Biology subjects

Otsubo, K.

Publications and source records attributed to Otsubo, K..

4 recordsLinked to original sources

bioRxiv2026

m1A58 governs two steps of human initiator-methionine tRNA metabolism: maturation and XRN2-mediated decay

N{superscript 1}-methyladenosine at position 58 (m{superscript 1}A58), installed by the TRMT6/TRMT61A complex, is a highly conserved structural modification implicated in tRNA stability and human disease. In yeast, loss of m{superscript 1}A58 disrupts initiator methionine tRNA (tRNA) metabolism through defects in precursor processing and rapid tRNA decay, but whether these mechanisms operate in human cells has remained unclear. Here, using acute degron-mediated depletion of TRMT6 in human HCT116 cells combined with precursor-resolved tRNA sequencing, we show that m{superscript 1}A58 controls two distinct steps of tRNA metabolism. TRMT6 depletion selectively reduces mature tRNA while causing accumulation of precursor species retaining both 5'-leader and 3'-trailer sequences, consistent with impaired maturation. In parallel, the nuclear 5'[->]3' exonuclease XRN2 selectively degrades the residual mature hypomodified tRNA pool without affecting precursor accumulation. Loss of mature tRNA activates the integrated stress response and impairs proliferation, which is restored by XRN2 co-depletion. Together, our findings identify m{superscript 1}A58 as a coordinator of human initiator-tRNA maturation and surveillance, establishing a two-step pathway that maintains tRNA homeostasis in human cells.

biochemistry↗

bioRxiv2025

The mammalian rapid tRNA decay pathway is critical for N⁷-methylguanosine-hypomodified tRNA degradation under physiological conditions

Chemical modifications of transfer RNAs (tRNAs) are integral to their stability and to translation. Loss of N7-methylguanosine (m7G) on specific tRNAs reduces their steady-state abundance and impairs translation in mammals, but whether these decreases reflect active degradation under physiological growth conditions is unresolved. Here, using human HCT116 cells, we show that knockdown of the 5'[->]3' exonuclease, XRN2, restores tRNA levels diminished by METTL1 depletion. Leveraging conditional protein knockdown, we performed time-resolved measurements of mature tRNA levels and directly quantified decay kinetics. We show that in the absence of heat stress, mG-hypomodified tRNAs undergo XRN2-dependent accelerated decay. Finally, partial loss of the Drosophila XRN2 ortholog, Rat1, genetically rescues male sterility of mettl1 mutants, demonstrating organismal relevance. These findings define a conserved constitutive rapid tRNA decay pathway in mammals and indicate inhibition of tRNA decay as a potential therapeutic strategy in disorders caused by tRNA hypomodification.

molecular biology↗

bioRxiv2025

Spatial dynamics of the tumor microenvironment in emerging resistance to targeted therapy in EGFR-mutated NSCLC

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) provide therapeutic benefit in EGFR mutation-positive non-small cell lung cancer, but some individuals develop early resistance. We performed spatial transcriptomics analysis of pre- and posttreatment tumor samples from the same patients to explore the underlying mechanisms of such early resistance. The proportion and activation of fibroblasts increased in association with the development of early resistance, whereas a distinct tumor cell cluster showed activation of tumor necrosis factor- signaling via the NF-{kappa}B pathway even before treatment. Also in the early resistance sample, specific tumor cell clusters interacted with immune and stromal cells. Immature tertiary lymphoid structures (TLSs) were enriched in the early resistance sample, whereas mature TLSs were observed in the long-term response sample. These findings implicate tumor heterogeneity and an inflammatory tumor microenvironment in early EGFR-TKI resistance, providing insight into potential therapeutic strategies to improve treatment outcomes.

cancer biology↗

bioRxiv2023

The role of desmoplakin for neuronal function in the dentate gyrus and anxiety-related behavior

Desmoplakin (Dsp) is a component of desmosomal cell-cell junctions that interacts with the cadherin complex and cytoskeletal intermediate filaments. In addition to its function as an adhesion component, Dsp is involved in various biological processes, such as gene expression, differentiation, and migration. Dsp is specifically expressed in the hippocampal dentate gyrus (DG) in the central nervous system. However, it is unclear how Dsp impacts hippocampal function and its related behaviors. Using an adeno-associated virus knockdown system in mice, we provide evidence that Dsp in the DG maintains hippocampal functions, including neuronal activity and adult neurogenesis, and contributes to anxiolytic-like effects. Dsp protein is mostly localized in mature granule cells in the adult DG. Dsp knockdown in the DG resulted in a lowered expression of an activity-dependent transcription factor FosB, and an increased expression of mature neuronal markers, such as calbindin. In addition, the suppression of Dsp decreases serotonin responsiveness at the DG output mossy fiber synapses and alters adult neurogenic processes in the subgranular zone of the DG. Moreover, DG- specific Dsp knockdown mice showed an increase in anxiety-like behaviors. Taken together, this research uncovers an unexplored function for Dsp in the central nervous system and suggests that Dsp in the DG may function as a regulator to maintain proper neuronal activation and adult neurogenesis, and contribute to the adaptation of emotion-related behavior.

neuroscience↗