Characterization of Extracellular Vesicle Cargo in Sjögren's Syndrome through a SWATH-MS Proteomics Approach.

Francesco Finamore,Chiara Baldini,Antonella Cecchettini,Francesco Ferro,Silvia Rocchiccioli,Giovanni Signore,Elisa Ceccherini

doi:10.3390/ijms22094864

Francesco Finamore, Chiara Baldini + Show 5 more

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https://doi.org/10.3390/ijms22094864

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Abstract

Primary Sjögren’s syndrome (pSS) is a complex heterogeneous disease characterized by a wide spectrum of glandular and extra-glandular manifestations. In this pilot study, a SWATH-MS approach was used to monitor extracellular vesicles-enriched saliva (EVs) sub-proteome in pSS patients, to compare it with whole saliva (WS) proteome, and assess differential expressed proteins between pSS and healthy control EVs samples. Comparison between EVs and WS led to the characterization of compartment-specific proteins with a moderate degree of overlap. A total of 290 proteins were identified and quantified in EVs from healthy and pSS patients. Among those, 121 proteins were found to be differentially expressed in pSS, 82% were found to be upregulated, and 18% downregulated in pSS samples. The most representative functional pathways associated to the protein networks were related to immune-innate response, including several members of S100 protein family, annexin A2, resistin, serpin peptidase inhibitors, azurocidin, and CD14 monocyte differentiation antigen. Our results highlight the usefulness of EVs for the discovery of novel salivary-omic biomarkers and open novel perspectives in pSS for the identification of proteins of clinical relevance that could be used not only for the disease diagnosis but also to improve patients’ stratification and treatment-monitoring. Data are available via ProteomeXchange with identifier PXD025649.

Highlights

Primary Sjögren’s syndrome is a complex heterogeneous disease characterized by a wide spectrum of glandular and extra-glandular manifestations, potentially leading to parotid MALT lymphoma [1]
Qualitative/quantitative analysis of proteins extracted from whole saliva (WS) and EV enriched saliva of five healthy controls was carried out by SWATH-mass spectrometry (MS) to investigate on the different proteomics profiles of these two biological compartments
The EVs dataset was compared with Vesiclepedia and ExoCarta (TOP100 most common human EV proteins) databases and 35 proteins resulted comprised in this database (Supplemental Table S1)

Summary

Introduction

Primary Sjögren’s syndrome (pSS) is a complex heterogeneous disease characterized by a wide spectrum of glandular and extra-glandular manifestations, potentially leading to parotid MALT lymphoma [1]. Little is known about the protein composition of salivary EVs in pSS, nor to what extent their content may disclose pathogenetic pathways involved in the disease development and progression In this pilot study, we used a sequential window acquisition of all the theoretical fragment ion spectra (SWATH-MS) approach to monitor the dynamics of EVs sub-proteome in pSS salivary samples in order to assess their value as a source of disease-related biomarkers in comparison with WS. We focused on EV enriched saliva and, besides the assessment of differential expressed proteins between pSS and healthy control EVs samples, a co-expression network analysis (WGCNA) was adopted to identify those groups of proteins with similar expression patterns that may be functionally related and associated with pSS These key proteins could be of clinical importance as diagnostic biomarkers or therapeutic targets

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