Re-Analysis of Public Transcriptomes Identifies a Candidate Histone-Cluster Signal in Eutopic Endometrium: A Hypothesis-Generating Link to Chronic Pelvic Pain

Abstract

Background Endometriosis is a leading cause of chronic pelvic pain (CPP), but the public transcriptomic datasets analysed here contain no pain phenotype, links to CPP are therefore hypothesis-generating. Methods We re-analysed GSE153739 (four endometriosis, three controls) and tested replication in GSE51981 (77 cases, 34 disease-free controls). Non-reproducible differential-expression results from the original submission were removed. Both cohorts were rebuilt from source processed matrices. Histone-cluster scores were modelled with menstrual-cycle and proliferation covariates, and ranked enrichment was tested before and after histone-gene depletion. A separate ion-channel analysis was pre-specified before execution. Results Histone scores were higher in endometriosis in GSE153739 (β = 1.108, P = 0.047) and GSE51981 (β = 0.321, P = 0.0025; phase-adjusted β = 0.394, P = 0.00021). In GSE51981 the effect was concentrated in proliferative-phase endometrium (β = 0.665, P = 0.00083), with a disease-by-phase interaction (P = 0.020). S-phase or proliferation-PC1 adjustment attenuated the effect below nominal significance. In phase-adjusted analyses, SLE enrichment had q = 0.038, whereas NET formation was not enriched (q =0.73); removing clustered histones abolished enrichment in GSE51981 and reversed NET enrichment to negative. The pre-specified ion-channel endpoint was positive (phase-adjusted β = 0.240, P = 8 × 10−6; voltage-gated potassium NES = 1.550, q = 0.013), but the histone and ion-channel scores both covaried with proliferation measures and the same array-level technical axis. Conclusion A reproducible, proliferative-phase-concentrated histone-cluster signal is present in eutopic endometrium, but its biological and technical components cannot be separated in these data. Histone-rich KEGG annotations should not be interpreted as independent pathways. The data do not establish extracellular histone release, NETosis, or a causal mechanism for pelvic pain.