Potocnik, A. | Search bioRxiv

bioRxiv2026

Rapid Mechanistic Bridging of an Alzheimer's Disease Plasma Protein Staging Panel Across Brain Proteomics Cohorts

Background: Blood-based biomarkers are transforming Alzheimer's Disease (AD) diagnosis and staging. Recent multi-protein plasma panels accurately identify individuals with advanced Braak pathology, but whether these circulating biomarkers truly reflect the molecular remodeling underlying AD neuropathology remains unclear. Pre-existing datasets could answer such questions, but their reuse requires harmonized protein expression data, standardized sample annotations, and consistent study metadata. Methods: A recently reported seven-protein plasma staging panel was evaluated across multiple post-mortem proteomics brain cohorts using pre-structured datasets on the Tesorai platform. Five datasets with Braak stage data were identified and re-analyzed. A linear model was used to distinguish late (V-VI) from early Braak stage (0-IV). Because phosphorylated tau 217 (p-tau217) and amyloid beta 1-40 (A{beta}40) were not reported for any studies, raw spectra were reprocessed to quantify these proteoforms. Results: Across the cohorts, the plasma-derived biomarker panel consistently discriminated early from late disease despite heterogeneous protein coverage. Reprocessing of raw spectra recovered tau phosphopeptides absent from the original protein summaries, enabling inclusion of p-tau217, while A{beta}40 remained undetected. Together, these findings show that proteins comprising a recently proposed blood-based staging panel are associated with proteomic remodeling in the AD brain across independent cohorts. Conclusions: These findings provide biological validation for a recently proposed blood-based seven-protein staging panel by demonstrating that its constituent biomarkers are associated with disease-stage proteomic changes in AD brain tissue. More broadly, re-mining legacy mass spectrometry data for disease-relevant proteoforms, combined with pre-structured datasets, can accelerate evaluation of emerging blood-based biomarkers against neuropathological and molecular features of disease.

neuroscience↗

bioRxiv2023

Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA

In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+ or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In the Short prokaryotic Argonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, suppressing SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation. KEY POINTSO_LIInactive monomeric SPARTA is autoinhibited by the C-terminal tail of TIR-APAZ C_LIO_LITarget DNA recognition causes C-terminal tail release, pAgo restructuring, and dimerization C_LIO_LITIR domain rotation enables catalytic activation and cooperative tetramer formation C_LI

biochemistry↗