SWATH-MS analysis of cerebrospinal fluid to generate a robust battery of biomarkers for Alzheimer’s disease

Abstract

Cerebrospinal fluid (CSF) Aβ42 and tau protein levels are established diagnostic biomarkers of Alzheimer's disease (AD). However, their inadequacy to represent clinical efficacy in drug trials indicates the need for new biomarkers. Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-based mass spectrometry (MS) is an advanced proteomic tool for large-scale, high-quality quantification. In this study, SWATH-MS showed that VGF, chromogranin-A, secretogranin-1, and opioid-binding protein/cell adhesion molecule were significantly decreased in 42 AD patients compared to 39 controls, whereas 14-3-3ζ was increased (FDR < 0.05). In addition, 16 other proteins showed substantial changes (FDR < 0.2). The expressions of the top 21 analytes were closely interconnected, but were poorly correlated with CSF Aβ42, tTau, and pTau181 levels. Logistic regression analysis and data mining were used to establish the best algorithm for AD, which created novel biomarker panels with high diagnostic value (AUC = 0.889 and 0.924) and a strong correlation with clinical severity (all p < 0.001). Targeted proteomics was used to validate their usefulness in a different cohort (n = 36) that included patients with other brain disorders (all p < 0.05). This study provides a list of proteins (and combinations thereof) that could serve as new AD biomarkers. Cerebrospinal fluid (CSF) levels of Aβ1-42 (Aβ42), total Tau (tTau), and phosphorylated Tau181 (pTau181) are diagnostic markers of Alzheimer's disease (AD) 1,2. These biomarkers are currently used to confirm the core pathology of AD, i.e., Aβ and tau pathology, in deceased patients while they are alive 3 , and are also monitored in AD therapeutic trials 4. However, accumulating evidence has demonstrated a lack of utility of these markers after clinical onset of AD due to early concentration plateaus 5 and poor reflection of the clinical benefits of therapeutics that target them 6. CSF proteins related to synaptic function, neurodegeneration, inflammation, and Aβ metabolism have recently been suggested as supplementary biomarkers 7 ; however, they have not yet been clinically adopted.

Unbalanced Regulation of α7 nAChRs by Ly6h and NACHO Contributes to Neurotoxicity in Alzheimer's Disease

“…However, an important caveat is that the CSF we analyzed was pooled from multiple patients, so it is possible that certain individuals skewed our results. On the other hand, Ly6h was recently identified by mass spectrometry as among 21 proteins that are most significantly changed in CSF of AD patients relative to age-matched controls (Park et al, 2020). Thus, in this context our data suggest that Ly6h may be a novel biomarker of AD that could be collected from CSF of living patients to monitor disease progression.…”

Dense core vesicle markers in CSF and cortical tissues of patients with Alzheimer’s disease

“…In the CSF of AD patients, we detected that five out of the six analyzed proteins are significantly lowered compared with controls. Decreased levels of PC1/3, PC2 and SgIII have very recently been found in large-scale proteomic CSF screens from AD patients, but this has not been immunologically verified yet [ 24 , 70 – 74 ], whereas variable results for CysC, CPE and SgII have been obtained [ 24 , 71 , 75 – 78 ]. In general, decreased levels of different DCV cargos (i.e.…”

“…Interestingly, a major and ubiquitous constituent of the DCV matrix, CgA, was one of the first biochemical biomarker candidates for AD synaptic degeneration [ 22 , 23 ]. Recent advances in proteomic technology have identified secreted DCV proteins in CSF screens for AD patients, such as the prototype granins CgA and CgB and the non-classical granin SgVII (usually called VGF, the nerve growth factor inducible protein VGF) [ 24 , 25 ]. These observations suggest that DCV proteins may be promising biomarkers of synaptic loss in AD.…”

Neurodegeneration and Astrogliosis in the Human CA1 Hippocampal Subfield Are Related to hsp90ab1 and bag3 in Alzheimer’s Disease

“…Recently, sequential window acquisition of all theoretical mass spectrometry (SWATH-MS) has been developed as a robust proteomic technique that provides not only the broad identification of thousands of proteins, but also a ratio of expression for each one. Different sets of proteins either in cerebrospinal fluid [ 43 ] or restricted to the synaptic proteome [ 44 ] have been obtained in AD by performing SWATH-MS, establishing a panel of biomarkers with clinical utility and a list of 30 unique synaptic proteins differentially expressed in AD HIPP. Nevertheless, a proteomic analysis of the whole HIPP using SWATH-MS might provide a helpful catalog of protein alterations in the diseased HIPP.…”