Karl Ocius

Sci Adv. 2025 Oct 24;11(43):eadx1751. doi: 10.1126/sciadv.adx1751. Epub 2025 Oct 24.

ABSTRACT

The interaction between human leukocyte antigens (HLAs) and T cell receptor (TCR) is essential for adaptive immune recognition. While it is known that one TCR can map to multiple HLA alleles, the extent of this cross-reactivity remains poorly understood. Here, we introduce THNet, a TCR-based HLA similarity network, and present a comprehensive analysis of HLA-TCR cross-reactivity, which is built upon more than 9 million significantly associated HLA-TCR pairs. We created similarity networks for both class I and class II HLA alleles, illustrating how peptide cross-presentation contributes to HLA-TCR cross-reactivity. Our analysis revealed disease susceptibilities missed by single-HLA enrichment analyses, especially in the Black population. Last, we demonstrated that THNet can prioritize optimal HLA mismatch candidates across different transplantation contexts, supporting its potential utility in donor selection strategies. In summary, our investigation of the HLA-TCR cross-reactive network provides useful insights into autoimmune risk prediction and improved transplantation outcomes.

PMID:41134880 | PMC:PMC12551698 | DOI:10.1126/sciadv.adx1751

Nat Commun. 2025 Oct 24;16(1):9405. doi: 10.1038/s41467-025-64071-0.

ABSTRACT

A microbe is pathogenic when it manages to survive in its host and, often, is able to proliferate. Thus, virulence entails coping with host defenses in parallel to dissemination and/or attack of the host. How the pathogen endures the attack by effectors of the immune response remains insufficiently understood. Here, we report that planktonic Pseudomonas aeruginosa is not immediately virulent in a Drosophila model of acute infection. Bacteria undergo a maturation step called priming, which is required for transition to virulence. Primed bacteria switch to a bacillus shape, only in vivo, proliferate and resist the action of a specific combination of antimicrobial peptides. This priming mechanism requires an interplay between two major effectors of the type IV pili (T4P), FimV and Vfr, which enhance lateral cell wall peptidoglycan synthesis. Interestingly, N-acetyl-muramic acid (NAM) abolishes the virulence of the injected bacteria, which become round, and prevents the localization of the T4P hub protein FimV at bacterial poles, and cAMP signaling. In contrast, N-acetyl glucosamine (NAG) counteracts the action of NAM by promoting FimV polar placement. In fact, NAG alone accelerates the speed of P. aeruginosa priming in a PilJ-dependent manner. This suggests that the NAG sensed by microorganisms is a common signal that promotes virulence through a morphological switch, both in bacteria and pathogenic dimorphic yeasts.

PMID:41136403 | PMC:PMC12552656 | DOI:10.1038/s41467-025-64071-0

Eur J Immunol. 2025 Oct;55(10):e70080. doi: 10.1002/eji.70080.

ABSTRACT

At birth, the mucosal immune system of neonates is not fully developed, making them more susceptible to respiratory and intestinal diseases. Previously described host-directed therapies using toll-like receptor (TLR) activation-based strategies have proven effective in controlling neonatal diseases, including cryptosporidiosis. In this study, we investigated the effect of nucleotide-binding oligomerization domain (NOD) receptors stimulation on the control of enteric infection by the protozoan Cryptosporidium parvum in neonatal mice. NOD2 stimulation by intraperitoneal injection of muramyl dipeptide (MDP) resulted in a rapid reduction in the parasite burden. The protective effect was associated with increased pro-inflammatory cytokine and antimicrobial peptide gene expression and a rapid influx of neutrophils to the site of infection, whereas NOD1 stimulation did not show a protective effect. The protective mechanism did not involve microbiota participation but involved IFN-γ and IL-22 cytokines and was associated with increased intestinal epithelium renewal in infected neonates. Our findings showed that stimulating neonatal mice with the bacterial ligand MDP, which targets the NOD2 receptor, actively contributes to the nonspecific clearance of C. parvum infection by eliminating or renewing infected epithelial cells.

PMID:41116307 | PMC:PMC12538031 | DOI:10.1002/eji.70080

Eur J Pharm Sci. 2025 Dec 1;215:107330. doi: 10.1016/j.ejps.2025.107330. Epub 2025 Oct 14.

ABSTRACT

Cell-penetrating peptides (CPPs) have the capacity to transport cargos into cells either through endocytosis or direct translocation across the plasma membrane. CPPs entering via endocytosis remain generally trapped within endosomes and lysosomes. This entrapment can be alleviated by coupling the CPPs to endosomal escape promoting cargos or by using small molecules that permeate endosomes or lysosomes. L-Leucyl-L-Leucine methyl ester (LLOMe) is an example of such a molecule. The assessment of CPP endosomal escape into the cytosol is not trivial as cytosolic acquisition can also occur via CPP direct translocation across the plasma membrane. Moreover, visualization of CPP cytosolic acquisition often requires the CPP to be tagged with a fluorophore that can affect the behavior of the CPP and that can also be released from the CPP in the degradative environment of endosomes and lysosomes. In the present work, we have explored various parameters that can potentially affect the recording of CPP endosomal escape, such as the chirality of the amino acids making the CPPs, the nature of the fluorophore coupled to the CPPs, and the timing of the recording. For this purpose, we have used three commonly used CPPs: R9 (a synthetic CPP made of 9 arginines), TAT, and penetratin. We have used LLOMe as the endosomal escape promoter. This study presents guidelines for the assessment of CPP endosomal escape. We also provide a framework for selecting appropriate combinations of amino acid chirality, fluorophore type, and assessment timing based on what researchers want to achieve when the CPP-cargo is released from vesicles into the cytosol.

PMID:41101513 | DOI:10.1016/j.ejps.2025.107330

Anal Chem. 2025 Oct 28;97(42):23370-23380. doi: 10.1021/acs.analchem.5c04297. Epub 2025 Oct 16.

ABSTRACT

Imaging endogenous peptides with the chiral selectivity of their component amino acids remains an unmet analytical challenge. d-amino acid-containing peptides (DAACPs), formed by post-translational isomerization of l- to d-amino acids, make up a functionally important class of neuropeptides whose spatial distribution remains poorly understood. Here, we introduce untargeted imaging of neuropeptide stereoisomers using matrix-assisted laser desorption/ionization-trapped ion mobility mass spectrometry imaging (MALDI-TIMS-MSI). We mapped neuropeptides and their DAACP forms in the central nervous system (CNS) of Aplysia californica at single-cell resolution. We found that while both stereoisomeric forms of known neuropeptides were colocalized in nerves and neuropil, DAACPs were not detected in the neuronal soma. For example, the l-form of small cardioactive peptide B was detected at high levels in the B1 and B2 neurons of the buccal ganglion but the DAA-containing form was not detected; however, the DAACP form of small cardioactive peptide B was found in the neuropil of several ganglia. To confirm our assignments and eliminate isobaric interferences, we performed tandem MS with MALDI-TIMS-MSI. In total, we resolved 13 peptide stereoisomers from 6 endogenous neuropeptides. These results demonstrate that MALDI-TIMS-MSI is an effective approach for characterizing and mapping peptide stereoisomers in situ, providing critical insight into the spatial regulation of neuropeptide isomerization.

PMID:41099662 | PMC:PMC12579433 | DOI:10.1021/acs.analchem.5c04297