Differential expression profiles and function prediction of tRNA-derived fragments in fibrous dysplasia

Ziji Ling; Na Xiao; Yangjie Li; Hanyu Xie; Tao Xiao; Hongbing Jiang; Yu Fu

doi:10.1016/j.archoralbio.2022.105347

Differential expression profiles and function prediction of tRNA-derived fragments in fibrous dysplasia

Arch Oral Biol. 2022 Mar:135:105347. doi: 10.1016/j.archoralbio.2022.105347. Epub 2022 Jan 7.

Authors

Ziji Ling¹, Na Xiao², Yangjie Li¹, Hanyu Xie¹, Tao Xiao³, Hongbing Jiang², Yu Fu⁴

Affiliations

¹ Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing 210029, China.
² Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing 210029, China.
³ Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China.
⁴ Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing 210029, China. Electronic address: siyu_528@163.com.

PMID: 35026649
DOI: 10.1016/j.archoralbio.2022.105347

Abstract

Objective: Fibrous dysplasia (FD) is a bone disease featuring that normal bone matrix is replaced by fibrous tissue and immature bone tissue. Transfer RNA-derived RNA fragments (tRFs) and tRNA halves (tiRNAs) are types of small non-coding RNA that produced by specific shearing of mature tRNA. Here, we conducted a comparative analysis of the expression of tRFs/tiRNAs in BMSCs and FD BMSCs.

Designs: The differential expression of tRFs/tiRNAs was detected by high-throughput sequencing technique, and validated by qRT-PCR. Bioinformatics analyses including prediction of target genes, gene ontology (GO) enrichment and KEGG pathway analysis and protein-protein interaction (PPI) network analysis were performed.

Results: The results detected 1 significantly upregulated tDR (tRNA-derived small RNA) and 3 downregulated tDRs in FD BMSCs. Predictions of target genes, GO and KEGG pathway analysis indicated that these tRFs were mainly involved in regulation of immune response, osteoclast differentiation, calcium ion transport, apoptotic signaling pathway, cell proliferation and endocrine system development. The PPI network analysis showed that PPP2R5A, ADAMTS1, PPARA, and POLR2C were the most frequently interacted proteins in target genes.

Conclusions: Our findings provided a comprehensive analysis of the expression of tRFs/tiRNAs in FD BMSCs and BMSCs, and they could serve as potential therapeutic targets.

Keywords: Bioinformatics analysis; Fibrous dysplasia; tRNA halves; tRNA-derived fragments.

MeSH terms

Cell Proliferation
Gene Ontology
High-Throughput Nucleotide Sequencing
RNA, Transfer* / genetics
Signal Transduction*

Substances

RNA, Transfer