Advisor(s)

Anindya Dutta

Committee Member(s)

Eun Young Ahn
John Parant
William Placzek
Zhangli Su

Document Type

Dissertation

Date of Award

6-1-2026

Degree Name

Doctor of Philosophy (PhD)

School

Joint Health Sciences (Interdisciplinary)

Department

Genetics

Abstract

Small noncoding RNAs are increasingly recognized as key regulators of tumor programs, yet the functional contributions of tRNA-derived fragments (tRFs) in tumor progression, particularly in gliomas, remain poorly defined. This dissertation focuses on tRF-3021a, a tRNA-Ala–derived small RNA. In an initial analysis of TCGA small RNA-seq data, we found that higher expression of tRF-3021a, tRF-3009a or tRF-3030a, are associated with poorer prognosis in low-grade glioma patients. The overall goal of this work is to define the biological function of tRF-3021a and elucidate the cellular pathways through which it supports GBM aggressiveness. Using gain-of-function and loss-of-function studies in GBM cell lines, we show that depletion of tRF-3021a suppresses tumor cell growth and invasive behavior and is associated with enhanced apoptosis and increased DNA damage. Importantly, tRF-3021a knockdown markedly reduces global protein synthesis, as measured by puromycin labeling. This occurs earlier than the apoptotic changes and is associated with activation of stress-response pathways. Transcriptomic profiling (RNA-seq) reveals broad remodeling of gene-regulatory programs after tRF-3021a depletion, including signatures consistent with impaired translation being the early and apoptosis the late response. Functional rescue experiments further support this model. Restoring tRF-3021a activity reverses key phenotypes, indicating that tRF-3021a specifically helps maintain a pro-survival, pro-growth state in glioma cells. Finally, we report an unexpected observation that parental tRNAs (including the tRNA source of tRF-3021a) appear increased in RT-based assays after tRF-3021a depletion, raising the possibility that altered tRNA modification or charging states influence tRNA detection and/or translational output. Together, these findings identify tRF-3021a as an oncogenic regulatory small RNA in GBM that supports invasion and proliferation, in part by sustaining efficient protein synthesis and limiting stress-activated, pro-apoptotic programs, and they establish a framework for future mechanistic studies aimed at pinpointing the direct molecular partners and minimal functional determinants of this tRF.

Keywords

Apoptosis;Glioma;Protein Synthesis;tRF-3021a;tRFs;tRNA derived fragments

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