Biology subjects

Gregory, R. I.

Publications and source records attributed to Gregory, R. I..

4 recordsLinked to original sources

bioRxiv2026

Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis

tRNAs play a critical role in protein synthesis, influencing mRNA translation dynamics to shape proteomes. Emerging evidence links dysregulated tRNA activity to cancer progression, with tRNA-Arg-TCT identified as an oncogenic driver when ectopically overexpressed in non-malignant cells. The requirement of endogenous tRNA-Arg-TCT in cancer biology, however, remains untested. Moreover, considering that the tRNA-Arg-TCT family comprises six genes in humans, the importance of an individual tRNA isodecoder in cancer remains unknown. Here, we find elevated levels of tRNA-Arg-TCT-4-1 isodecoder are associated with poor patient prognosis across multiple cancer types. We demonstrate that, using different antisense RNA strategies, specific inhibition of tRNA-Arg-TCT-4-1 suppresses the growth of glioblastoma (GBM) and liposarcoma (LPS) cancer cells. Mechanistically, we find that tRNA-Arg-TCT-4-1 inhibition leads to a codon-biased remodeling of mRNA translation and the proteome, preferentially suppressing expression of growth-promoting genes and pathways encoded by mRNAs enriched in arginine AGA codons. Strikingly, intratumoral delivery of an antisense oligonucleotide (ASO) targeting tRNA-Arg-TCT-4-1 suppresses tumor growth and extends survival in mouse xenograft experiments performed using either a human LPS cell line or a patient-derived soft tissue sarcoma model. This study provides a foundation for targeting tRNA dysregulation as a novel therapeutic approach for cancer. One Sentence SummaryThis study identifies tRNA-Arg-TCT-4-1 as a new anti-cancer therapeutic target and demonstrates that an antisense oligonucleotide (ASO) targeting this tRNA effectively suppresses tumorigenesis and extends survival in mouse xenograft models.

cancer biology↗

bioRxiv2025

EXOSC10-mediated pre-tRNA surveillance safeguards neuron survival

tRNA quality control pathways have been identified in yeast, whereby aberrant and hypomodified mature tRNAs are targeted for 5-3 degradation by the rapid tRNA decay (RTD) pathway involving the Xrn1 and Rat1/Xrn2 exonucleases, whereas aberrant precursor tRNAs (pre-tRNAs) are targeted for 3-5 degradation by the nuclear surveillance pathway involving the RNA Exosome. However, the pathways controlling tRNA and pre-tRNA degradation in mammals have not yet been defined and the relevance of pre-tRNA surveillance pathways for normal cell physiology remains largely unknown. The RNA Exosome comprises a core of nine non-catalytic subunits (EXOSC1-9) to which the distinct, DIS3 and EXOSC10, 3-5 exonucleases associate. Here we find that EXOSC10 deficiency leads to accumulation of unspliced precursor tRNAs (pre-tRNAs) in mouse embryonic stem cells (ESCs) and is required for pre-tRNA decay in biochemical assays. Pre-tRNA overexpression causes diminished motor neuronal survival in a mouse ESC differentiation model. Our results identify a pre-tRNA decay pathway that links Exosome deficiency with neuron survival and provides insight into possible pathological mechanisms underlying human neurodevelopmental disorders caused by mutations in Exosome subunits and genes involved in tRNA biogenesis. O_LIExosc10 is required for pre-tRNA surveillance in cells and degradation in biochemical assays C_LIO_LIPre-tRNA expression inhibits survival of neurons C_LIO_LIPre-tRNA decay pathway links exosome deficiency with neurodevelopmental disorders C_LI

molecular biology↗

bioRxiv2024

ADAT2/3-mediated tRNA editing promotes cancer cell growth and tumorigenicity

Transfer RNAs (tRNAs) are subject to various chemical modifications that influence their stability or function. Adenosine to Inosine (A-to-I) editing in the tRNA anticodon at position A34 is an important modification that expands anticodon-codon recognition at the wobble position and is required for normal mRNA translation. The relevance of tRNA editing in cancer remains unexplored. Here we show that the genes encoding the ADAT2/3 deaminase complex, responsible for A-to-I tRNA editing in humans, are commonly amplified and/or overexpressed in several tumor types including liposarcoma (LPS). We find that knockdown of the ADAT complex suppresses LPS cell growth and tumorigenicity. Mechanistically, we find that decreased tRNA editing upon ADAT2 depletion leads to defective translation of a subset of mRNAs. Thus, ADAT-mediated tRNA modification promotes oncogenesis by enhancing the translation of growth promoting mRNAs that are enriched in NNC codons that lack cognate tRNAs and therefore depend on A-I tRNA editing for decoding and mRNA translation. Our results uncover an oncogenic role of tRNA editing and identify ADAT2/3 as a potential new cancer therapeutic target.

cancer biology↗

bioRxiv2024

Mapping multiple RNA modifications simultaneously by proximity barcode sequencing

RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (m6A) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns. However, convenient methods that enable the simultaneous mapping of multiple different RNA marks within the same sample are generally lacking. Here we present EpiPlex RNA modification profiling, a bead-based proximity barcoding assay with sequencing readout that expands the scope of molecular recognition-based RNA modification detection to multiple targets, while providing relative quantification and enabling low RNA input. Measuring signal intensity against spike-in controls provides relative quantification, indicative of the RNA mod abundance at each locus. We report on changes in the modification status of HEK293T cells upon treatment with pharmacological inhibitors separately targeting METTL3, the dominant m6A writer enzyme, and the EIF4A3 component of the exon junction complex (EJC). The treatments resulted in decreased or increased m6A levels, respectively, without effect on inosine levels. Inhibiting the helicase activity of EIF4A3 and EIF4A3 knockdown both cause a significant increase of m6A sites near exon junctions, consistent with the previously reported role of EIF4A3 in shaping the m6A landscape. Thus, EpiPlex offers a reliable and convenient method for simultaneous mapping of multiple RNA modifications to facilitate epitranscriptome studies.

genomics↗