Characterization of Proteasome-Generated Spliced Peptides Detected by Mass Spectrometry

Rational design of a near-infrared fluorescent probe for rapid monitoring of carboxylesterase in live cells and drug-induced liver injury mice

BACKGROUND

Carboxylesterase (CE) is an important enzyme that mainly exists in liver cells and can catalyze the hydrolysis of esters in a variety of pharmaceuticals and xenobiotics. Real-time and non-invasive imaging of CE is of great significance for the study of CE-related metabolic diseases. Although fluorescence sensing technology is considered a promising candidate, the slow response rate (> 60 min), low sensitivity, and short emission wavelength (<650 nm) of most CE probes limit their practical application. Therefore, it is significant and urgent to develop novel fluorescent probes for the rapid diagnosis of CE-related diseases.

RESULTS

Herein, a near-infrared fluorescent probe, CF3-BDP-CE, has been developed by introducing acetyl as the CE recognition unit into the fluorophore meso-trifluoromethyl-BODIP for the detection of CE. CF3-BDP-CE exhibited a remarkable fluorescence enhancement at 690 nm for CE with a limit of detection of 7.9 × 10-4 U/mL. Importantly, the fast response kinetics (within 3 min) make CF3-BDP-CE superior to most reported probes. The emission turn-on mechanism was confirmed by theoretical calculation, revealing that after the hydrolysis of CF3-BDP-CE, the intramolecular charge transfer process leads to strong fluorescence. Furthermore, CF3-BDP-CE has been successfully applied to real-time imaging of endogenous CE changes in living cells and to imaging CE activity differences between tumor and normal cells. In addition, CF3-BDP-CE has been successfully used to track CE abnormalities in acetaminophen-induced liver injury model mice.

SIGNIFICANCE

A NIR fluorescent probe CF3-BDP-CE was developed to effectively track the dynamic change of CE fluctuation in living cells and mice, with potential applications in the diagnosis of CE-related diseases.

InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides

Noncanonical epitopes presented by Human Leucocyte Antigen class I (HLA-I) complexes to CD8+ T cells attracted the spotlight in the research of novel immunotherapies against cancer, infection and autoimmunity. Proteasomes, which are the main producers of HLA-I-bound antigenic peptides, can catalyze both peptide hydrolysis and peptide splicing. The prediction of proteasome-generated spliced peptides is an objective that still requires a reliable (and large) database of non-spliced and spliced peptides produced by these proteases. Here, we present an extended database of proteasome-generated spliced and non-spliced peptides, which was obtained by analyzing in vitro digestions of 80 unique synthetic polypeptide substrates, measured by different mass spectrometers. Peptides were identified through invitroSPI method, which was validated through in silico and in vitro strategies. The peptide product database contains 16,631 unique peptide products (5,493 non-spliced, 6,453 cis-spliced and 4,685 trans-spliced peptide products), and a substrate sequence variety that is a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing. Potential artefacts and skewed results due to different identification and analysis strategies are discussed.