Newly Identified Transcriptomic Biomarkers and Gene Signature of Pathological Complete Response to Induction Chemoimmunotherapy in Locally Advanced Head and Neck Squamous Cell Carcinoma

Neoadjuvant therapies incorporating immune checkpoint inhibitors (ICIs) have shown promise in locally advanced head and neck squamous cell carcinoma (HNSCC). However, biomarkers for pathological complete response (pCR) remain undefined. In the CheckRad-CD8 trial (NCT03426657), we performed RNA sequencing on pre- and post-treatment biopsies from 77 locally advanced HNSCC patients treated with induction chemoimmunotherapy. Of these, 42 patients achieved pCR, while 35 had residual disease (RD). Differentially expressed genes (DEGs) and pathways were identified using DESeq2 and gene set enrichment analysis. Tumor immune microenvironment analysis, utilizing eight RNAseq deconvolution methods, assessed 266 gene signatures and 38 curated immunotherapy signatures. Baseline intratumoral CD8+ T-cell density, stromal tumor lymphocyte infiltration, and combined PD-L1 proportion score were associated with pCR. Pretreatment analysis identified 830 DEGs between pCR and RD, with T and B-cell-related pathways enriched in pCR samples. Logistic regression models indicated the significance of T and B cells and IFN-gamma signaling in predicting pCR. Furthermore, a new CheckRad-7-gene signature, with an AUC of 0.902 in the training cohort, effectively predicted pCR and survival, serving as a robust biomarker for prognosis and treatment response in HNSCC.