Single-Cell Transcriptome Analysis Reveals Inter-Tumor Heterogeneity in Bilateral Papillary Thyroid Carcinoma

Abstract

BackgroundThe tumor microenvironment (TME) plays a pivotal role in cancer progression in papillary thyroid carcinoma (PTC), yet the composition and the phenotype of cells within the TME in bilateral PTC are poorly understood.MethodsWe performed unbiased transcriptome-wide single-cell RNA sequencing (scRNA-seq) analysis on 29,561 cells from 3 pairs of bilateral PTC and 1 non-tumor thyroid sample. The results of the analysis were validated by a large-scale bulk transcriptomic dataset deposited in The Cancer Genome Atlas (TCGA) database.ResultsOur integrative analysis of thyroid follicular cells revealed 42 signaling pathways enriched in malignant follicular cells, including cytokine–cytokine receptor interaction, PI3K/Akt signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and tumor necrosis factor (TNF) signaling pathway. A 6-gene signature (CXCL3, CXCL1, IL1A, CCL5, TNFRSF12A, and IL18) in the cytokine–cytokine receptor interaction pathway was constructed to predict the prognosis of patients with PTC, with high risk scores being associated with decreased overall survival [hazard ratio (HR) = 3.863, 95% CI = 2.233−6.682, p < 0.001]. Gene set variation analysis (GSVA) indicated that the pathways enriched in bilateral PTC were significantly different, indicating great heterogeneity in bilateral PTC, even with the same BRAF V600E mutation. Comprehensive analysis of T cells revealed that the proportion of CD8+ tissue-resident memory T cells expressing IFNG decreased in tumor samples with advanced N stage. Within the myeloid compartment, the ratio of suppressive M2-like to pro-inflammatory M1-like macrophages increased with advanced disease stage, which was confirmed in the bulk dataset using transcriptomic profiles. In addition, we also identified numerous biologically critical interactions among myeloid cells, T cells, and follicular cells, which were related to T-cell recruitment, M2-like macrophage polarization, malignant follicular cell progression, and T-cell inhibitory signaling.ConclusionOur integrative analyses revealed great inter-tumor heterogeneity within the TME in bilateral PTC, which will offer assistance for precise diagnosis and treatment.

Development and validation of potential molecular subtypes and signatures of thyroid carcinoma based on aging-related gene analysis

“…BRAF gene mutations are prominent in thyroid cancer, with an incidence exceeding 40%, followed closely by N-RAS and H-RAS mutations [35], consistent with the analysis of the top 3 mutations in our high-risk group. Proteins driven by mutations in the Braf gene encode proteins that activate downstream mitogenactivated protein kinase (MAPK) signaling pathways, promoting malignant tumor progression and recurrence risk [36,37].…”

Exploring the advances of single-cell RNA sequencing in thyroid cancer: a narrative review

“…During the advanced disease stage, a decrease in IFNG-expressing CD8+ tissue-resident memory T cells is observed, coupled with an increased ratio of suppressive M2-to-pro-inflammatory M1-like macrophages [25]. Several key biological interactions among myeloid cells, T cells, and follicular cells have been detected, related to T-cell recruitment, M2-like macrophage polarisation, malignant follicular cell progression, and T-cell inhibitory signalling [25].…”

“…During the advanced disease stage, a decrease in IFNG-expressing CD8+ tissue-resident memory T cells is observed, coupled with an increased ratio of suppressive M2-to-pro-inflammatory M1-like macrophages [25]. Several key biological interactions among myeloid cells, T cells, and follicular cells have been detected, related to T-cell recruitment, M2-like macrophage polarisation, malignant follicular cell progression, and T-cell inhibitory signalling [25]. Of particular interest is the potential regulatory role of fibroblasts in immune cell functions via the Macrophage Migratory Inhibition Factor (MIF) signalling pathway in the TME, promoting thyroid cancer development [15].…”

The Immune Landscape of Papillary Thyroid Cancer in the Context of Autoimmune Thyroiditis

“…An initial comprehensive analysis of CD8+ TRM cells, as another subset of TILs, in PTC samples, revealed a lower proportion of this population in the more advanced stage of disease, consistent with an anti-tumor phenotype [ 112 , 113 ], but further work is required to better understand their prognostic value.…”