Glycopeptides

Pulmonary fibrosis (PF) is a disease characterized by dysregulated extracellular matrix deposition and aberrant fibroblast activation. Emerging evidence implicates that dysregulated copper metabolism contributed to fibrotic pathogenesis, yet its role and the therapeutic potential of copper modulation remain underexplored. This study investigated the involvement of cuproptosis, a programmed cell death induced by intracellular copper overload, in PF and evaluated the therapeutic efficacy of the copper chelator tetrathiomolybdate (TTM). In a bleomycin (BLM)-induced murine PF model, intratracheal BLM administration elevated lung copper levels, upregulated oligomerized DLAT, and exacerbated fibrosis, as evidenced by collagen deposition, α-smooth muscle actin, and transforming growth factor-beta expression. TTM treatment significantly attenuated fibrotic progression, reduced oxidative stress, and suppressed Olig-DLAT accumulation. In vitro, copper ionophores induced cuproptosis in bronchial epithelial cells, characterized by reduced viability, elevated intracellular Cu⁺, and Olig-DLAT aggregation, which were reversed by TTM. Furthermore, TTM mitigated TGF-β-driven epithelial-mesenchymal transition (EMT) and fibroblast-to-myofibroblast transition (FMT), downregulating collagen-1 and restoring E-cadherin expression. These findings establish cuproptosis as a novel mechanistic contributor to PF and highlight TTM's dual role in restoring copper homeostasis and inhibiting fibrogenic pathways, offering a promising therapeutic strategy for fibrotic lung diseases.

Glycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. While these fragment ions are often straightforward to observe by eye, few tools exist to systemically explore these common glycopeptide spectral features or explore their relationships with each other. Instead, most studies rely on manual inspection to understand glycan-informative ion content in their data, or they are restricted to evaluating the presence of these ions only in the small fraction of spectra that are identified by glycopeptide search algorithms. Here we introduce GlyCounter as a freely available, open-source tool to rapidly extract oxonium, Y-type, and custom ion information from raw data files. We highlight GlyCounter's utility by evaluating glycan-specific fragments in a diverse selection of publicly available datasets to demonstrate how others in the field can make immediate use of this software. In several cases, we show how conclusions drawn in these publications are evident simply through GlyCounter's extracted ion information without requiring database searches or experiment-specific programs. Although one of our goals is to decouple spectral evaluation from glycopeptide identification, we also show that evaluating oxonium ion content with GlyCounter can supplement a database search as valuable spectral evidence to validate conclusions. In all, we present GlyCounter as a user-friendly platform that can be easily incorporated into most glycoproteomic workflows to refine sample preparation, data acquisition, and post-acquisition identification methods through straightforward evaluation of the glycan content of glycoproteomic data. Software and instructions are available at https://github.com/riley-research/GlyCounter.

The spirochete Borrelia burgdorferi causes Lyme disease. In some patients, an excessive, dysregulated proinflammatory immune response can develop in joints leading to persistent arthritis even after antibiotic therapy. In such patients, persistence of antigenic B. burgdorferi peptidoglycan (PGBb) fragments within joint tissues may contribute to immunopathogenesis pre- and post-antibiotic treatment. In live B. burgdorferi cells, the outer membrane shields the polymeric PGBb sacculus from exposure to the immune system. However, unlike most diderm bacteria, B. burgdorferi releases PGBb turnover products into its environment due to the absence of recycling activity. In this study, we identified the released PGBb fragments using a mass spectrometry-based approach. By characterizing the l,d-carboxypeptidase activity of B. burgdorferi protein BB0605 (renamed DacA), we found that PGBb turnover largely occurs at sites of PGBb synthesis. In parallel, we demonstrated that the lytic transglycosylase activity associated with BB0259 (renamed MltS) releases PGBb fragments with 1,6-anhydro bond on their N-acetylmuramyl residues. Stimulation of human cell lines with various synthetic PGBb fragments revealed that 1,6-anhydromuramyl-containing PGBb fragments are poor inducers of a NOD2-dependent immune response relative to their hydrated counterparts found in the polymeric PGBb isolated from dead bacteria. We also showed that the activity of the human N-acetylmuramyl-l-alanine amidase PGLYRP2, which reduces the immunogenicity of PGBb material, is low in joint (synovial) fluids relative to serum. Altogether, our findings suggest that MltS activity helps B. burgdorferi evade PG-based immune detection by NOD2 during growth despite shedding PGBb fragments and that PGBb-induced immunopathology likely results from host sensing of PGBb material from dead (lysed) spirochetes. Additionally, our results suggest the possibility that natural variation in PGLYRP2 activity may contribute to differences in susceptibility to PG-induced inflammation across tissues and individuals.

Current analytical techniques are limited in their ability to interrogate the mechanistic relationship between aberrant mucin glycosylation and malignancy. Herein, we describe a method for mapping specific mucin glycoforms in diseased tissue, enabling correlation of the tumor glycan profile with malignant features. Following on-tissue digestion with mucinase StcE, matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) deduces the spatial distribution of mucinous O-glycopeptides that are subsequently identified using liquid chromatography coupled to mass spectrometry (LC-MS). Our coupled MS approach reveals a striking mucin 2 (MUC2) expression pattern in three colorectal mucinous adenocarcinomas, in which different glycoforms clearly stratify regions within each tumor. The LC-MS experiments obtain glycoproteomic sequence coverage of MUC2's mucin domains in unprecedented depth, and we also present evidence for an endogenous O-acetylated GalNAc. Overall, this proof-of-concept work underscores the potential of this technique to drive research in oncology and beyond.