Comparative transcriptomic and immune profiling identifies a shared molecular identity in clear cell odontogenic carcinoma and hyalinizing clear cell carcinoma
Year: 2026
Type: software
Abstract: This capsule reproduces the spatial transcriptomic analysis pipeline for CCOC, HCCC, and seven comparator head-and-neck/soft-tissue tumor types, profiled via NanoString GeoMx Digital Spatial Profiler (Whole Transcriptome Atlas) across 80 FFPE samples from 78 patients (1,192 tumor AOIs post-QC). The pipeline includes GeoMx data QC and TMM normalization (standR), PCA, differential expression (limma-voom with duplicateCorrelation), gene set enrichment analysis (fgsea against MSigDB collections), PROGENy pathway activity inference, drug-target nomination against the Open Targets Platform. Outputs include the heatmaps, volcano plots, PCA projections, GSEA/PROGENy visualizations, and drug-target plots presented in the associated manuscript. Environment: R 4.5.2 with standR, limma, fgsea, msigdbr, progeny, scater, and SpatialExperiment.
Source: Code Ocean
Authors: Helen X. Hou, Annie Li, Bidish K. Patel, Emily E. Ackerman, Tom Bisson, Samantha Flynn, Samyukta Singh, Afrah M. Ahmed, Navkiran Deol, Camron Rivera, Yasusei Kudo, Chloe Bertolus, Ajiravudh Subarnbhesaj, Antonio Villanueva, Karla Rubio, Peter M. Richieri, Liron Bar-Peled, David T. Ting, William C. Faquin, Maria J. Troulis, Miguel N. Rivera, A. John Iafrate
Institutions: Massachusetts General Hospital, Institute of Photonics and Human Health Frontier, Tokushima University, Tokushima University, Sorbonne Université, Assistance Publique – Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Khon Kaen University, Harvard University, Beth Israel Deaconess Medical Center
Language: English
Subfield: Oral Surgery
Field: Dentistry
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7204481137