Spatially Informed Immuno-Oncology Analysis Framework

This archive provides data resources supporting a spatial transcriptomics study of immune checkpoint blockade in recurrent/metastatic head and neck squamous cell carcinoma (RM-HNSCC). The deposited materials include curated gene expression signatures and processed data products used for external validation in bulk RNA-seq immunotherapy cohorts. These data accompany the associated manuscript and were used to validate spatially informed gene expression signatures derived from spatial tumor–immune architecture. Computational workflows and analysis code are hosted separately and are not included in this archive. Patient-level raw data are not redistributed due to privacy and consent restrictions. Public Validation Datasets All raw datasets used in this pipeline are hosted on ORCESTRA (https://www.orcestra.ca/clinical_icb), a reproducible biomedical data platform. The dataset includes: - Normalized RNA-seq expression profiles (TPM) - Clinical annotations for immune checkpoint blockade (ICB) studies - Associated metadata and processing documentation Private Validation Datasets In addition to publicly available cohorts, selected private bulk RNA-seq datasets were used for external validation of spatially informed gene expression signatures. These datasets consist of pre-treatment whole-transcriptome RNA-seq with associated clinical outcome annotations and were obtained through institutional and collaborative immunotherapy studies.Access to these data is restricted and governed by institutional review board (IRB) approvals and data-sharing agreements. All private cohorts were processed using the same harmonization, normalization, and scoring procedures as public validation datasets. Raw data are not redistributed due to patient privacy and consent restrictions. Gene Expression Signatures To perform signature scoring, association and meta-analysis, this project uses a curated collection of RNA-based gene signatures (e.g., IO-responsive, IO-resistant). IO signatures - https://github.com/bhklab/SignatureSets