Ubiquitin-proteasome system in the different stages of dominantly inherited Alzheimer's disease

Abstract

Introduction: This study investigated the role of the ubiquitin-proteasome system (UPS) in dominantly inherited Alzheimer's disease (DIAD) by examining cerebrospinal fluid (CSF) levels of UPS proteins.

Method: The SOMAscan assay was used to detect changes in UPS proteins in mutation carriers (MCs) relative to disease progression; imaging and CSF biomarkers of amyloid, tau, and neurodegeneration measures; and Clinical Dementia Rating scale.

Results: Subtle increases in specific ubiquitin enzymes were detected in MCs up to two decades before symptom onset, with more pronounced elevations in UPS-activating enzymes near symptom onset. Significant correlations were found between UPS proteins and Alzheimer's disease (AD) biomarkers, especially between autophagy markers and late-stage tau biomarkers, microglia, and axonal degeneration.

Discussion: The rise in UPS proteins alongside tau-related markers suggests UPS involvement in tau neurofibrillary tangles. Elevated CSF UPS proteins in DIAD MCs may serve as indicators of disease progression, and may support the UPS as a therapeutic target in AD.

Highlights: This study investigates the ubiquitin-proteasome system (UPS) in Dominantly Inherited Alzheimer's Disease (DIAD), highlighting early molecular changes linked to disease progression. Using SOMAscan proteomics, we identified significant UPS protein alterations in cerebrospinal fluid of mutation carriers, notably up to 20 years before clinical symptom onset. Correlations between UPS protein levels and Alzheimer's biomarkers, particularly tau and neurodegeneration markers, suggest a strong association between UPS dysregulation and tau pathology in DIAD. Dynamic UPS changes align with A/T biological staging: UPS proteins were shown to increase across Aβ/tau (A/T) groups, with largest increases in the A+/T+ group, reinforcing their role in late-stage tau pathology and disease progression. These findings underscore the potential of UPS proteins as early biomarkers for Alzheimer's disease progression and as novel therapeutic targets, especially in tau-pathology-driven neurodegeneration. This work contributes to understanding AD pathogenesis, by emphasizing the importance of protein quality control systems and by offering avenues for future biomarker discovery and therapeutic development in Alzheimer's disease.

Keywords: amyloid beta; amyloid precursor protein; autophagy–lysosome pathway; biomarker discovery; dominantly inherited Alzheimer's disease; genetic mutations; neurodegeneration; presenilin 1; presenilin 2; protein aggregation; protein degradation; proteomic analysis; proteostasis; tau pathology; ubiquitin–proteasome system.

FIGURE 1

UPS protein levels relative to EYO at baseline: Depicted are asymptomatic mutation carriers, (green triangles, n = 179), symptomatic mutation carriers (red triangles, n = 104), and non‐carriers (blue circles, n = 172). Rows are organized by EYO when UPS protein levels began showing statistically significant elevation in mutation carriers (red line) compared to non‐carriers (blue line). The dotted line at 0 years indicates the anticipated symptom onset, with best‐fit curves represented by LOESS. A–C, E2H (–19 EYO each), SUMO4 (–18 EYO), and ubiquitin ligases: SMURF1 (–17 EYO). D‐F: E SUMO2, and SUMO3 (–16 EYO each). G–K, N, UBE2Z, UBE2N (–15 EYO each), UBE2N/Uev1a, UBE2N/UBE2V2 (–14 EYO each), UFC1 and deubiquinating enzyme VCIP135 (both –13 EYO). L–M, USP‐14 (–9 EYO), E2Q1, and PSMA4 close to EYO 0. Note: Parenthetical time points specify when proteins had significantly elevated levels in mutation carriers. DIAN, Dominantly Inherited Alzheimer Network; EYO, estimated years from symptom onset; MC, mutation carrier; NC, non‐carrier; UPS, ubiquitin–proteasome system.

FIGURE 2

Heat map of Spearman correlations adjusted for age and sex between UPS proteins and neurological markers. This heatmap illustrates the results of a Spearman correlation analysis conducted between various UPS proteins and an array of AD biomarkers specific to the MC group. Each cell in the heatmap shows the Spearman correlation coefficient, with the scale indicated by the color gradient on the right: strong positive correlations are shown in red, strong negative correlations in purple, and no correlation in light blue. The UPS proteins are listed on the y axis, while the AD biomarkers are on the x axis, which includes amyloid and tau pathology markers, neurodegenerative markers from PET scans and MRI, as well as clinical assessment scales. The chart highlights statistically significant correlations (r values) across multiple dimensions, such as CSF Aβ42/40 ratio, Aβ40, Aβ42, cortical PiB PET SUVR, and various phosphorylated tau (pTau) ratios, alongside MTBR‐tau243, total tau (tTau), tau PET, CSF and serum NfL on a logarithmic scale, relative soluble TREM2 levels, MRI of the precuneus (left), and the Clinical Dementia Rating‐Sum of Boxes (CDR‐SB) in the MC group. All illustrated correlations are significant with a false discovery rate (FDR)–adjusted p value of < 0.05. Aβ, amyloid beta; AD, Alzheimer's disease; CSF, cerebrospinal fluid; FDG, fluorodeoxyglucose; MC, mutation carrier; MRI, magnetic resonance imaging; NfL, neurofilament light chain; PET, positron emission tomography; PiB, Pittsburgh compound B; SUVR, standardized uptake value ratio; TREM2, triggering receptor expressed on myeloid cells 2; UPS, ubiquitin–proteasome system.

FIGURE 3

UPS protein levels across A/T biological stages. The box plots illustrate the log₁₀‐transformed protein levels of 14 UPS proteins across four amyloid PET/total tau (A/T) classification groups: A–/T–, A+/T–, A+/T+, and A–/T+. The following proteins are shown: (A) VCIP135, (B) USP‐14, (C) SMURF1, (D) UBE2Q1, (E) SUMO3, (F) SUMO2, (G) SUMO4, (H) UFC1, (I) UBE2Z, (J) UBE2N/Uev1a, (K) UBE2N/UBE2V2, (L) PSMA4, (M) UBE2N, (N) UBE2H. The x axis represents the A/T groups, while the y axis denotes the log₁₀‐transformed protein levels. Statistical significance was assessed using analysis of variance for overall differences, followed by Tukey's honestly significant difference test for pairwise comparisons. The p values for each protein are indicated in each plot, with significant pairwise differences marked by different symbols, representing different levels of significance. A represents amyloid PET, T refers to total tau. Statistical significance is denoted as follows: *, +, ^, &, $ for p < 0.05; **, ^^, ++, &&, $$ for p < 0.001; ***, +++, ^^^, &&&, $$$ for p < 0.000; and ****, ++++, ^^^^, &&&&, for p < 0.00001. PET, positron emission tomography; UPS, ubiquitin–proteasome system.

FIGURE 4

Pathophysiological progression of UPS in DIAD. This figure depicts the temporal progression of UPS alterations in DIAD from 20 years before symptom onset (EYO –20) to 10 years after (EYO 10). It contrasts the homeostatic and dysregulated states of the UPS and autophagy pathways, as illustrated in panels C and D. The schema underscores the pathological evolution from amyloid beta accumulation into plaques (A) to the aggregation of tau protein into neurofibrillary tangles (B). Early ubiquitination with neuritic plaque development may represent an adaptive response to tau phosphorylation/plaque development (EYO –20 to –10; C); however, with disease progression and the development of more widespread intraneuronal NFTs, the UPS system may become overwhelmed or impaired, precipitating a compensatory increase in autophagic activity. This hypothesis posits that the interplay between UPS and autophagy reflects a dynamic cellular attempt to mitigate the escalating tauopathy and amyloid plaques, with an initial robust UPS reaction potentially yielding to a heightened autophagic response as the disease progresses. Created with BioRender.com. The DIAN‐EYO timeline is denoted in years. A⁻, amyloid negative; A⁺, amyloid positive; DIAD, Dominantly inherited Alzheimer's disease; DIAN, Dominantly Inherited Alzheimer's Network; EYO, estimated years from symptom onset; NFT, neurofibrillary tangle; T⁻, tau negative; T⁺, tau positive; UPS, ubiquitin–proteasome system.