APOE ε4 carriers share immune-related proteomic changes across neurodegenerative diseases, 2025, Shvetcov et al

[forestglip]

APOE ε4 carriers share immune-related proteomic changes across neurodegenerative diseases

Artur Shvetcov, Erik C. B. Johnson, Laura M. Winchester, Keenan A. Walker, Heather M. Wilkins, Terri G. Thompson, Jeffrey D. Rothstein, Varsha Krish, Farhad B. Imam, The Global Neurodegeneration Proteomics Consortium (GNPC), Jeffrey M. Burns, Russell H. Swerdlow, Chad Slawson & Caitlin A. Finney

[Line breaks added]

Abstract
The APOE ε4 genetic variant is the strongest genetic risk factor for late-onset Alzheimer’s disease (AD) and is increasingly being implicated in other neurodegenerative diseases.

Using the Global Neurodegeneration Proteomics Consortium SomaScan dataset covering 1,346 cerebrospinal fluid (CSF) and 9,924 plasma samples, we used machine learning-based proteome profiling to identify an APOE ε4 proteomic signature shared across individuals with AD, frontotemporal dementia (FTD), Parkinson’s disease dementia (PDD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS) and nonimpaired controls. This signature was enriched in pro-inflammatory immune and infection pathways as well as immune cells, including monocytes, T cells and natural killer cells.

Analysis of the dorsolateral prefrontal cortex proteome for 262 donors from the Accelerating Medicines Partnership for AD UPenn Proteomics Study revealed a consistent APOE ε4 phenotype, independent of neurodegenerative pathology, including amyloid-β tau and gliosis for all diseases, as well as TDP-43 in ALS and FTD cases, and α-synuclein in PD and PDD cases.

While systemic proteomic changes were consistent across APOE ε4 carriers, their relationship with clinical and lifestyle factors, such as hypertension and smoking, varied by disease.

These findings suggest APOE ε4 confers a systemic biological vulnerability that is necessary but not sufficient for neurodegeneration, emphasizing the need to consider gene–environment interactions.

Overall, our study reveals a conserved APOE ε4-associated pro-inflammatory immune signature persistent across the brain, CSF and plasma irrespective of neurodegenerative disease, highlighting a fundamental, disease-independent biological vulnerability to neurodegeneration. This work reframes APOE ε4 as a pleiotropic immune modulator rather than an AD-specific risk gene, providing a foundation for precision biomarker development and early intervention strategies across neurodegenerative diseases.

Link | PDF (Nature Medicine) [Open Access]

 

[forestglip]

Nature: 'One potent gene raises risk of Alzheimer’s, Parkinson’s and other brain diseases'

'Massive proteomics database links gene variant APOE4 to chronic inflammation.'

'A gene variant known to increase the risk of Alzheimer’s disease also makes people vulnerable to a host of other age-related brain disorders, from Parkinson’s disease to motor neuron disease. The gene variant, a version of apolipoprotein E called APOE ε4, produces a distinct set of proteins that contribute to chronic inflammation, finds an analysis using the largest proteomics database for neurodegenerative disease.

Neurodegenerative diseases affect more than 57 million people worldwide. Researchers know that people who carry the APOE ε4 variant have an increased risk of developing late-onset Alzheimer’s disease, but studies are beginning to implicate this version, or allele, of APOE in other neurodegenerative diseases.'