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RNA-seq analysis of U251 cells following tRF-3021a knockdown at 8 and 48 hours

ABSTRACT: tRNA-derived fragments (tRFs) are relatively recently discovered small RNAs implicated in gene-regulatory processes in diverse biological contexts, but there have been few reports of clear phenotypic roles for these small RNAs in cancer progression. High expression of the 3' tRFs tRF-3009a, tRF-3021a, and tRF-3030a is associated with poor overall survival in low-grade glioma. In glioblastoma cells, these tRFs enhance invasion and migration, while tRF-3021a is uniquely required for cell proliferation, suppression of apoptosis, and maintenance of global protein synthesis. This RNA-seq study profiles transcriptomic changes following tRF-3021a knockdown in U251 cells at early and late time points (8 hours and 48 hours)

ORGANISM(S): Homo sapiens

PROVIDER: GSE335248 | GEO | 2026/09/25

REPOSITORIES: GEO

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Project description:Context: Papillary thyroid cancer (PTC) is the most common thyroid cancer with dramatically increasing worldwide. Accurate diagnosis is crucial to avoid unnecessary overtreatment for low-risk patients, but the currently available markers are still insufficient. tRNA-derived fragments (tRFs) are emerging as a new class of small non-coding RNAs due to their potential roles as novel biomarkers and therapeutic targets in cancer. However, their involvement in papillary thyroid carcinoma (PTC) is still unclear. Objectives: This study was performed to identify differentially expressed tRFs in PTC and investigate the role of serum tRFs to discriminate PTC from nodular goiters (NGs).Methods and Materials: tRF expression profiles were measured in pooled sera from patients with PTCs (n=6), NGs (n=6) and healthy subjects (n=6) using high-throughput sequencing (cohort1). One selected tRF candidate was validated in the same individual samples (cohort1) by qRT-PCR. The confirmed tRF was further validated in a larger second cohort including patients with PTCs (n=30), NGs (n=20) and healthy individuals (n=18).Results: Our sequencing results showed that circulating tRFs were differentially expressed in patients with PTC compared with those with NG and healthy people. After the validation in individual samples, tRF-Pro-AGG-018 was confirmed as differentially elevated in serum samples of patients with PTC. These results were further confirmed in a larger second cohort. Moreover, tRF-Pro-AGG-018 exhibited good diagnostic performance with a sensitivity of 0.7222 and a specificity of 0.8846 for PTC and it was associated with several targeted genes of PTC. Conclusions: Our study identified that the serum tRFs were differentially expressed in PTC compared with NG and healthy individuals. Notably, circulating tRF-Pro-AGG-018 was found to have a significant elevation in patients with PTC and exhibited good diagnostic performance with relatively high sensitivity and specificity for PTC. Our findings suggest tRFs might serve as novel circulating biomarkers in predicting patients with PTC, which may prevent unnecessary thyroid surgeries for low-risk and benefit from optimal

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RNA-seq analysis of U251 cells following tRF-3021a knockdown at 8 and 48 hours

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