Single-cell RNA sequencing in thyroid cancer: a methodological review and thyroid specific dissociation protocol

Thyroid cancer is the most prevalent endocrine malignancy. In contrast to the more prevalent papillary thyroid carcinoma, high grade thyroid carcinomas including poorly differentiated and anaplastic thyroid cancers have a more aggressive clinical behaviour with decreased survival. Multikinase inhibitors can stabilize radioactive iodine-refractory disease, but responses are often not durable. The molecular mechanisms underlying differences among histologic subtypes remain incompletely understood. Single-cell RNA sequencing (scRNA-seq) offers higher-resolution characterization of tumor cellular composition than conventional methods of bulk RNA sequencing, RT-PCR, or multiplex immunohistochemistry, yet its application to thyroid cancer has been limited. This review critically evaluates published scRNA-seq studies in thyroid cancer to identify methodological gaps and presents a detailed, optimized tissue processing protocol for generating high-quality single-cell suspensions from thyroid specimens.MethodsWe conducted a focused search of PubMed and Embase to identify original scRNA-seq studies of primary thyroid tumours published from 2020 to 2025. From 22 studies that profiled primary specimens collected by the authors, we assessed the level of methodological detail reported for tissue dissociation.Informed by these findings, we developed an optimized thyroid tissue dissociation protocol that appears to yield high-viability single-cell suspensions compatible with droplet-based scRNA-seq platforms, however formal validation studies will be required.ResultsMany published studies provided concise descriptions of dissociation methods without technical detail. Our optimized protocol replaces conventional red blood cell (RBC) lysis buffers with an immunomagnetic depletion step, which improved cell recovery and viability compared with standard lysis in limited clinical specimens, although broader benchmarking across sample types is still warranted. When combined with contemporary bioinformatics workflows, these cell preparations enable robust single-cell characterization of thyroid tissues including developmental trajectories, intercellular signalling networks, and immune infiltration with the potential to reveal biomarkers of progression, mechanisms for therapeutic resistance and to identify novel therapeutic targets.ConclusionsThe optimized dissociation protocol is practical and well suited to precious patient-derived thyroid samples. By improving single-cell data quality and cellular representation, it facilitates discovery of biomarkers of disease progression and treatment resistance and supports identification of new therapeutic targets across thyroid cancer subtypes.