tRNA derived fragment (tRF)-3009 participates in modulation of IFN-α-induced CD4(+) T cell oxidative phosphorylation in lupus patients

BACKGROUND: Accumulating evidence suggests tRNA-derived fragments (tRFs) play important roles in cellular homeostasis. Here we aimed to explore aberrant expression of tRFs in CD4(+) T cells from patients with systemic lupus erythematosus (SLE) and their potential function in the SLE pathogenesis. METHODS: First, small RNA sequencing was performed on CD4(+) T cells from four SLE patients and three healthy controls (HCs). Candidate tRFs were then validated in CD4(+) T cells from 97 SLE patients and their relevant disease controls using qRT-PCR. Then sequencing was used to investigate the profiles of HC-derived CD4(+) T cells transfected with tRF-3009. Lastly, tRF-3009 siRNA or tRF-3009 mimics were transfected into CD4(+) T cells with/without IFN-α. Changes in oxygen consumption rate (OCR), ATP, and ROS production were analyzed. RESULTS: We identified 482 differentially expressed tRFs from SLE CD4(+) T cells and chose tRF-3009 for further analysis due to its upregulation and the positive correlations between its expression and SLEDAI, active lupus nephritis and serum IFN-α levels. In vitro, tRF-3009 over-expressing CD4(+) T cell profiling and putative analysis linked this product to the type I IFN and oxidative phosphorylation (OXPHOS) pathways. Interestingly, IFN-α is capable of inducing ROS and ATP production in CD4(+) T cells, while knockdown of tRF-3009 reversed this process. Overexpression of tRF-3009 in CD4(+) T cells alone was sufficient to upregulate OCR, ROS, and ATP production. CONCLUSIONS: Our study is the first to link aberrant tRF expression and SLE. tRF-3009 may participate in metabolic modulation of IFN-α-induced CD4(+) T cell OXPHOS in lupus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-021-02967-3.