluvolu U, Voet D, Walter V, Wan Y, Wang Z, Warth A, Weis C, Weisenberger D, Wilkerson M, Wise L, Wong T, Wu H, Wu Y, Yang L, Zhang J, Zmuda E, Fujimoto J, Scapulatempo-Neto C, Moreira A, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao M, Marx A, Tsao A, Loehrer P. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell 2018, 33: 244-258.e10. PMID: 29438696, PMCID: PMC5994906, DOI: 10.1016/j.ccell.2018.01.003.Peer-Reviewed Original ResearchConceptsThymic epithelial tumorsEpithelial tumorsWorld Health Organization (WHO) histological subtypeAutoimmune disease myasthenia gravisDisease myasthenia gravisMuscle autoantigensThymic carcinomaMyasthenia gravisAutoimmune diseasesHistological subtypesAdult malignanciesTumoral overexpressionMarked prevalenceTumorsThymomaSubtypesEnrichment of mutationsGenomic landscapeBiological effectsGenomic hallmarksMolecular linkUnique associationAssociationMulti-platform analysisGravis
2016
Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nature Communications 2016, 7: 12601. PMID: 27574101, PMCID: PMC5013636, DOI: 10.1038/ncomms12601.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntineoplastic AgentsCarcinogenesisCarcinoma, Squamous CellDisease ProgressionDNA Mutational AnalysisExome SequencingFemaleGene Expression ProfilingGenomicsHigh-Throughput Nucleotide SequencingHumansKeratosis, ActinicMiceMice, HairlessMolecular Targeted TherapyPrecancerous ConditionsSequence Analysis, RNASkinSkin NeoplasmsUltraviolet RaysConceptsCross-species genomic analysisCross-species identificationCross-species analysisKey genomic changesGenomic analysisGenomic changesTranscriptional driversDistinct precancerous lesionsGenomic driversPotential targetSquamous cell carcinoma developmentMolecular similarityActinic keratosisAccessible modelDiverse sitesCutaneous squamous cell carcinomaHuman samplesSquamous cell carcinomaHairless mouse modelProgression sequenceMouse modelCarcinoma developmentCell carcinomaPrecancerous lesionsCommon treatment
2015
Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer
Neskey DM, Osman AA, Ow TJ, Katsonis P, McDonald T, Hicks SC, Hsu TK, Pickering CR, Ward A, Patel A, Yordy JS, Skinner HD, Giri U, Sano D, Story MD, Beadle BM, El-Naggar AK, Kies MS, William WN, Caulin C, Frederick M, Kimmel M, Myers JN, Lichtarge O. Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer. Cancer Research 2015, 75: 1527-1536. PMID: 25634208, PMCID: PMC4383697, DOI: 10.1158/0008-5472.can-14-2735.Peer-Reviewed Original ResearchConceptsTP53 mutationsDistant metastasisP53 mutationsNeck squamous cell carcinomaSquamous cell carcinomaPoor survival outcomesAggressive tumor behaviorEvolutionary action scoreHigh-risk mutationsLung metastasesPrognostic significanceSurvival outcomesCell carcinomaNeck cancerClinical prognosisHigh incidenceLower riskTumor behaviorDecreased survivalKey cellular pathwaysTumor cellsMetastasisRisk mutationsPatientsTumorsComprehensive genomic characterization of head and neck squamous cell carcinomas
Lawrence M, Sougnez C, Lichtenstein L, Cibulskis K, Lander E, Gabriel S, Getz G, Ally A, Balasundaram M, Birol I, Bowlby R, Brooks D, Butterfield Y, Carlsen R, Cheng D, Chu A, Dhalla N, Guin R, Holt R, Jones S, Lee D, Li H, Marra M, Mayo M, Moore R, Mungall A, Gordon Robertson A, Schein J, Sipahimalani P, Tam A, Thiessen N, Wong T, Protopopov A, Santoso N, Lee S, Parfenov M, Zhang J, Mahadeshwar H, Tang J, Ren X, Seth S, Haseley P, Zeng D, Yang L, Xu A, Song X, Pantazi A, Bristow C, Hadjipanayis A, Seidman J, Chin L, Park P, Kucherlapati R, Akbani R, Casasent T, Liu W, Lu Y, Mills G, Motter T, Weinstein J, Diao L, Wang J, Hong Fan Y, Liu J, Wang K, Todd Auman J, Balu S, Bodenheimer T, Buda E, Neil Hayes D, Hoadley K, Hoyle A, Jefferys S, Jones C, Kimes P, Liu Y, Marron J, Meng S, Mieczkowski P, Mose L, Parker J, Perou C, Prins J, Roach J, Shi Y, Simons J, Singh D, Soloway M, Tan D, Veluvolu U, Walter V, Waring S, Wilkerson M, Wu J, Zhao N, Cherniack A, Hammerman P, Tward A, Sekhar Pedamallu C, Saksena G, Jung J, Ojesina A, Carter S, Zack T, Schumacher S, Beroukhim R, Freeman S, Meyerson M, Cho J, Chin L, Getz G, Noble M, DiCara D, Zhang H, Heiman D, Gehlenborg N, Voet D, Lin P, Frazer S, Stojanov P, Liu Y, Zou L, Kim J, Sougnez C, Gabriel S, Lawrence M, Muzny D, Doddapaneni H, Kovar C, Reid J, Morton D, Han Y, Hale W, Chao H, Chang K, Drummond J, Gibbs R, Kakkar N, Wheeler D, Xi L, Ciriello G, Ladanyi M, Lee W, Ramirez R, Sander C, Shen R, Sinha R, Weinhold N, Taylor B, Arman Aksoy B, Dresdner G, Gao J, Gross B, Jacobsen A, Reva B, Schultz N, Onur Sumer S, Sun Y, Chan T, Morris L, Stuart J, Benz S, Ng S, Benz C, Yau C, Baylin S, Cope L, Danilova L, Herman J, Bootwalla M, Maglinte D, Laird P, Triche T, Weisenberger D, Van Den Berg D, Agrawal N, Bishop J, Boutros P, Bruce J, Averett Byers L, Califano J, Carey T, Chen Z, Cheng H, Chiosea S, Cohen E, Diergaarde B, Marie Egloff A, El-Naggar A, Ferris R, Frederick M, Grandis J, Guo Y, Haddad R, Hammerman P, Harris T, Neil Hayes D, Hui A, Jack Lee J, Lippman S, Liu F, McHugh J, Myers J, Kwok Shing Ng P, Perez-Ordonez B, Pickering C, Prystowsky M, Romkes M, Saleh A, Sartor M, Seethala R, Seiwert T, Si H, Tward A, Van Waes C, Waggott D, Wiznerowicz M, Yarbrough W, Zhang J, Zuo Z, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Yena P, Black A, Bowen J, Frick J, Gastier-Foster J, Harper H, Leraas K, Lichtenberg T, Ramirez N, Wise L, Zmuda E, Baboud J, Jensen M, Kahn A, Pihl T, Pot D, Srinivasan D, Walton J, Wan Y, Burton R, Davidsen T, Demchok J, Eley G, Ferguson M, Mills Shaw K, Ozenberger B, Sheth M, Sofia H, Tarnuzzer R, Wang Z, Yang L, Claude Zenklusen J, Saller C, Tarvin K, Chen C, Bollag R, Weinberger P, Golusiński W, Golusiński P, Ibbs M, Korski K, Mackiewicz A, Suchorska W, Szybiak B, Wiznerowicz M, Burnett K, Curley E, Gardner J, Mallery D, Penny R, Shelton T, Yena P, Beard C, Mitchell C, Sandusky G, Agrawal N, Ahn J, Bishop J, Califano J, Khan Z, Bruce J, Hui A, Irish J, Liu F, Perez-Ordonez B, Waldron J, Boutros P, Waggott D, Myers J, William W, Lippman S, Egea S, Gomez-Fernandez C, Herbert L, Bradford C, Carey T, Chepeha D, Haddad A, Jones T, Komarck C, Malakh M, McHugh J, Moyer J, Nguyen A, Peterson L, Prince M, Rozek L, Sartor M, Taylor E, Walline H, Wolf G, Boice L, Chera B, Funkhouser W, Gulley M, Hackman T, Neil Hayes D, Hayward M, Huang M, Kimryn Rathmell W, Salazar A, Shockley W, Shores C, Thorne L, Weissler M, Wrenn S, Zanation A, Chiosea S, Diergaarde B, Marie Egloff A, Ferris R, Romkes M, Seethala R, Brown B, Guo Y, Pham M, Yarbrough W. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 2015, 517: 576-582. PMID: 25631445, PMCID: PMC4311405, DOI: 10.1038/nature14129.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Squamous CellDNA Copy Number VariationsDNA, NeoplasmFemaleGene Expression Regulation, NeoplasticGenome, HumanGenomicsHead and Neck NeoplasmsHumansMaleMolecular Targeted TherapyMutationOncogenesRNA, NeoplasmSignal TransductionSquamous Cell Carcinoma of Head and NeckTranscription FactorsConceptsNeck squamous cell carcinomaSquamous cell carcinomaCell carcinomaCopy number alterationsMutations of HRASFavorable clinical outcomeFrequent copy number alterationsComprehensive genomic characterizationNumber alterationsFunction TP53 mutationsCancer Genome AtlasSomatic genomic alterationsClinical outcomesLaryngeal tumorsOral cavityFunction alterationsTP53 mutationsCandidate alterationsOncogene PIK3CALoss of TRAF3Novel alterationsCDKN2A inactivationGenome AtlasGenomic alterationsDomain mutations
2014
Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma
Pickering CR, Zhou JH, Lee JJ, Drummond JA, Peng SA, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma. Clinical Cancer Research 2014, 20: 6582-6592. PMID: 25303977, PMCID: PMC4367811, DOI: 10.1158/1078-0432.ccr-14-1768.Peer-Reviewed Original ResearchConceptsAggressive cutaneous squamous cell carcinomaCutaneous squamous cell carcinomaSquamous cell carcinomaCell carcinomaCandidate tumor suppressorNeck squamous cell carcinomaNovel therapeutic targetNovel candidate tumor suppressorTumor suppressorWhole-exome sequencingBone invasionPoor outcomeTherapeutic targetLethal diseaseTumor suppressor geneCarcinomaKMT2C mutationsHigh mutational backgroundGene TP53Mutational landscapePutative linkDriver genesDiseaseMutational spectrumUV exposure
2013
Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers
Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, Zhao M, Alves M, Chang K, Drummond J, Cortez E, Xie TX, Zhang D, Chung W, Issa JP, Zweidler-McKay PA, Wu X, El-Naggar AK, Weinstein JN, Wang J, Muzny DM, Gibbs RA, Wheeler DA, Myers JN, Frederick MJ. Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers. Cancer Discovery 2013, 3: 770-781. PMID: 23619168, PMCID: PMC3858325, DOI: 10.1158/2159-8290.cd-12-0537.Peer-Reviewed Original ResearchConceptsOral squamous cell carcinomaCaspase-8Integrative Genomic CharacterizationGenomic alterationsSquamous cell carcinomaComprehensive genomic analysisTumor suppressor geneCopy number changesSomatic driversKey genesGenomic analysisCell carcinomaGene expressionNotch pathwayGenomic characterizationSuppressor geneDriver pathwaysCopy numberPoint mutationsGenesSomatic eventsNumber changesSurvival of patientsOSCC cell linesSubset of head