Five pathophysiological Alzheimer’s disease subtypes detected with unsupervised clustering of CSF proteomics

Abstract Background We previously identified three CSF proteomic Alzheimer’s disease (AD) subtypes: one with increased amyloid metabolism and aberrant neuronal plasticity, one with innate immune activation and one with blood‐brain barrier dysfunction. We studied their replicability in another cohort, and whether increasing the number of proteins (from 556 to 1059) would enable detecting more subtypes. Method We selected 419 AD individuals with abnormal CSF abeta42 and 187 controls (normal cognition and normal AD biomarkers) from Alzheimer center Amsterdam studies. With 16‐plex TMT‐MS we detected 3987 proteins in CSF, of which we clustered 1059 proteins with complete observations that were associated with AD (all p<.05). Subtypes were compared on all 2906 proteins with at least 10 observations per subgroups. Potential upstream drivers of molecular subtypes were identified with ENRICHR. Result We found 5 subtypes with distinct protein profiles, of which three subtypes were highly concordant with our previously observed subtypes (figure1: subtype 1a, 2a and 2b) and two were new (1b and 1c). Compared to controls, subtype 1a, 1b and 1c had high levels of neuronal plasticity proteins, and subtype 2a and 2b had low levels of plasticity proteins. Thirty‐one proteins were increased in all subtypes (figure 2). Subtype 1a individuals (n=137, 32%) also showed increased amyloid processing. Their 827 proteins associated with REST and SUZ12 as potential upstream drivers. Subtype 1b individuals (n=124, 30%) also showed increased levels of inflammation proteins. Their 988 proteins converged on SOX2 as potential upstream driver. Subtype 1c individuals (n=24,6%), also showed proteasome dysfunction. Their 517 proteins were associated with TAF1 and MYC as potential upstream drivers. Subtype 2a individuals (n=78, 19%) showed increased levels of 469 proteins, of which 45% is expressed by the choroid plexus. These converged on NFE2L2. Subtype 2b individuals (n=56, 13%) showed high levels of 649 proteins that associated with blood‐brain barrier (BBB) leakage. These proteins converged on ERG1 and ESR1 as potential upstream drivers. Conclusion In this new dataset we replicated three AD subtypes, and detected two new subtypes. Subtypes differed on plasticity proteins, immune activation, choroid plexus function and BBB function. Each AD subtypes may require a different treatment.