Top-Down Proteomics Detection of Potential Salivary Biomarkers for Autoimmune Liver Diseases Classification

Abstract

(1) Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases characterized by chronic hepatic inflammation and progressive liver fibrosis. The possible use of saliva as a diagnostic tool has been explored in several oral and systemic diseases. The use of proteomics for personalized medicine is a rapidly emerging field. (2) Salivary proteomic data of 36 healthy controls (HCs), 36 AIH and 36 PBC patients, obtained by liquid chromatography/mass spectrometry top-down pipeline, were analyzed by multiple Mann—Whitney test, Kendall correlation, Random Forest (RF) analysis and Linear Discriminant Analysis (LDA); (3) Mann—Whitney tests provided indications on the panel of differentially expressed salivary proteins and peptides, namely cystatin A, statherin, histatin 3, histatin 5 and histatin 6, which were elevated in AIH patients with respect to both HCs and PBC patients, while S100A12, S100A9 short, cystatin S1, S2, SN and C showed varied levels in PBC with respect to HCs and/or AIH patients. RF analysis evidenced a panel of salivary proteins/peptides able to classify with good accuracy PBC vs. HCs (83.3%), AIH vs. HCs (79.9%) and PBC vs. AIH (80.2%); (4) RF appears to be an attractive machine-learning tool suited for classification of AIH and PBC based on their different salivary proteomic profiles.

The Post-Translational Modifications of Human Salivary Peptides and Proteins Evidenced by Top-Down Platforms

“…The study was performed on patients affected by autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC), two autoimmune liver diseases characterized by chronic hepatic inflammation and progressive liver fibrosis, to establish a panel of salivary proteins/peptides able to classify with good accuracy PBC patients vs HCs, AIH patients vs HCs, and PBC vs AIH patients. Among the other data, they revealed significantly different levels of PRP-3 desArg 106 by comparing the two patient groups [ 76 ].…”

Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms

“…In light of this, it is not surprising that the application of TDP has seen a rapid expansion in translational studies over the past decade . Intact protein analysis by MS has been used on a variety of clinical samples and tissues, including (but not limited to) cerebrospinal fluid, cardiac tissue, , gingival crevicular fluid, brain tissue, , and saliva. − Kelleher and co-workers analyzed the various proteoforms of peripheral blood mononuclear cells (PBMCs) in an attempt to identify biomarkers for transplant rejection . Such work has recently led to the creation of the largest proteoform repository to date, the Blood Proteoform Atlas, which includes >30 000 unique proteoforms …”

Orbitrap mass spectrometry and high-field asymmetric waveform ion mobility spectrometry (FAIMS) enable the in-depth analysis of human serum proteoforms

“…[8] Intact protein analysis by MS has been used on a variety of clinical samples and tissues, including (but not limited to) cerebrospinal fluid, [9] cardiac tissue, [10,11] gingival crevicular fluid, [12] brain tissue [13,14] and saliva. [15][16][17][18] Kelleher and co-workers analyzed the various proteoforms of peripheral blood mononuclear cells (PBMCs) in the attempt to identify biomarkers for transplant rejection. [19] Such work has recently led to the creation of the largest proteoform repository to date, the Blood Proteoform Atlas, which includes >30,000 unique proteoforms.…”