Most papillary thyroid microcarcinomas (PTMCs) remain indolent, but a subset shows progression such as new lymph node metastasis or extrathyroidal extension during follow-up. Identifying molecular characteristics that differentiate indolent from progressive PTMCs is crucial for clinical decision-making. This study aimed to explore the proteomic landscape of PTMC and to identify biomarkers that distinguish low-risk PTMC (LR-PTMC) from non-low-risk PTMC (nonLR-PTMC) and larger papillary thyroid carcinoma (>1 cm, PTC>1).

Formalin-fixed paraffin-embedded tumor tissues were analyzed by global proteomics using LC-MS/MS. A total of 185 samples were included: LR-PTMC (N=39), nonLR-PTMC (N=73), and PTC>1 (N=73), with normal thyroid tissue as reference. LC-MS/MS identified 8,055 proteins, of which 7,100 remained after filtering and normalization. Missing values were imputed, and quantile normalization was applied. Differentially expressed proteins (DEPs) were identified using Student’s t-test, followed by functional enrichment analyses to define biological pathways.

Proteomic profiling revealed a largely overlapping background of protein expression across LR-PTMC, nonLR-PTMC, and PTC>1; however, each subgroup displayed distinct biological signatures. NonLR-PTMC exhibited specific enrichment of pathways related to tumor progression and invasion that were not observed in LR-PTMC or PTC>1. Comparative analyses identified sets of upregulated and downregulated proteins that differentiated LR-PTMC from nonLR-PTMC, with 23 pathways enriched in the upregulated group and 11 in the downregulated group. Visualization analyses demonstrated that nonLR-PTMC samples tended to cluster separately from LR-PTMC and PTC>1, supporting their biological distinction. Importantly, these differences suggest that nonLR-PTMC constitutes a subgroup with unique molecular behavior, distinct from both indolent PTMCs and larger papillary thyroid carcinomas.

Global proteomic analysis identified molecular differences that distinguish nonLR-PTMC from LR-PTMC and PTC>1. These findings highlight the potential of proteomic signatures to stratify PTMC patients by risk of progression and support clinical decision-making regarding active surveillance versus surgical management.