Papillary thyroid carcinoma (PTC) is less aggressive when associated with lymphocytic thyroiditis (LT), even in the presence of oncogenic BRAF, including smaller tumours, less lymph node involvement, and reduced extrathyroidal extension (1). To investigate possible immune mechanisms underlying this association, we compared the tumour microenvironment of PTC-BRAF with and without LT using single-cell RNA sequencing (scRNA-seq). Single-cell libraries were generated from fresh and fixed tumour samples with post-dissociation viability >70% using the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq 6000. We analysed scRNA-seq data from 11 PTC-BRAF tumours, including four with LT (one publicly available sample) and seven without LT. Downstream analyses included quality control, batch correction, dimensionality reduction, and differential gene expression analysis.
PTC-BRAF tumours without LT were characterised by abundant neutrophils, the predominant myeloid population. Thyrocytes from these tumours showed increased expression of the neutrophil-recruiting chemokine ECRG4, while neutrophils exhibited oncogenic transcriptional programmes associated with adverse clinical outcomes. In contrast, thyrocytes with LT demonstrated increased MHC-II antigen-presentation, consistent with effective immune surveillance. Both thyrocytes and macrophages with LT showed enrichment of interferon gamma response pathways. In tumours with LT, T cells displayed a highly organised, antigen-driven immune environment characterised by coordinated T–B cell interactions, germinal centre activity, and increased checkpoint molecule expression, reflecting active immune engagement rather than dysfunction. Conversely in tumours without LT, T cells exhibited disorganised, stress-adapted immune states associated with pro-tumorigenic transcriptional programmes, irreversible terminal differentiation (‘exhaustion’), and enhanced myeloid trafficking.
Collectively, these findings are consistent with improved clinical outcomes being associated with active immune surveillance in tumours with LT; whereas in the absence of LT, adverse features included myeloid infiltration and exhausted T cells within a stress-adapted immune microenvironment. Furthermore, we identify previously under-recognised myeloid population and transcriptomic features that represent novel therapeutic targets in treatment-refractory differentiated thyroid cancer.