领域：学术论文 · 自然科学

The GNPC dataset represents a substantial advancement in neuro­degenerative disease research, by providing a real-world clinical pro­ teomic dataset that comprises over 35,000 (11,270 with APOE genotype) individuals across AD, FTD, PDD, PD, ALS and normal aging from across more than 20 clinical sites in the US, UK and Europe. This enabled us to ask whether the APOE ε4-associated proteomic signature is shared across multiple neurodegenerative diseases. Our results demonstrate that all APOE ε4 carriers, irrespective of neurodegenerative disease, have a unique proteome signature that extends across the plasma and CSF. Unlike prospectively designed cohorts, the GNPC dataset reflects real-world clinical heterogeneity, highlighting the robustness and generalizability of our findings. This signature is associated with pro-inflammatory immune dysregulation and an enrichment for circulating immune cells, including monocytes, memory CD8 and γδ T cells, Tregs and NK cells. This molecular phenotype extends to the brains of APOE ε4 carriers in a similar disease-independent manner and is not associated with the presence of any disease-specific brain pathology. Although all APOE ε4 carriers have a systemic immune-related proteome signature, we find that the relationships between proteins within this signature are uniquely associated with demographic, lifestyle, and clinical variables in a neurodegenerative disease-specific manner. Notably, this suggests that although the biological changes associated with APOE ε4 carriage are essential for neurodegeneration, broadly, interactions with underlying biological vulnerability and the environment may be key for driving the pathogenesis of the specific neurodegenerative disease.

There is evidence that the APOE ε4 genotype is a modern-day example of antagonistic pleiotropy. In younger adults, APOE ε4 is associated with increased survival and fertility in environments with high levels of infectious disease. For example, healthy individuals who are APOE ε4 heterozygotes exhibit heightened cytokine release, increased plasma TNF levels, a more pronounced hyperthermic response and an earlier onset of IL-6 production following immune challenge with TLR2/TLR4/TLR5 ligands or lipopolysaccharide. While this immune response protects younger APOE ε4 carriers from infectious diseases, prolonged states of inflammation and cytokine release are likely deleterious with age. Although this study identified a proteomic signature indicative of a pro-inflammatory phenotype, a limitation is the absence of direct measures of routine inflammatory markers such as C-reactive protein or cytokines. Future studies should incorporate these markers in prospectively designed cohorts to clarify their association with APOE ε4.

To date, the biological effects of APOE ε4 carriage have largely only been studied in the context of AD. A notable finding of our study is that the pro-inflammatory molecular phenotype associated with APOE ε4 extends to individuals with other neurodegenerative diseases, including FTD, PDD, PD and ALS. This raises two key considerations. First, our findings underscore the need to shift focus from the continued identification of genetic risk loci via genome-wide association studies toward functional characterization of established variants. Notably, the absence of a statistically significant association between a variant and a specific disease phenotype does not preclude biological relevance. Despite APOE ε4 being overrepresented in the AD cohort, we observe a consistent molecular signature associated with APOE ε4 across multiple neurodegenerative diseases, highlighting an underrecognized role for this variant beyond AD that may have been overlooked due to its historically strong link with AD risk. Second, our data support reconceptualizing APOE ε4 not only as a disease-specific risk factor but also as a broader susceptibility allele contributing to shared pathogenic mechanisms across neurodegenerative diseases. It remains unclear, however, why APOE ε4 is more strongly associated with AD in terms of prevalence despite exhibiting systemic biological effects across neurodegenerative diseases. One possibility is that interactions between APOE ε4 and additional age-related, environmental, or comorbid factors may selectively amplify neurodegenerative pathways characteristic of AD. Another possibility is that CNS-specific vulnerabilities or cellular contexts (for example, in hippocampal circuits or dopaminergic neurons) modulate how the APOE ε4 inflammatory phenotype manifests clinically. Thus, while APOE ε4 confers a shared biological susceptibility, disease expression likely depends on a combination of genetic background, cellular context(s), and lifetime exposures. Large-scale integrative efforts, such as the GNPC, which harmonize data across distinct disease cohorts into unified datasets, provide a powerful framework for advancing this line of inquiry. By enabling cross-disease comparisons, such efforts may help delineate modifiers that influence why some APOE ε4 carriers develop AD while others remain healthy or develop different neurodegenerative diseases. This has important implications for prognosis and risk stratification in midlife individuals who carry APOE ε4.

A limitation of our study is the absence of validated biomarkers (for example, CSF p-tau217) to confirm clinical diagnoses, which reflects both the nature of the GNPC dataset and global heterogeneity in clinical practice. However, several features mitigate concerns regarding potential misdiagnosis. First, the APOE ε4 signature was derived from nonimpaired individuals. While it is possible that a minority of these nonimpaired individuals harbored asymptomatic pathology (for example, asymptomatic AD), the majority would be free of overt disease, reducing the likelihood of confounding results. Second, the consistent presence of the signature across all APOE ε4 carriers, irrespective of clinical diagnosis, supports its generalizability and suggests it reflects a broader APOE ε4-related biological phenotype rather than disease-specific changes. Finally, we validate our findings using postmortem brain proteomics and histopathology, where diagnostic certainty is highest. Here APOE ε4 status was not associated with hallmark pathologies, including amyloid-β, tau, TDP-43 or α-synuclein, across respective disease groups. This postmortem validation reinforces the robustness of our findings. Future studies would benefit from prospective cohorts incorporating validated CSF or plasma biomarkers to confirm and extend these observations.

An unexpected finding of our study was that plasma neurofilament light (NEFL) levels were lower in APOE ε4 carriers across neurodegenerative diseases, despite NEFL’s growing recognition as a biomarker of neurodegeneration. Prior studies have reported conflicting results— some found no association, another reported increased levels in APOE ε4 carriers, while others using the SomaScan and Simoa assays observed decreased levels, consistent with our findings. These discrepancies may reflect differences in sample size, with studies reporting decreased NEFL levels generally including larger cohorts (~600 to 5,000 participants, and 9,924 in our study). Alternatively, APOE ε4-related blood–brain barrier (BBB) or metabolic dysfunction may alter peripheral clearance of NEFL and affect its plasma or CSF concentration. These results raise important questions about the reliability of NEFL as a stand-alone biomarker and underscore the need for mechanistic studies and a shift toward precision biomarkers that integrate genetic and environmental context.

In our study, key peripheral inflammatory states in APOE ε4 carriers were mirrored in the CNS. Notably, brain proteomics performed using label-free MS orthogonally validated findings from SomaScan-based CSF and plasma analyses. While SomaScan aptamer technology offers high-throughput protein quantification, it is relatively insensitive to proteoform diversity, including post-translational modifications, a limitation when examining signaling pathways and protein networks where such modifications are functionally significant. In contrast, MS enables the detection of broader proteoforms, offering an independent assessment of protein abundance and pathway enrichment. The concordance of APOE ε4-associated protein signatures and enrichment patterns across plasma, CSF and brain proteomic datasets suggests that our findings are not artifacts of platform-specific biases but likely reflect underlying biology. Supporting this interpretation, we observed enrichment of APOE ε4-associated proteins in both hepatocytes and Kupffer cells in the CSF, but only in Kupffer cells and T cells in plasma. This pattern implies that plasma reflects chronic peripheral immune activation, whereas the CSF may capture liver-brain axis-mediated inflammatory signaling in APOE ε4 carriers. Further experimental studies are warranted to validate these mechanisms. Prospective cohort studies incorporating cross-platform, multi-tissue analyses from the same individuals will be essential to confirm and expand upon these observations.

While the exact mechanisms underlying the mirroring of peripheral and central pro-inflammatory states remain unclear, they may involve interactions between pro-inflammatory peripheral immune cells and the BBB. A recent study of individuals with long COVID-19 demonstrated that hyperactive peripheral blood mononuclear cells adhere to the endothelial cells of the BBB, driving inflammation, degradation, and symptoms of brain fog. In support of this, cognitively healthy APOE ε4 carriers exhibit early markers of BBB dysfunction in the hippocampus and medial temporal lobe. As the BBB becomes increasingly compromised, it allows the infiltration of blood-derived proteins and pro-inflammatory immune cells into the brain, contributing to exacerbated neuroinflammation and neurodegeneration. In our study, we identify enriched pro-inflammatory immune cell subpopulations, including nonclassical and intermediate monocytes, memory CD8+ T cells, γδ T cells and NK cells. These immune cell types may represent peripheral blood mononuclear cells that interact with the BBB to promote neurodegeneration in APOE ε4 carriers. Given that APOE ε4 is linked to a shared molecular phenotype across neurodegenerative diseases, this hypothesis is consistent with current understanding. Healthy, nonimpaired APOE ε4 carriers have a systemic pro-inflammatory phenotype (and as we have shown here), early signs of BBB disruption, alterations in brain activity and connectivity, and sleep disturbances, all of which are known to be risk factors for neurodegenerative diseases, broadly. Further supporting this is the recent evidence that vaccinations protect against dementia, including the shingles vaccines Zostavax and Shingrix. Although none of these studies explicitly examined the interactive effects between vaccination status and APOE ε4 genotype, the fact that more than 60% of individuals with dementia are APOE ε4 carriers suggests that APOE ε4 may represent a critical modifier of the observed associations, warranting further investigation. Future studies in human disease-relevant models, such as patient stem cell-derived organoids, are needed to further elucidate these mechanisms.

翻译考点：
考点1：:“expression”根据语境翻译为“临床表现”更加合适
考点2：“vulnerability”根据语境翻译为“易感性”更加合适
考点3:“APOE ε4 carriage”推荐翻译为“APOE ε4基因携带者/APOE ε4基因携带状态”，勿翻译为“运载体” 
考点4:“prospectively designed cohorts”中的“prospectively”推荐翻译为“前瞻性”
考点5:“disease-specific risk factor”推荐翻译为“疾病特异性风险因素”
考点6:“postmortem validation”必须翻译为“尸检验证”，不能译为“死后验证”
考点7:“proteoform diversity”推荐翻译为“蛋白质异构体多样性”
考点8:“label-free MS”翻译为“无标记质谱”
考点9:“orthogonally validated”推荐翻译为“交叉验证”
考点10：“GNPC” 应该译为 “全球神经退行性疾病蛋白质组学联盟”，不能保留原文不译
考点11：“individuals across AD, FTD, PDD, PD, ALS and normal aging”中“AD”应译为“阿尔茨海默病”或“阿尔茨海默病（AD）”，不能保留原文不译
考点12：“individuals across AD, FTD, PDD, PD, ALS and normal aging”中“FTD”应译为“额颞叶痴呆”或“额颞叶痴呆（FTD）”，不能保留原文不译
考点13：individuals across AD, FTD, PDD, PD, ALS and normal aging”中“PDD”应译为“帕金森病痴呆”或“帕金森病痴呆（PDD）”，不能保留原文不译
考点14：individuals across AD, FTD, PDD, PD, ALS and normal aging”中“PD”应译为“帕金森病”或“帕金森病（PD）”，不能保留原文不译
考点15：individuals across AD, FTD, PDD, PD, ALS and normal aging”中“ALS”应译为“肌萎缩侧索硬化症”或“肌萎缩侧索硬化症（ALS）”，不能保留原文不译