Functional Analysis of Novel Small Non-Coding RNAs Derived from Transfer RNAs in Neuronal Stress Responses: Relevance as Biomarkers and Therapeutics for Neurodegeneration

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disease characterised by the loss of motor neurons in the brain and spinal cord. The aetiology of the disease remains poorly understood and to date, there is no cure or effective treatment options. Emerging studies suggest important roles of small non-coding RNAs (sncRNAs) in the pathogenesis of ALS. Of particular interest is a recently discovered class of sncRNAs called transfer RNA (tRNA)-derived small RNAs (tsRNAs). These have been found to regulate a wide range of biological processes including translation, gene expression and neuronal survival. In a series of studies, our group identified angiogenin, a tsRNA-generating enzyme, as a candidate susceptibility- and stress-response gene in ALS, indicating that defects in tsRNA production may promote neurodegeneration. However, the full spectrum of tsRNAs and their regulatory roles in ALS remain largely unknown. 

This study used a combination of functional in vitro studies, transcriptomics and proteomics to perform a comprehensive analysis of the genome-wide regulation of stress response by tsRNAs in primary neurons. Functional interrogation of specific ALS-associated tsRNAs demonstrated that although these are produced in neurons in response to various disease-relevant stresses they do not efficiently impact on nascent protein synthesis or neuronal survival under such conditions. Systems-wide analysis of gene and protein expression suggests that 5’tiRNA^Gly-GCC, a stress-induced ALS-associated tsRNA, fine-tunes neuronal gene expression at the post-transcriptional and translational level by regulating translation initiation, ribosome biogenesis and mRNA stability. Finally, the repertoire of tsRNAs and other sncRNAs was profiled in cellular models of neurodegenerative diseases using small RNA-seq, which identified a subgroup of tsRNAs, tRF-3s, as potential novel regulators of gene expression in ALS and neurodegeneration. Together, this work provides novel insight into the genome-wide regulation of stress responses by tsRNAs and their potential as biomarkers and therapeutic targets of ALS.