{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE279nnn/GSE279017/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279017"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Spatial transcriptomic analysis of head and neck squamous cell carcinoma reveals novel regulators of hybrid epithelial-to-mesenchymal transition","description":"Head and neck squamous cell carcinoma (HNSCC) is characterized by a high degree of intra- and inter-tumoral heterogeneity. Here we use spatial transcriptomics (ST) to profile both HPV-positive and HPV-negative HNSCC, uncovering distinct patterns of spatial organization of malignant cells and the surrounding tumor microenvironment across groups of tumors. First, we find that HPV-positive HNSCC is characterized by high cellular density in all cellular compartments with distinct expression of hypoxia, senescence, and cell cycle-associated genes in the malignant compartment. In HPV-negative HNSCC, we find two distinct spatial patterns of a partial epithelial-to-mesenchymal transition (p-EMT) program. One pattern is spatially associated with fibroblasts, characterized by p-EMT at the leading edge of tumor nests (“p-EMT edge”), and mediated by TGFB-signaling. The other pattern features high p-EMT expression in the core of tumor nests (“p-EMT core”). In p-EMT core tumors, we observe high co-localization of p-EMT cells with an inflammatory response program including neutrophils and macrophages, as well as differential expression of distinct ligands, including OSM. In vitro experiments demonstrate that OSM can induce the p-EMT state in multiple HNSCC models. Together these findings suggest that multiple p-EMT phenotypes exist across HPV-unrelated HNSCC and are mediated by distinct cell-to-cell signaling mechanisms, highlighting potential novel therapeutic vulnerabilities.","dates":{"publication":"2026/06/21"},"accession":"GSE279017","cross_references":{"GSM":["GSM8559688","GSM8559677","GSM8559689","GSM8559678","GSM8559679","GSM8559684","GSM8559673","GSM8559685","GSM8559674","GSM8559675","GSM8559686","GSM8559676","GSM8559687","GSM8559680","GSM8559681","GSM8559670","GSM8559682","GSM8559671","GSM8559672","GSM8559683"],"GPL":["34295"],"GSE":["279017"],"taxon":["Homo sapiens"]}}