Proteomic signatures of Alzheimer's disease and Lewy body dementias: A comparative analysis

Abstract

Introduction: We aimed to identify unique proteomic signatures of Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia (PDD).

Methods: We conducted a comparative proteomic analysis of 33 post mortem brains from AD, DLB, and PDD individuals without dementia focusing on prefrontal, cingulate, and parietal cortices, using weighted gene co-expression network analyses with differential enrichment analysis.

Results: Network modules revealed hub proteins common to all dementias. Lewy body dementias differed from AD by reduced levels of the autophagy protein p62 (SQSTM1), whereas DLB was distinguished from both AD and PDD by altered TRIM33 and cysteine/glutamate transporter (SLC7A11) across brain regions. An increase in mitochondrial and synaptic proteins was related to better cognition whereas enrichment in the extracellular matrix, complement system, and autophagy proteins was associated with greater cognitive impairment.

Discussion: Our study offers valuable insights into the network-based biomarker characterization of molecular signatures of AD, DLB, and PDD.

Highlights: Reduced levels of the autophagy protein p62 (SQSTM1) differentiated Lewy body dementias from Alzheimer's disease (AD) across multiple brain regions. Dementia with Lewy bodies (DLB) was distinguished from both AD and Parkinson's disease dementia (PDD) by altered TRIM33 and cysteine/glutamate transporter (SLC7A11) levels across brain regions. Key mitochondrial oxidative phosphorylation proteins (e.g., COX7A2, TOMM40L, NDUFV1), and synaptic proteins (e.g., GABRB3, GABRB2, GLUA3, GLUA4, SNAP47, dynamin1) were more abundant in preserved cognitive states. Extracellular matrix proteins and members of the complement system (decorin, biglycan, C4A, C4B) showed a strong positive correlation with cognitive decline.

Keywords: Alzheimer's disease; Lewy body dementias; cognitive impairment; co‐expression network analysis; mass spectrometry; synaptic proteins.

FIGURE 1

Schematic overview of the study design, analysis strategy, and results. Samples used in this study are coming from a prospectively followed cohort of patients diagnosed with AD, LBD, PDD, or cognitively normal (C) participants (A). Labeled shotgun proteomics analyses were performed in the prefrontal cortex, anterior cingulate cortex, and parietal cortex revealing > 11,000 proteins expressed across the brain regions. WGCNA network analysis was used to determine modules based on similar co‐expression pattern in a trans‐diagnostic and trans‐brain regional fashion (A). Differential protein expression analyses revealed decreased abundance in pathways related to synaptic, innate immunity, and mitochondrial respiration, with increased metabolic functions across the three dementias. Several differentially expressed synaptic and mitochondrial proteins have been positively correlated with the last MMSE score, while metabolic‐ and autophagy‐related proteins have been negatively correlated to cognitive scores. Twenty‐five percent missing values were allowed during all data analysis revealing 6289 proteins commonly expressed across the three brain regions (B). t‐SNE visualizing the diagnosis and brain regional clusters, highlights a better sample separation based on brain regions and mixed clustering across the three dementias (C). DEPs compared to non‐demented controls reveal various amount of overlap across the dementia groups in the three brain regions (D). AD, Alzheimer's disease; DEPs, differentially expressed proteins; DLB, dementia with Lewy bodies; MMSE, Mini‐Mental State Examination; PDD, Parkinson's disease dementia; t‐SNE, t‐distributed stochastic neighbor embedding; WGCNA, weighted gene co‐expression network analysis.

FIGURE 2

Module trait‐correlation summary in the three brain regions. Correlations between the modules’ genes and the traits in the parietal cortex (A), the prefrontal cortex (B), and the anterior cingulate gyrus (C). Traits correspond to years of dementia, diagnosis (AD, PDD, DLB), Braak stage, lMMSE, MMSEd, and APOE ε4 genotype. Various module eigengene proteins were correlated with neuropathological hallmarks, cognitive traits, and APOE ε4 genotype in all three brain regions. P values of significant correlations are indicated. The scale indicates negative (blue) and positive (red) significant correlations. AD, Alzheimer's disease; APOE, apolipoprotein E; DLB, dementia with Lewy bodies; lMMSE, last Mini‐Mental State Examination; MMSEd, Mini‐Mental State Examination decline; PDD, Parkinson's disease dementia.

FIGURE 3

Module trait‐correlation and module eigengene value comparison summary in AD. Correlation between the modules’ genes and the traits in AD (A), where traits correspond to years of dementia, Braak stage, lMMSE, MMSEd, and APOE ε genotype. P values of significant correlations are indicated. The scale indicates negative (blue) and positive (red) significant correlations. Immune response, metabolic, and protein folding MEs correlated negatively with the last MMSE scores across the brain regions, while RNA splicing and cytoskeleton related ME correlated negatively with Braak stages. ME value comparisons of synaptic and mitochondrial modules M5, M3, M4, and M7 showed significant brain regional differences (B). AD, Alzheimer's disease; APOE, apolipoprotein E; lMMSE, last Mini‐Mental State Examination; ME, module eigengenes; MMSEd, Mini‐Mental State Examination decline.

FIGURE 4

Module trait‐correlations and module eigengene value comparison summary in Lewy body dementias. Correlation between the modules’ genes and the traits in DLB (A) and PDD (B), where traits correspond to years of dementia, Braak stage, lMMSE, MMSEd, and APOE ε genotype. Various module eigengene were correlated with neuropathological and cognitive traits across DLB and PDD, with strong positive correlation for RNA splicing and immune response modules and years of dementia in DLB. Module eigengene value comparisons between the brain regions for module M9 in DLB (C) and module M1 in PDD (D) showed significant differences across brain regions. APOE, apolipoprotein E; DLB, dementia with Lewy bodies; lMMSE, last Mini‐Mental State Examination; MMSEd, Mini‐Mental State Examination decline; PDD, Parkinson's disease dementia.

FIGURE 5

Differential expression of proteins across dementia and brain regions compared to non‐demented individuals. DEPs in AD (A), DLB (B), and PDD (C) compared to non‐demented controls are visualized for each dementia and brain region revealing < 5% to 10% overlap across the various brain regions. GO biological terms (D) and KEGG pathways (E) highlight positively (red dots) and negatively enriched (ES, blue dots) biological processes (mustard color), cellular component (green), and metabolic functions across brain regions and dementias compared to non‐demented individuals. AD, Alzheimer's disease; DEPs, differentially expressed proteins; DLB, dementia with Lewy bodies; ES, enrichment score; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; PDD, Parkinson's disease dementia.

FIGURE 6

Differential expression of proteins across dementia and brain regions. Differentially regulated proteins in DLB versus AD (A), DLB versus PDD (B), and PDD versus AD (C) show few overlaps across the brain regions with p62 stably downregulated across Lewy body dementias compared to AD. Significantly dysregulated proteins specific for AD (D, represents significant alterations only present in AD compared to DLB and PDD), DLB (E, includes significant alterations simultaneously present in DLB compared to AD and PDD) or PDD (F, showing alterations simultaneously present in PDD compared to AD and DLB) highlight a handful proteins with differentiating potential among dementias. GO biological terms (G) and KEGG pathways (H) highlight positively (red dots) and negatively enriched (ES, blue dots) biological processes (mustard color), cellular component (green) and metabolic functions across brain regions and dementias compared to each other. AD, Alzheimer's disease; ES, enrichment score; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; LB, dementia with Lewy bodies; PDD, Parkinson's disease dementia.

FIGURE 7

Synaptic dysfunction in AD and Lewy body dementias. Differential protein heat map and synaptic protein profile shows brain regional synergies and differences across dementias compared to control cases for the most commonly altered synaptic proteins for SNARE and SV, dopaminergic, GABA‐ergic (A) and glutamatergic (B) synaptic functions. Differentially up‐ (blue) or downregulated (brown) synaptic proteins across the brain regions highlight conserved and disease‐specific signature proteins (C–E). Sunburst plot of gene enrichment analysis of synaptic proteins revealing alterations in presynaptic and postsynaptic functions, signaling and synapse organization in AD (F), DLB (G), and PDD (H). Presynaptic membrane potential and calcium levels are more dysregulated in AD compared to non‐demented individuals than in Lewy body dementias. AD, Alzheimer's disease; DLB, dementia with Lewy bodies; PDD, Parkinson's disease dementia.