A new de novo‐assisted mass spectrometry method for novel antimicrobial peptide expression profiling in cerebrospinal fluid (CSF) of demented subjects

Abstract

AbstractBackgroundActivation of innate immunity is a pathological hallmark of Alzheimer’s disease (AD). Antimicrobial peptides (AMPs), small (12‐50 amino acid) peptides, are essential components of the innate immune system and provide the first line of defense against microbial infections in immune‐privileged tissues, like brain. Many proteins with antimicrobial activity have been shown to be involved in AD. We developed a new mass spectrometry (MS)‐based method to profile known and novel AMPs in CSF. Here we report differentially expressed AMPs in CSF of Ab+ (AD) and Ab‐ (non‐AD) dementia.MethodWe created a custom (Swiss‐Prot + human AMP) database for our de novo‐assisted proteomics platform. MS data (PRIDE archive PXD016278) from CSF of cognitively impaired subjects with or without amyloid positivity were analyzed. Peptide raw peak area intensities were quantile normalized and log2 transformed to reduce technical variation and ensure distribution symmetry. Differentially expressed peptides were identified via analysis of covariance after adjusting for age and gender, with the significant criteria based on 20% false discovery rate. Multiscale Embedded Gene Co‐expression Network Analysis (MEGENA) was used to identify AMPs with the potential to regulate the molecular changes in AD.ResultWe identified 24 differentially expressed AMPs in CSF of Ab‐driven dementia mapping to 6 proteins. These include the AMPs released by the chromaffin cells of the adrenal medulla (Chromogranin A and B, Ubiquitin), Beta‐2 macroglobulin, Amyloid‐beta A4, and Clustrin proteins. The antimicrobial activity containing sequence from Chromogranin A was represented in top two modules identified by MEGENA network analysis. These modules exhibited high correlation with peptides from a dementia‐linked neurosecretory protein VGF. The top 5 pathways enriched in MEGENA modules include cell adhesion, system development, nervous system development, regulation of nervous system development, and neurogenesis.ConclusionThis study reports the first unbiased analysis of dementia‐linked AMP diversity that can be monitored in CSF. Contribution of these AMPs and the associated pathways in the AD pathophysiology warrants further investigation.