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. 2024 Sep 10;25(1):337.
doi: 10.1186/s12931-024-02933-9.

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis

Sarah Samorodnitsky  1 , Monica Kruk  2 , Eric F Lock  1 , Ken M Kunisaki  2   3 , Alison Morris  4 , Janice M Leung  5 , Danielle Weise  2 , Subina Mehta  6 , Laurie L Parker  6 , Pratik D Jagtap  6 , Timothy J Griffin  6 , Chris H Wendt  7   8
Affiliations

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis

Sarah Samorodnitsky et al. Respir Res. .

Abstract

Background: Obstructive lung disease (OLD) is increasingly prevalent among persons living with HIV (PLWH). However, the role of proteases in HIV-associated OLD remains unclear.

Methods: We combined proteomics and peptidomics to comprehensively characterize protease activities. We combined mass spectrometry (MS) analysis on bronchoalveolar lavage fluid (BALF) peptides and proteins from PLWH with OLD (n = 25) and without OLD (n = 26) with a targeted Somascan aptamer-based proteomic approach to quantify individual proteases and assess their correlation with lung function. Endogenous peptidomics mapped peptides to native proteins to identify substrates of protease activity. Using the MEROPS database, we identified candidate proteases linked to peptide generation based on binding site affinities which were assessed via z-scores. We used t-tests to compare average forced expiratory volume in 1 s per predicted value (FEV1pp) between samples with and without detection of each cleaved protein and adjusted for multiple comparisons by controlling the false discovery rate (FDR).

Findings: We identified 101 proteases, of which 95 had functional network associations and 22 correlated with FEV1pp. These included cathepsins, metalloproteinases (MMP), caspases and neutrophil elastase. We discovered 31 proteins subject to proteolytic cleavage that associate with FEV1pp, with the top pathways involved in small ubiquitin-like modifier mediated modification (SUMOylation). Proteases linked to protein cleavage included neutrophil elastase, granzyme, and cathepsin D.

Interpretations: In HIV-associated OLD, a significant number of proteases are up-regulated, many of which are involved in protein degradation. These proteases degrade proteins involved in cell cycle and protein stability, thereby disrupting critical biological functions.

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Conflict of interest statement

Not applicable.

Figures

Fig. 1
Fig. 1
Venn diagram of proteases that correlate with FEV1pp from the various BALF proteomic analyses
Fig. 2
Fig. 2
a) STRING diagram demonstrating protein–protein associations of the 26 proteases identified in BALF by LC–MS/MS and SomaScan that associate with FEV1pp. b) STRING diagram demonstrating protein–protein associations of the 31 substrate proteins mapped to endogenous peptides that associate with FEV1pp
Fig. 3
Fig. 3
Proteases targeting proteins whose degradation was associated with FEV1pp and the total number of substrate proteins mapped to the endogenous peptides
See this image and copyright information in PMC

Update of

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