Plasma enzymatic activity, proteomics and peptidomics in COVID-19-induced sepsis: A novel approach for the analysis of hemostasis

Abstract

Introduction: Infection by SARS-CoV-2 and subsequent COVID-19 can cause viral sepsis. We investigated plasma protease activity patterns in COVID-19-induced sepsis with bacterial superinfection, as well as plasma proteomics and peptidomics in order to assess the possible implications of enhanced proteolysis on major protein systems (e.g., coagulation).Methods: Patients (=4) admitted to the intensive care units (ICUs) at the University of California, San Diego (UCSD) Medical Center with confirmed positive test for COVID-19 by real-time reverse transcription polymerase chain reaction (RT-PCR) were enrolled in a study approved by the UCSD Institutional Review Board (IRB# 190699, Protocol #20-0006). Informed consent was obtained for the collection of blood samples and de-identified use of the data. Blood samples were collected at multiple time points and analyzed to quantify a) the circulating proteome and peptidome by mass spectrometry; b) the aminopeptidase activity in plasma; and c) the endopeptidase activity in plasma using fluorogenic substrates that are cleaved by trypsin-like endopeptidases, specific clotting factors and plasmin. The one patient who died was diagnosed with bacterial superinfection on day 7 after beginning of the study.Results: Spikes in protease activity (factor VII, trypsin-like activity), and corresponding increases in the intensity of peptides derived by hydrolysis of plasma proteins, especially of fibrinogen degradation products and downregulation of endogenous protease inhibitors were detected on day 7 for the patient who died. The activity of the analyzed proteases was stable in survivors.Discussion: The combination of multiomics and enzymatic activity quantification enabled to i) hypothesize that elevated proteolysis occurs in COVID-19-induced septic shock with bacterial superinfection, and ii) provide additional insight into malfunctioning protease-mediated systems, such as hemostasis.

A Reduced Proteomic Signature in Critically Ill Covid-19 Patients Determined With Plasma Antibody Micro-array and Machine Learning

“…The novelties of this study include the protein biomarkers identi ed, the immune microarray platform utilized, and several of the analytic techniques. Previous proteomics studies have also identi ed biomarker models that differentiate COVID-19 patients from non-COVID-19 sepsis controls and healthy control participants (174)(175)(176)(177). While these studies identify a number of important biomarkers, they did not evaluate their effectiveness in a single combined model, which decreases the likelihood of crossidentity concerns with other diseases.…”

“…While these studies identify a number of important biomarkers, they did not evaluate their effectiveness in a single combined model, which decreases the likelihood of crossidentity concerns with other diseases. The novel proteins identi ed in our study may be attributed to our use of an immune microarray platform, while other studies utilized mass spectrometry or proximity extension assays (174)(175)(176)(177)(178)(179). Pathway analysis was used in previous studies to help understand COVID-19 pathophysiology (176, 178, 179); however, our approach utilized NLP to identify organ and cell expression patterns.…”

Data mining antibody sequences for database searching in bottom-up proteomics

“…Database search was conducted using FragPipe [29][30][31][32][33][34][35][36][37] with the above databases and six PRIDE datasets including four blood plasma datasets (PXD031813, PXD029181, PXD023175, and PXD020354) [38][39][40], two depleted blood plasma datasets (PXD036491 [41] and PXD022296) and one brain dataset (PXD039808) [42]. Depleted blood plasma samples were samples of which most abundant proteins (e.g., antibody, fibrinogen, etc.)…”

Rationally Designed Functionalization of Single‐Walled Carbon Nanotubes for Real‐Time Monitoring of Cholinesterase Activity and Inhibition in Plasma

“…Enzymes, prevalent in biological fluids like blood plasma, play pivotal roles in numerous physiological functions, and any deviations in their activity are intricately linked to the emergence of various DOI: 10.1002/smll.202309481 diseases. [1][2][3][4][5][6][7][8][9] Furthermore, a multitude of chemical agents have been identified as interacting, either reversibly or irreversibly, with essential enzymes, leading to their inactivation and thereby impeding their vital biological functionality. [10][11][12][13][14][15][16] Consequently, monitoring of enzyme inhibition arises as an equally essential challenge as tracking their activity.…”