BackgroundGene expression is dysregulated in Alzheimer’s disease (AD) patients, both in peripheral blood and post mortem brain. We investigated peripheral whole-blood gene (co)expression to determine molecular changes prior to symptom onset.MethodsRNA was extracted and sequenced for 65 cognitively healthy F-PACK participants (65 (56–80) years, 34APOE4non-carriers, 31APOE4carriers), at baseline and follow-up (interval: 5.0 (3.4–8.6) years). Participants received amyloid PET at both time points and amyloid rate of change derived. Accumulators were defined with rate of change ≥ 2.19 Centiloids. We performed differential gene expression and weighted gene co-expression network analysis to identify differentially expressed genes and networks of co-expressed genes, respectively, with respect to traits of interest (APOE4status, amyloid accumulation (binary/continuous)), and amyloid positivity status, followed by Gene Ontology annotation.ResultsThere were 166 significant differentially expressed genes at follow-up compared to baseline inAPOE4carriers only, whereas 12 significant differentially expressed genes were found only inAPOE4non-carriers, over time. Among the significant genes inAPOE4carriers, several had strong evidence for a pathogenic role in AD based on direct association scores generated from the DISQOVER platform:NGRN,IGF2,GMPR,CLDN5,SMIM24. Top enrichment terms showed upregulated mitochondrial and metabolic pathways, and an exacerbated upregulation of ribosomal pathways inAPOE4carriers compared to non-carriers. Similarly, there were 33 unique significant differentially expressed genes at follow-up compared to baseline in individuals classified as amyloid negative at baseline and positive at follow-up or amyloid positive at both time points and 32 unique significant differentially expressed genes over time in individuals amyloid negative at both time points. Among the significant genes in the first group, the top five with the highest direct association scores were as follows:RPL17-C18orf32,HSP90AA1,MBP,SIRPB1, andGRINA. Top enrichment terms included upregulated metabolism and focal adhesion pathways. Baseline and follow-up gene co-expression networks were separately built. Seventeen baseline co-expression modules were derived, with one significantly negatively associated with amyloid accumulator status (r2=  − 0.25,p= 0.046). This was enriched for proteasomal protein catabolic process and myeloid cell development. Thirty-two follow-up modules were derived, with two significantly associated withAPOE4status: one downregulated (r2=  − 0.27,p= 0.035) and one upregulated (r2= 0.26,p= 0.039) module. Top enrichment processes for the downregulated module included proteasomal protein catabolic process and myeloid cell homeostasis. Top enrichment processes for the upregulated module included cytoplasmic translation and rRNA processing.ConclusionsWe show that there are longitudinal gene expression changes that implicate a disrupted immune system, protein removal, and metabolism in cognitively intact individuals who carryAPOE4or who accumulate in cortical amyloid. This provides insight into the pathophysiology of AD, whilst providing novel targets for drug and therapeutic development.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13195-023-01242-5.