The study reports a comparative subcellular proteomics workflow developed to map protein localisation in human brain tissue. The method was applied to the dorsolateral prefrontal cortex, enabling proteome-wide interrogation of subcellular distribution rather than relying solely on bulk protein abundance. This spatially informed proteomic strategy is positioned to reveal intracellular remodelling associated with neurodegenerative pathology and resilience.
The analysis used dorsolateral prefrontal cortex samples from 75 individuals selected to represent a spectrum of clinical and pathological states across Alzheimer's disease and resilience. The cohort design allowed modelling of localisation changes across disease progression and resilience phenotypes, permitting identification of proteins with altered subcellular distribution linked to disease state.
Using comparative subcellular fractionation and proteomic analysis, the authors modelled protein localisation across the cohort. This approach provides a quantitative readout of where proteins are enriched within cellular compartments in tissue samples. The pipeline enables detection of proteome-wide spatial reorganisation that may not be apparent from whole-tissue abundance measurements.
Across the cohort, the authors identified 217 disease-associated localisation shifts. These localisation changes were enriched for functional categories including endolysosomal pathways, intracellular trafficking, and RNA processing. The enrichment pattern points to broad intracellular remodelling affecting vesicle and membrane trafficking systems as well as RNA-related machinery in association with the Alzheimer's disease–resilience spectrum.
Notably, many of the strongest localisation candidates exhibited only modest differences in whole-tissue protein abundance. This observation underscores the limitation of conventional abundance-based proteomics for uncovering disease biology that manifests primarily as spatial reorganisation rather than net change in protein levels.
The subcellular proteomics workflow enabled resolution of tau proteoforms within insoluble aggregates extracted from tissue. Detection of distinct tau species in insoluble fractions provides spatial and biochemical context for pathological tau, complementing existing knowledge about tau aggregation in Alzheimer's disease and demonstrating the method's ability to interrogate insoluble, pathology-associated proteoforms.
The authors validated selected localisation findings in tissue. They demonstrated co-localisation of CSNK1A1 with pathological tau, supporting a spatial association between this kinase and tau aggregates in affected cortex. Additionally, the study identified an unexpected neuronal localisation for SCAI, a protein previously associated with cancer biology and not characterised in human brain tissue. The finding for SCAI illustrates the discovery potential of subcellular proteomics to reveal novel protein localisations in the central nervous system.
Findings emphasize that disease-relevant biology can be encoded in the spatial distribution of proteins rather than in altered total abundance. The detection of 217 localisation shifts—many without large abundance changes—highlights the added value of subcellular resolution for studies of neurodegeneration. By providing insight into intracellular trafficking, endolysosomal function, RNA processing, and the spatial context of tau proteoforms, the approach can reveal mechanisms and candidate proteins not accessible to bulk proteomic surveys.
The preprint was posted on August 21, 2026. Funding acknowledgements reported include Alzheimer’s Research UK, the National Institute on Aging, the National Institute of Neurological Disorders and Stroke, and the UK Medical Research Council. The authors declared competing interests for some contributors, including sponsored research funding and consulting roles; those organisations had no involvement in this study. Other authors declared no competing interests.
In sum, this population-scale subcellular proteomic study of dorsolateral prefrontal cortex across 75 individuals reveals widespread intracellular remodelling on the Alzheimer's disease–resilience spectrum. With 217 localisation shifts enriched for endolysosomal, trafficking, and RNA-processing pathways, and with spatial resolution of tau proteoforms and validated co-localisation of CSNK1A1 and neuronal localisation of SCAI, the work demonstrates that subcellular spatial proteomics can reveal disease biology not captured by whole-tissue abundance measures.