Emerging TME phenotypes and their characteristics in the HNSCC cohort. A, The heat map displays the immune cell enrichment/depletion in bulk tumor samples from the cohort, as inferred from the expression of cell type–specific markers using ConsensusTME and ssGSEA (single-sample gene set enrichment analysis). Every column corresponds to a sample and every row depicts an immune subpopulation. Samples are clustered on the basis of the predicted enrichment/depletion of immune cell populations. Relevant clinical features, Immunoscore (CD3 and CD8 quantification), PD-L1 staining by IHC (TC – tumor cell and IC – immune cell positivity) and TCR repertoire characteristics (productive clonality, observed richness) are annotated. Five subgroups with distinct immunity emerge: highly cytotoxic and exhausted, PC rich, DC rich, macrophage rich, and immune-excluded. Key clinical characteristics are also annotated. B, Markers of immune exhaustion and TCR repertoire differ significantly among the immune subgroups defined in A. Higher TCR clonality and exhaustion is generally observed in the highly cytotoxic group (exhausted, PC high). The y axis depicts PD-L1 staining measurements by IHC; TBET, EOMES, and TCF7 expression from NanoString; and computed TCR productive clonality and observed richness, respectively. Kruskal–Wallis test P values comparing the five groups are displayed underneath the plots. ****, P < 0.0001; ***, P < 0.001; **, P < 0.01; *, P < 0.05; ns, nonsignificant (P > 0.05). C, Enriched characteristics in the five immunity subgroups. Red circles denote significant enrichments from a Fisher exact test. Dotted circles represent infinite ORs.
ARTICLE ABSTRACTHead and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumor microenvironment (TME) of 162 HNSCC primary tumors of diverse etiologic and spatial origin, through gene expression and IHC profiling of relevant immune proteins, T-cell receptor (TCR) repertoire analysis, and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (i) cytotoxic, (ii) plasma cell rich, (iii) dendritic cell rich, (iv) macrophage rich, and (v) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T-cell infiltration and immune checkpoint expression (e.g., PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history, and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents.
Here we present our findings on the genomic and immune landscape of primary disease in a cohort of 162 patients with HNSCC, benefitting from detailed molecular and clinical characterization. By employing whole-exome sequencing and gene expression analysis of relevant immune markers, TCR profiling, and staining of relevant proteins involved in immune response, we highlight how distinct etiologies, cell intrinsic, and environmental factors combine to shape the landscape of HNSCC primary disease.