Lecanemab Engages a Proliferative Human Microglial Program in Alzheimer's Disease, Divergent from Active-Immunisation Signatures: Code, Tables, and Figures

This repository accompanies the manuscript: Dulčić D, Likić R, Strikić D, Dumančić L, Merčep I. "Lecanemab engages a proliferative human microglial program in Alzheimer's disease, divergent from active-immunization signatures." Submitted to Glia.This is a third-party computational re-analysis of two publicly deposited datasets (GSE297665, GSE297667; Albertini, Zielonka, De Strooper et al., Nature Neuroscience, 2025). No new experimental work was performed.The master R script (lecanemab_master_RELEASE.R) reproduces the full analytical pipeline: (1) ingestion of scRNA-seq (.h5ad) and Nova-ST spatial transcriptomic data from GEO; (2) pseudobulk differential expression (edgeR) across four plaque-distance zones (0–25, 25–50, 50–100, 100–250 µm); (3) Reactome pathway enrichment using fgsea; (4) microglial state scoring against Sun 2023 (MG0--MG12) and Green 2024 (Mic.1--Mic.16) taxonomies; (5) Fc-dependent spatial amplification analysis (lecanemab vs LALA-PG); and (6) generation of all publication figures (Figures 1--5 plus supplementary).The deposit also contains curated reference tables, per-zone differential expression and pathway results, sensitivity analyses (S1--S3), and all manuscript figures. All input data are publicly available from NCBI GEO. Scripts require R ≥ 4.3 and standard Bioconductor/CRAN dependencies as detailed in README.md.University of Zagreb School of Medicine, Zagreb, Croatia.