Identification of potential LncRNAs as papillary thyroid carcinoma biomarkers based on integrated bioinformatics analysis using TCGA and RNA sequencing data

• Published in: Scientific reports Vol. 13; no. 1; p. 4350
• Main Authors: Feng, Jia-Lin, Zheng, Wen-Jie, Xu, Le, Zhou, Qin-Yi, Chen, Jun
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.03.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/67; Bioinformatics; Biomarkers; Gene Expression Regulation, Neoplastic; Genes; Genomes; Humanities and Social Sciences; Humans; Lymph nodes; Metastases; multidisciplinary; Non-coding RNA; Papillary thyroid cancer; Papillary thyroid carcinoma; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Science; Science (multidisciplinary); Sequence Analysis, RNA; Thyroid; Thyroid cancer; Thyroid Cancer, Papillary - diagnosis; Thyroid Cancer, Papillary - genetics; Thyroid Cancer, Papillary - pathology; Thyroid Neoplasms - diagnosis; Thyroid Neoplasms - genetics; Thyroid Neoplasms - pathology
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-30086-0

The roles and mechanisms of long non-coding RNAs (lncRNAs) in papillary thyroid cancer (PTC) remain elusive. We obtained RNA sequencing (RNA-seq) data of surgical PTC specimens from patients with thyroid cancer (THCA; n = 20) and identified differentially expressed genes (DEGs) between cancer and cancer-adjacent tissue samples. We identified 2309 DEGs (1372 significantly upregulated and 937 significantly downregulated). We performed Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment, and protein–protein interaction network analyses and screened for hub lncRNAs. Using the same methods, we analyzed the RNA-seq data from THCA dataset in The Cancer Genome Atlas (TCGA) database to identify differentially expressed lncRNAs. We identified 15 key differentially expressed lncRNAs and pathways that were closely related to PTC. Subsequently, by intersecting the differentially expressed lncRNAs with hub lncRNAs, we identified LINC02407 as the key lncRNA. Assessment of the associated clinical characteristics and prognostic correlations revealed a close correlation between LINC02407 expression and N stage of patients. Furthermore, receiver operating characteristic curve analysis showed that LINC02407 could better distinguish between cancerous and cancer-adjacent tissues in THCA patients. In conclusion, our findings suggest that LINC02407 is a potential biomarker for PTC diagnosis and the prediction of lymph node metastasis.