ArticlePDF Available

Distinct Stress‐Dependent Signatures of Cellular and Extracellular tRNA‐Derived Small RNAs (Adv. Sci. 17/2022)

June 2022
Advanced Science 9(17)

DOI:10.1002/advs.202270109

License
CC BY-NC 4.0

Authors:

Massachusetts General Hospital and Harvard Medical School

University of California, Santa Cruz

Show all 19 authorsHide

Extracellular tRNA‐Derived Small RNAs In article number 2200829, Saumya Das and co‐workers provide a comprehensive landscape for the signature of cellular and extracellular tRNA‐derived small RNAs (tDRs) in response to different stressors. They also determine a distinct fragmentation pattern for extracellular tDRs distinct from cellular tDRs and investigate the basis of their biogenesis and stability.

Available via license: CC BY-NC 4.0

Content may be subject to copyright.

www.advancedscience.com

EXTRACELLULAR tRNA-DERIVED SMALL RNAs

In article number 2200829, Saumya Das and co-workers provide a comprehensive landscape

for the signature of cellular and extracellular tRNA-derived small RNAs (tDRs) in response to

different stressors. They also determine a distinct fragmentation pattern for extracellular tDRs

distinct from cellular tDRs and investigate the basis of their biogenesis and stability.

ResearchGate has not been able to resolve any citations for this publication.

ResearchGate has not been able to resolve any references for this publication.

Article

Full-text available

Distinct Stress‐Dependent Signatures of Cellular and Extracellular tRNA‐Derived Small RNAs

April 2022 · Advanced Science

The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA‐derived small RNAs (tDRs) play pivotal roles in stress responses. However, RNA modifications present on tDRs are barriers to ... [Show full abstract] accurately quantifying tDRs using traditional small RNA sequencing. Here, AlkB‐facilitated methylation sequencing is used to generate a comprehensive landscape of cellular and extracellular tDR abundances in various cell types during different stress responses. Extracellular tDRs are found to have distinct fragmentation signatures from intracellular tDRs and these tDR signatures are better indicators of different stress responses than miRNAs. These distinct extracellular tDR fragmentation patterns and signatures are also observed in plasma from patients on cardiopulmonary bypass. It is additionally demonstrated that angiogenin and RNASE1 are themselves regulated by stressors and contribute to the stress‐modulated abundance of sub‐populations of cellular and extracellular tDRs. Finally, a sub‐population of extracellular tDRs is identified for which AGO2 appears to be required for their expression. Together, these findings provide a detailed profile of stress‐responsive tDRs and provide insight about tDR biogenesis and stability in response to cellular stressors. Using AlkB‐facilitated methylation sequencing, this work uncovers the distinct extracellular transfer RNA‐derived small RNA (tDR) fragmentation patterns from cellular tDRs and provides a detailed profile of stress‐responsive tDRs in a variety of cell culture systems and human patients. This work also provides insights about the biogenesis and stability of cellular and extracellular tDRs in response to cellular stressors.

Preprint

Full-text available

Distinct stress-dependent signatures of cellular and extracellular tRNA-derived small RNAs (tDRs)

September 2021

The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may yield novel biomarkers for different diseases, and potentially identify key signaling pathways important for disease progression. tRNAs and tRNA-derived small RNAs (tDRs) comprise one of the most abundant RNA species in cells and have been ... [Show full abstract] associated with cellular stress responses. The presence of RNA modifications on tDRs has been an obstacle for accurately identifying tDRs with conventional small RNA sequencing. Here, we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDR expression in a variety of human and rat cells during common stress responses, including nutritional deprivation, hypoxia, and oxidative stress. We found that extracellular tDRs have a distinct fragmentation signature with a predominant length of 31-33 nts and a highly specific termination position when compared with intracellular tDRs. Importantly, we found these signatures are better discriminators of different cellular stress responses compared to extracellular miRNAs. Distinct extracellular tDR signatures for each profiled stressor are elucidated in four different types of cells. This distinct extracellular tDR fragmentation pattern is also noted in plasma extracellular RNAs from patients on cardiopulmonary bypass. The observed overlap of these patient tDR signatures with the signatures of nutritional deprivation and oxidative stress in our cellular models provides preliminary in vivo corroboration of our findings and demonstrates the potential to establish novel extracellular tDR biomarkers in human disease models.

Article

Abstract P384: Distinct Roles Of Cellular And Extracellular TRNA-derived Small RNAs In Myocardial Fi...

September 2021 · Circulation Research

Heart failure (HF) remains the leading cause of morbidity and mortality in the US, affecting approximately 6.2 million Americans with an anticipated 46% increase in overall prevalence by 2030. Myocardial fibrosis, defined as increased cardiac fibroblast (CF) activation and excessive extracellular matrix (ECM) deposition, is a leading contributor to the progression of adverse heart remodeling that ... [Show full abstract] leads to HF. Despite this clinical importance, no FDA-approved antifibrotic drug is available to prevent the development of HF. There is therefore an urgent need to understand pathways important in myocardial fibrosis that can be targeted with novel therapies. Non-coding RNAs, particularly miRNAs and lincRNAs, have emerged as promising novel biomarkers or therapeutic targets for myocardial fibrosis. As an emerging category of small regulatory non-coding RNAs that was discovered only a decade ago, tRNA-derived small RNAs (tDRs), have been shown to play important roles in cancer and neurological disorders. However, the knowledge of tDRs in myocardial remodeling remains scarce. Here, by using a recently developed tDR sequencing technique, called ARM-seq, we have discovered the unique extracellular tDR fragmentation profile and created an atlas of stress-specific cellular and extracellular tDR signatures in both CFs and cardiomyocytes (CMs). Notably, we identified a nutritional deprivation-induced cellular tRNA-Asp-GTC-3’tDR (cl-tRNA-Asp-GTC-3’tDR) that demonstrates potent antifibrotic effects. In vitro mechanistic studies and transcriptome analysis suggest that the lysosome-localized cl-tRNA-Asp-GTC-3’tDR inhibits CF activation through targeting ECM deposition program and cellular response to TGFβ stimulus and the G-quadruplex motifs are required for its functionality. Meanwhile, a related extracellular tDR derived from the same canonical tRNA, ex-tRNA-Asp-GTC-3’tDR, which has two additional nucleotides at both 5’ and 3’ end of cl-tRNA-Asp-GTC-3’tDR, is specifically enriched in the extracellular vesicles derived from CFs and CMs. Our pilot data suggest that the secretion of ex-tRNA-Asp-GTC-3’tDR may be required for maintaining the homeostasis of CFs and CMs. Importantly, we found that cardiac ischemia significantly decreases the circulating ex-tRNA-Asp-GTC-3’tDR level in both cell culture models and human patients during cardiopulmonary bypass surgery or following acute coronary syndrome. Together, our findings identify a cellular tDR that represents an attractive therapeutic target against myocardial fibrosis and an extracellular tDR with the same origin that has a distinct function and may be translated into novel biomarkers for cardiac ischemia.

Preprint

Full-text available

tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNA...

July 2022

Recent high-throughput sequencing protocols have facilitated increased accuracy in measurements of transfer tRNAs (tRNAs) and tRNA-derived RNAs (tDRs) from biological samples. However, commonly used RNA-seq analysis pipelines overlook special considerations given the unique features of tRNA metabolism. We present tRAX (tRNA Analysis of eXpression), a user-friendly analytic package for streamlined ... [Show full abstract] processing and graphic presentation of small-RNA sequencing data. Here, we apply it to both tRNAs and tDRs from mouse tissues to illustrate the extensive analysis and visualization features. Biologically compelling results demonstrate tRAX as an effective and accessible tool for in-depth characterization of tRNA and tDR transcriptomes.

Last Updated: 21 Aug 2023