Q: How would you summarize your study for a lay audience?
Cells contain helper molecules called transfer RNAs (tRNAs), which carry building blocks (amino acids) to make proteins. These tRNAs can be broken down into smaller pieces called tRNA-derived RNAs (tsRNAs or tDRs) that have new jobs - to help cells deal with stress and challenging situations.
In this study, we focused on one specific tDR, called tRNA-Asp-GTC-3'tDR, which becomes more abundant during stress. tRNA-Asp-GTC-3'tDR is present at baseline in kidney cells and increases in response to disease-related stress signals in cell culture and several mouse models of kidney diseases. Importantly, its levels are also higher in human conditions like preeclampsia and early kidney disease.
tRNA-Asp-GTC-3'tDR helps protect kidney cells by regulating a critical process called autophagy, where cells break down and reuse their own parts. Blocking tRNA-Asp-GTC-3'tDR in kidney disease models led to more kidney damage, including cell death, inflammation, and scarring.
To test if boosting this tDR could help, we developed a way to increase its levels in mouse kidneys. Mice had more kidney protection with less scarring, inflammation, and injury when this tDR was present at higher levels.
We also learned that the tDR's unique folded shape, called a G-quadruplex, is essential for its protective effect. This shape helps it bind to proteins that manage autophagy, making it a potential new target for kidney disease treatments in the future.
Q: What question were you investigating?
We sought to determine the regulation and function of the novel tRNA-Asp-GTC-3'tDR that increases markedly with stress in different cell types and is expressed at high levels at baseline in metabolically active tissues and cells.
Q: What methods or approach did you use?
We developed new tools to assess its biogenesis, reagents to silence this molecule selectively using machine learning approaches and deliver/increase its levels. These tools allow precise control of its levels to investigate its role and therapeutic potential in cell culture and disease models.
Q: What did you find?
We found that the hypoxia-responsive tRNA-Asp-GTC-3'tDR maintains cellular homeostasis in kidney cells by regulating autophagic flux and plays a key role in the stress response. The levels of tRNA-Asp-GTC-3'tDR increased acutely in animal models and human cell cultures to enhance autophagic flux and protect against cellular injury, inflammation and fibrosis.
Q: What are the implications?
We identified a promising RNA molecule that could be therapeutically targeted to treat patients with kidney diseases, such as chronic kidney disease.
Q: What are the next steps?
We are developing platforms and tools to study the therapeutic potential of this tDR in kidney and heart disease. These new tools will help determine safety, durability and any toxicity of treatments. Additionally, we are developing Cas13-based RNA editing tools to enhance the expression of the endogenous tDR, a far more efficient way to manipulate the cell's own tDR.
Authorship: In addition to Li and Das, Mass General Brigham authors include Lingfei Sun, Cuiyan Xin, Tian Hao, Prakash Kharel, Priyanka Gokulnath, Chunyang Xiao, Hanna Y. Wang, Emeli Chatterjee, Seungbin Yim, Leo B. Ren, Michail Spanos, Haobo Li, Oluwaseun Akeju, Pavel Ivanov and Joseph V. Bonventre.
Paper cited: Li, G., et al. "A hypoxia-responsive tRNA-derived small RNA confers renal protection via RNA autophagy." Science. DOI: 10.1126/science.adp5384
Funding: This work was supported by grants from the American Heart Association (23CDA1045944, 20CDA35310184 and 24SCEFIA1253853), the National Institutes of Health (R21DK137432, R01DK072381, AG077040, UG3CA241687, R01GM126150, R01GM146997, NHLBI R35HL150807, NCATS UG3TR002878, NIDDK R21DK137432, R01DK39773, R01DK072381 and R00HD096125), the Preeclampsia Foundation Canada Vision Grant 2021 and the National Institutes of Health/National Cancer Institute (P30CA33572).
Disclosures: Ravi V. Shaw has equity ownership in Thryv Therapeutics. Shaw is a co-inventor on pending patents or disclosures on cardiometabolic disease and RNA biomarkers. Akeju is a consultant and holds equity in Reversal Therapeutics. Bonventre is an inventor on KIM-1 patents assigned to Mass General Brigham. Bonventre is a consultant to Sarepta, Mitsubishi-Tanabe, GentiBio and Praxis and has equity interests in Renalytix, DxNow, Oisin, VeriNano, Autonomous, Medical Devices, Pacific Biosciences, Medibeacon and Cascade Medical Systems. Das is a founding member and has equity and consulting agreements for Thryv Therapeutics and Switch Therapeutics, neither of which is relevant to this study. Li and Das. are co-inventors on a U.S. provisional patent application (WO2024264035A2) relating to tsRNA/tDR generation and engineering technology filed by Mass General Brigham.
