Bioinformatics analysis of downstream circRNAs and miRNAs regulated by Runt-related transcription factor 1 in papillary thyroid carcinoma

Jiajie Xu; Guowan Zheng; Haiwei Guo; Kexin Meng; Wanchen Zhang; Ru He; Chuanming Zheng; Minghua Ge

doi:10.21037/gs-22-219

Bioinformatics analysis of downstream circRNAs and miRNAs regulated by Runt-related transcription factor 1 in papillary thyroid carcinoma

Gland Surg. 2022 May;11(5):868-881. doi: 10.21037/gs-22-219.

Authors

Jiajie Xu^{1

2

3}, Guowan Zheng³, Haiwei Guo^{2

3}, Kexin Meng^{2

3}, Wanchen Zhang², Ru He², Chuanming Zheng^{2

3}, Minghua Ge^{1

2

3}

Affiliations

¹ Department of Clinical Medicine, Medical College of Soochow University, Suzhou, China.
² Otolaryngology and Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
³ Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, China.

Abstract

Background: This study sought to clarify the role of Runt-related transcription factor 1's (RUNX1's) regulation of downstream circular ribonucleic acid (circRNA) in the occurrence and development of papillary thyroid carcinoma (PTC) and to explore its mechanism of action.

Methods: The levels of RUNX1 were analyzed in PTC tumor tissues and adjacent non-tumor tissues in different types and at different stages via reverse-transcription quantitative polymerase chain reaction (RT-qPCR). The expression pattern and functional role of RUNX1 were analyzed in PTC cells via RT-qPCR, Western blotting, and Transwell assays. This study explored the differential expression of circRNA and microRNA (miRNA) in cells after knocking down RUNX1 through high-throughput sequencing and examined the changes in downstream signaling pathways through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

Results: RUNX1 was upregulated in PTC tissues, and the expression levels of RUNX1 were related to PTC stage. The knockdown of RUNX1 inhibited the proliferation, migration, and invasion of cells. The high-throughput sequencing results showed that after RUNX1 knockdown, 29 circRNAs (11 upregulated and 18 downregulated) and 20 miRNAs (8 upregulated and 12 downregulated) had the most significant differential expression. The GO analysis of the differential circRNA downstream genes showed that the iron channel-related pathways, endosomal transport, learning, and memory pathways had the largest number of differential genes, and the most significant changes. The KEGG analysis showed that there were 2 pathways with P values <0.05; that is, the glycosaminoglycan synthesis and transcription dysregulation pathways. The GO analysis of the differential miRNA downstream genes showed that the protein binding and cytoplasmic pathways had the largest number of differential genes and the greatest level of difference. The KEGG analysis showed that the tumor-related pathways, phosphatidylinositol-3-kinase and protein kinase B, glycoprotein, cytoskeleton, Ras, and Rap1 pathways changed the most significantly.

Conclusions: RUNX1 is highly expressed in PTC. We conducted high-throughput sequencing to analyze the effect of knocking down RUNX1 on the levels of circRNA and miRNA in PTC. The GO and KEGG analyses revealed that the iron channel-related pathways, endosomal transport, learning and memory, glycosaminoglycan synthesis, and transcriptional disorder-related signaling pathways were enriched.

Keywords: Papillary thyroid carcinoma (PTC); Runt-related transcription factor 1 (RUNX1); bioinformatic analysis; circular RNA (circRNA); microRNA (miRNA).