RNA Sequencing Reveals Key Genes and Pathways Associated with Thyroid Cancer

BACKGROUND: Molecular distinctions between malignant and benign thyroid lesions remain inadequately characterised, particularly in Indian populations, while preoperative cytology has recognised diagnostic limitations. Transcriptomic profiling may uncover pathways of diagnostic and therapeutic relevance. METHODS: In this prospective study, fresh intraoperative thyroid tissue was obtained from 103 patients undergoing thyroidectomy (83 benign lesions, 20 malignant tumours). Paired-end RNA sequencing (150 bp) on live frozen samples was performed on the Illumina NovaSeq 6000 platform. Differential expression analysis was conducted using DESeq2, with functional enrichment assessed using KEGG and Gene Ontology databases. RESULTS: Thirty-one genes were differentially expressed between malignant and benign lesions (adjusted P ≤ 0.05; |log₂ fold change| ≥ 1), including 24 upregulated and 7 downregulated genes in malignant tissue. Upregulated transcripts were predominantly ribosomal protein–encoding genes, indicating enhanced ribosome biogenesis and translational capacity. Notably, MET and CDH6 were overexpressed among non-ribosomal genes. Downregulated genes included KIT, KDR, BCL2, PHLDA2, MLLT3 and RPS6KA1. Pathway analysis revealed enrichment of ribosome-related pathways with relative suppression of MAPK, PI3K–Akt, Ras, Rap1, focal adhesion and p53 signalling. CONCLUSION: Malignant thyroid lesions demonstrate a distinct transcriptomic signature characterised by enhanced ribosome biogenesis and translational reprogramming, highlighting protein synthesis–associated pathways as potential diagnostic and therapeutic targets. Funding: Indian Council of Medical Research (ICMR) Trial Registration: CTRI/2020/09/027607.