Related Experiment Video
Updated: Jun 20, 2026
Development of an Insert Co-culture System of Two Cellular Types in the Absence of Cell-Cell Contact
Published on: July 17, 2016
Profiling tRNA-derived fragments in LPS-induced microglia and their influence on immune response
Burak Ibrahim Arioz1, Leman Binokay1, Huseyin Kocakusak1
1Izmir Biomedicine and Genome Center, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey.
Abstract:
The resident macrophages of the brain, microglia, react to immunological responses and preserve homeostasis in the central nervous system. Microglia play a critical role in neuroinflammation, which occurs in neurological and neurodegenerative diseases. Microglial responses are associated with neurodegenerative diseases, autoimmune diseases, and cancer, and therefore require strict regulation. Transfer RNA-derived fragments (tRFs) are small non-coding regulatory RNA molecules generated from the cleavage of transfer RNAs. tRFs have recently emerged as one of the key regulators of gene expression and cellular function in various biological processes. Understanding the content of tRFs altered in microglia due to LPS exposure may provide insights into the mechanisms involved in disease pathogenesis, where neuroinflammation plays a role. We used next-generation sequencing to determine tRF profiles of three different fractions (lysate, extracellular vesicles, and extracellular vesicles-free supernatant) of LPS-induced microglial cells. A total of 345 tRFs were differentially expressed across these fractions after LPS stimulation, including 13 DE-tRFs shared by all three compartments. Gene Ontology analysis of these 13 tRFs suggests their potential involvement in the inflammatory responses of microglia. Among the 13 consistently dysregulated DE-tRFs, tDR-1:33-Glu-CTC-1-M2 was selected for preliminary candidate-level assessment based on its consistent differential expression across all three fractions in our NGS data and previous reports linking this fragment to neuroinflammatory contexts.Increased expression pattern of tDR-1:33-Glu-CTC-1-M2 was further confirmed in lysate samples of LPS-induced microglial cells via RT-qPCR. Inhibition of tDR-1:33-Glu-CTC-1-M2 attenuated LPS-induced cytokine expression and release in microglia, supporting an association between this candidate tRF and inflammatory readouts in this model.
Insights
Transfer RNA-derived fragments (tRFs) regulate gene expression in microglia. This study identified specific tRFs, including tDR-1:33-Glu-CTC-1-M2, involved in microglial inflammatory responses to LPS stimulation.
Area of Science:
- Neuroscience
- Molecular Biology
- Immunology
Background:
- Microglia, the brain's resident macrophages, are crucial for central nervous system homeostasis and neuroinflammation.
- Dysregulated microglial responses are implicated in neurodegenerative diseases, autoimmune disorders, and cancer.
- Transfer RNA-derived fragments (tRFs) are emerging regulators of gene expression and cellular functions.
Purpose of the Study:
- To investigate the alterations in tRF profiles within microglia upon lipopolysaccharide (LPS) exposure.
- To identify specific tRFs involved in LPS-induced microglial inflammatory responses.
- To explore the role of a candidate tRF, tDR-1:33-Glu-CTC-1-M2, in microglial inflammation.
Main Methods:
- Next-generation sequencing (NGS) was employed to profile tRFs in three cellular fractions (lysate, extracellular vesicles, supernatant) of LPS-treated microglia.
- Gene Ontology (GO) analysis was performed on differentially expressed tRFs (DE-tRFs).
- Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and functional inhibition assays were used to validate and assess the role of a specific tRF.
Main Results:
- A total of 345 tRFs were differentially expressed in LPS-induced microglia.
- Thirteen DE-tRFs were consistently found across all three analyzed fractions.
- GO analysis suggested these 13 tRFs are involved in microglial inflammatory responses.
- The tRF tDR-1:33-Glu-CTC-1-M2 showed consistent differential expression and its inhibition attenuated LPS-induced cytokine production.
Conclusions:
- LPS stimulation significantly alters tRF expression profiles in microglia.
- Specific tRFs, notably tDR-1:33-Glu-CTC-1-M2, play a role in regulating microglial inflammatory responses.
- These findings provide insights into the molecular mechanisms underlying neuroinflammation and potential therapeutic targets.
