tRNA regulatory ecosystem states shape tissue and circulating small-RNA landscapes in gastric cancer.

Background: Gastric cancer is a heterogeneous disease shaped by the co-evolution of malignant epithelial programs, stromal remodeling, and immune contexture. Transfer RNA (tRNA) regulation sits at a strategic junction in this biology: it governs translational capacity and selectivity while generating tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs)-a family of regulatory small RNAs detectable in both tissue and blood. Objective: We asked whether the coordinated machinery responsible for tRNA transcription, maturation, modification, charging, and cleavage defines biologically meaningful gastric cancer ecosystem states, and whether a corresponding circulating small-RNA phenotype can be detected across independent cohorts of chronic atrophic gastritis (CAG), early gastric cancer (EGC), and gastric cancer (GC). Methods: We integrated transcriptomic, genomic, proteomic, and tissue small-RNA data across complementary gastric cancer series and localized the program in single-cell expression maps. The clinical arm comprised independent serum samples from CAG, EGC, and GC participants. Results: A 70-gene tRNA-regulatory program resolved three ecosystem states (TRES-1, TRES-2, and TRES-3). TRES-3 exhibited high tRNA-regulatory activity coupled with proliferative and DNA-repair protein expression, whereas TRES-1 was enriched for receptor-signaling and cell-cycle-restraint proteins. These states also differed in copy-number alterations and non-synonymous variant burden at the program level. Direct tissue small-RNA profiling revealed a marked expansion of tRF output and repertoire breadth in TRES-2 and TRES-3, with state-specific tRF classes, parent-tRNA modules, and exact sequences. A shared set of 446 exact tRF sequences connected the tissue and serum catalogues. In an independent gastric cancer series, the three-state architecture aligned with ACRG molecular subtypes, RNA cargo selection, extracellular vesicle release, and stress-response programs. Single-cell mapping placed tRNA-regulatory activity across epithelial, stromal, and immune compartments. In our serum cohort, the 14-30-nt fraction declined from 47.4% in CAG to 37.8% in EGC and 33.6% in GC, while the 31-40-nt fraction rose from 52.6% to 62.2% and 66.4% (absolute Spearman rho = 0.791; BH-adjusted P = 0.0112; exact-permutation P = 0.0214). Conclusion: tRNA regulation defines gastric cancer ecosystem states with distinct genomic, proteomic, and tissue small-RNA correlates. In our serum cohort, the reciprocal shift in circulating tRF/tiRNA length composition-a decline in the 14-30-nt fraction and a rise in the 31-40-nt fraction-parallels the transition from CAG to EGC to GC. These findings establish a testable molecular framework for paired tissue-serum validation and position circulating tRF/tiRNA architecture as a candidate readout of gastric cancer ecosystem biology.