2024
Spatial transcriptomics in inflammatory skin diseases using GeoMx digital spatial profiling: a practical guide for applications in dermatology
Cho C, Haddadi N, Kidacki M, Woodard G, Shakiba S, Yıldız-Altay Ü, Richmond J, Vesely M. Spatial transcriptomics in inflammatory skin diseases using GeoMx digital spatial profiling: a practical guide for applications in dermatology. JID Innovations 2024, 100317. DOI: 10.1016/j.xjidi.2024.100317.Peer-Reviewed Original ResearchDigital spatial profilingInflammatory skin diseaseGeoMx Digital Spatial ProfilerSkin diseasesDiscoid lupus erythematosusNanoString GeoMx Digital Spatial ProfilingImmune milieuImmune microenvironmentLichen planusLupus erythematosusSingle cell RNA sequencingAberrant inflammationCell RNA sequencingSkin disease pathogenesisDisease pathogenesisManufacturer's guidelinesIndicators of diseaseDiseaseSpatial transcriptomics platformSkinTissue processing
2021
Discovering dominant tumor immune archetypes in a pan-cancer census
Combes A, Samad B, Tsui J, Chew N, Yan P, Reeder G, Kushnoor D, Shen A, Davidson B, Barczak A, Adkisson M, Edwards A, Naser M, Barry K, Courau T, Hammoudi T, Argüello R, Rao A, Olshen A, Consortium T, Spitzer M, Fong L, Nelson A, Kumar R, Lee J, Burra A, Hsu J, Hackett C, Tolentino K, Sjarif J, Johnson P, Shao E, Abrau D, Lupin L, Shaw C, Collins Z, Lea T, Corvera C, Nakakura E, Carnevale J, Alvarado M, Loo K, Chen L, Chow M, Grandis J, Ryan W, El-Sayed I, Jablons D, Woodard G, Meng M, Porten S, Okada H, Tempero M, Ko A, Kirkwood K, Vandenberg S, Guevarra D, Oropeza E, Cyr C, Glenn P, Bolen J, Morton A, Eckalbar W, Cai C, Zhan J, Davis K, Kelley R, Chapman J, Atreya C, Patel A, Daud A, Ha P, Diaz A, Kratz J, Collisson E, Fragiadakis G, Erle D, Boissonnas A, Asthana S, Chan V, Krummel M. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell 2021, 185: 184-203.e19. PMID: 34963056, PMCID: PMC8862608, DOI: 10.1016/j.cell.2021.12.004.Peer-Reviewed Original ResearchConceptsTumor immune microenvironmentIndividual tumorsTumor gene expression patternsCancer immunityImmune microenvironmentImmune compositionImmune systemTumor biologyUnique immuneTissue of originFlow cytometryCancer typesDriver mutationsImmune organizationDominant patternStandardized protocolTumorsSignificant heterogeneityCancerUniversity of CaliforniaTissueGene expression patternsCommon patternTherapyImmune