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Table 1_RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring in Staphylococcus aureus.xlsx Zhangfu Li (11080881) Huanmei Liu (24868381) Baicheng Yang (23095213) Shiqing Liu (4262017) Zhenfeng Li (5865902) Shengji Yu (9379768) Microbiology public transcriptomics RefSeq annotation response rewiring RNA–RNA interaction Staphylococcus aureus vancomycin Background<p>Staphylococcus aureus is a major cause of bone, joint and orthopaedic implant-associated infections, providing clinical motivation for understanding adaptive antibiotic-response states. However, the present study is a secondary analysis of public in vitro transcriptomic and RNA-interaction datasets rather than an infection-model or clinical-specimen study. Vancomycin remains important for serious MRSA infections, but adaptive responses to vancomycin may vary across environmental and evolutionary states. Here, we used a framework integrating RefSeq-harmonized transcriptomics and RNA–RNA interaction evidence to examine vancomycin response rewiring.</p>Materials and methods<p>In this secondary analysis, we performed a processed-expression reanalysis of public S. aureus transcriptomic and RNA-interaction datasets, using GSE149213 as the discovery dataset for medium-stratified vancomycin response modeling across cation-adjusted Mueller-Hinton broth (CA-MHB) and Roswell Park Memorial Institute medium supplemented with 10% lysogeny broth (RPMI + 10% LB) in wild-type, media-adapted control and analytically pooled vancomycin-evolved lineages/populations. Candidate identities were harmonized using USA300HOU RefSeq locus-tag annotations, clean GSE254530 was used for conservative cross-dataset assessment, and published RNase III-CLASH data were used to evaluate candidate-associated RNA-interaction evidence.</p>Results<p>In the exploratory GSE149213 processed-expression contrast analysis, analytically pooled vancomycin-evolved lineages/populations retained broad acute responses, with the strongest response-rewiring burden corresponding to the EVO-WT response shift in RPMI + 10% LB; EVO-MAC response shifts were much more limited. RefSeq locus-tag harmonization retained a predefined nine-locus candidate panel for evidence ranking. Conservative GSE254530 assessment provided strict cross-dataset differential-expression support for pyrR only, while glnA was uniquely mapped but not differentially expressed and the remaining seven candidates lacked conservative clean-feature mappings. RNase III-CLASH integration highlighted carbamoyl-P synthase, dihydroorotase and glnA as top-ranked candidate-associated CLASH hotspots. Module-level processed-expression analysis further localized evolved response shifts to RPMI-associated redox/stress, cell-wall/envelope and proteolysis/stress/virulence programs, with translation/ribosome showing a contrasting negative trend.</p>Conclusion<p>This study provides a RefSeq-corrected, evidence-ranked processed-expression map of vancomycin response rewiring in S. aureus. Although the findings remain hypothesis-generating rather than causal, they define prioritized candidate loci, candidate-associated RNA-interaction edges and functional modules for future experimental testing in matched in vitro systems and biologically relevant infection models, including bone- and implant-associated models.</p> 2026-09-14T05:40:29Z Dataset Dataset 10.3389/fmicb.2026.1930249.s001 https://figshare.com/articles/dataset/Table_1_RefSeq-corrected_transcriptomic_and_RNA-interaction_integration_maps_medium-associated_vancomycin_response_rewiring_in_Staphylococcus_aureus_xlsx/33718987 CC BY 4.0