Mitoxyperilysis-ARDS: analysis code, six-layer gene signature, and frozen statistical outputs for "Mitoxyperilysis-consistent L4 de-protection in human sepsis-associated ARDS blood: a compartment- and etiology-bounded transcriptomic boundary map" (archive v4; manuscript v2.30)

Abstract

This archive supports the manuscript "Mitoxyperilysis-consistent L4 de-protection in human sepsis-associated ARDS blood: a compartment- and etiology-bounded transcriptomic boundary map" (submission target: Critical Care, BMC; manuscript version v2.30, September 2026). Contents: (1) complete analysis code (R 4.6.1 / Python 3.11) covering score construction (ssGSEA/UCell), four-cohort meta-analysis with Hartung-Knapp inference, leave-one-gene-out robustness, three-method deconvolution, single-cell localization (Scissor, diffusion pseudotime), transcription-factor activity inference (decoupleR/DoRothEA, PROGENy), Mendelian randomization (eQTLGen instruments; ARDS GWAS GCST90700332; FinnGen R13 endpoints), pharmacological layers (DSigDB, CMap/LINCS, AutoDock Vina docking, DGIdb/Open Targets), and permissive-state cross-disease comparisons; (2) the six-layer mitoxyperilysis gene signature (GMT/CSV); (3) frozen statistical outputs (module CSV files plus eTables) serving as the audit anchor for every statistic reported in the manuscript; (4) data-lineage documentation, the pre-specified analysis plan, and contemporaneous analysis logs. Version v4 changes relative to v3: the frozen-output set and analysis code have been extended to cover the R35 extensions (sepsis-prognosis survival analysis in GSE65682; protein-layer coverage screen including pQTL colocalisation and Mendelian randomisation for the HMGCR-RhoA axis; structured plasma/phospho/ATAC screens), the R37 analyses, the R39 Task F.1 NETosis orthogonality benchmark, and the R40 sensitivity-endpoint analyses. The data-lineage document in metadata.zip has been updated accordingly (raw-archive manifest now 228 entries). A read-only metadata verifier for the associated OSF registration is included in the code archive. All frozen values reported in manuscript versions up to v2.30 are represented. Title correspondence: earlier manuscript versions and the associated OSF registration (osf.io/p3wcy, registered 2026-08-28) carry the former title "...in human sepsis-associated ARDS neutrophils: a shared stress program constrained by compartment and etiology". The first revision was wording-level (the compartment claim was narrowed to blood; the subtitle was removed) and altered no data, statistic, direction, or conclusion. The title was subsequently revised twice more, again without any change to the data, statistics, effect directions, frozen outputs, or conclusions: at v2.28 the headline claim was re-scoped from a uniform blood signature to a compartment- and etiology-bounded boundary map, the description of which was already reported, with the composite MAS score moved to a secondary readout in the abstract and the L4 arm named as the discriminating signal; and at v2.29 the modality name "mitoxyperilysis" was restored to the headline, with the v2.28 boundary-map framing retained as the subtitle. The OSF registration at osf.io/p3wcy was not retro-edited; the divergence between the submission title and the registered title is disclosed in the registered amendment osf.io/2qkg3 (doi:10.17605/OSF.IO/2QKG3, 2026-09-12) and in the manuscript itself. All primary datasets are publicly available (GEO accessions GSE66890, GSE32707, GSE10474, GSE76293, GSE235046, GSE200848, GSE326212, GSE145926, GSE151263, GSE167363, GSE188288, GSE65682; PRIDE PXD060437; Metabolomics Workbench ST002738; GWAS summary statistics via GWAS Catalog GCST90700332, FinnGen R13 and eQTLGen official portals) and are NOT redistributed here. GWAS summary statistics are not redistributed because FinnGen and eQTLGen distribute them under their own access terms; use the official portals. This record is the fourth version of a continuously versioned archive; the concept DOI 10.5281/zenodo.22135916 always resolves to the latest version, and the manuscript cites the concept DOI.