Colsen

bioRxiv [Preprint]. 2026 Apr 27:2026.04.26.720920. doi: 10.64898/2026.04.26.720920.

ABSTRACT

CRISPR-Cas systems use RNA-guided proteins for adaptive immunity through a mechanism whose origin is unknown. Here we report the discovery of Viral Interference Programmable Repeat (VIPR) systems consisting of a Vipr protein more ancient than CRISPR-Cas and vrRNAs comprising alternating GGY/NN motifs. Unlike canonical guide RNAs that base pair with nucleic acid targets using an uninterrupted sequence, vrRNAs recognize double-stranded DNA through a noncontiguous code in which the variable NNs of each repeat collectively specify a target that itself contains a gapped recognition sequence. Analysis of natural vrRNA targets suggests VIPR acts against competing phages. We demonstrate programmable phage defense by redirecting the complex for transcriptional repression. These results suggest that the roots of adaptive immunity lie in ancient warfare between viruses, and reveal a new logic for programmable genetic control.

PMID:42094414 | PMC:PMC13142463 | DOI:10.64898/2026.04.26.720920

Microorganisms. 2026 Mar 26;14(4):744. doi: 10.3390/microorganisms14040744.

ABSTRACT

Helicobacter pylori (H. pylori) is the primary etiological agent for chronic gastritis, peptic ulcers, and gastric adenocarcinoma. The alarming rise in multidrug-resistant (MDR) strains, particularly against clarithromycin (CLR), metronidazole (MNZ), and levofloxacin (LVX), has severely compromised standard therapies. Thus, there is an urgent clinical need for novel antimicrobial agents that operate through distinct mechanisms to bypass resistance pathways and mitigate gastric cancer risk. We designed and synthesized a series of antimicrobial peptides, focusing on the proteolytically stable all-D-amino acid enantiomer, DT7-3, derived from a probiotic-sourced template. Minimum inhibitory concentrations (MICs) were determined against standard strains and 11 clinical MDR isolates via the broth microdilution method. Antimicrobial mechanisms were elucidated using scanning electron microscopy (SEM) for morphology, fluorescence-based assays for anti-adhesion activity, and real-time qPCR to quantify virulence gene expression (babA, ureA, and vacA). Biocompatibility was assessed using defibrinated sheep erythrocytes, gastric epithelial cells (GES-1), and representative beneficial gut microbiota. Analysis of the clinical isolates revealed resistance rates of 63.6% for CLR/LVX and 81.8% for MNZ, with 54.5% identified as MDR. DT7-3 exhibited superior potency (MIC 1-32 µg/mL) against all strains, significantly outperforming its L-enantiomer counterparts. Mechanistic studies unveiled a "triple-hit" mechanism: (1) rapid membrane disruption; (2) potent inhibition of bacterial adhesion to host cells (~60% reduction at 0.5 × MIC); (3) significant downregulation of critical virulence factors (babA, ureA, and vacA). Furthermore, DT7-3 showed an excellent safety profile, with negligible hemolysis (<5% at 32 µg/mL) and minimal cytotoxicity toward GES-1 cells, yielding a high selectivity index (SI, MHC/MIC) > 32 relative to mammalian cells. Crucially, DT7-3 showed high selectivity for the pathogen over beneficial gut microbiota (MIC > 128 µg/mL, SI > 16). Crucially, DT7-3 maintained potent bactericidal activity (MIC ≤ 16 µg/mL) even under cholesterol-enriched conditions. The engineered D-peptide DT7-3 is a potent candidate for combating MDR H. pylori. Its multifaceted mechanism, targeting bacterial viability while suppressing core virulence factors, positions it as a robust lead compound for next-generation eradication therapies aimed at reducing the burden of H. pylori-associated diseases.

PMID:42075141 | DOI:10.3390/microorganisms14040744

Int J Mol Sci. 2026 Apr 18;27(8):3622. doi: 10.3390/ijms27083622.

ABSTRACT

Autoimmune diseases arise from the failure of self-tolerance. The recognition of self-antigen peptide-MHC (pMHC) complexes by the T-cell receptor (TCR) is the fundamental event triggering autoimmune pathogenesis. While traditional immunosuppressants provide broad systemic effects, they often compromise global immunity. Emerging molecular strategies aim to selectively disrupt the trimolecular complex-comprising the TCR, the antigenic peptide, and the MHC molecule-to induce antigen-specific tolerance. This review highlights the pMHC-TCR interaction as the primary molecular checkpoint for antigen-specific intervention. We discuss the structural basis of these interactions and their potential to redefine the therapeutic landscape for autoimmune diseases (ADs). We examine the molecular drivers of tolerance breakdown-including genetic susceptibility, molecular mimicry, post-translational modifications (PTMs), and ectopic MHC II expression-that shape the autoreactive T-cell landscape. This review examines current advancements in biological and pharmacological interventions, such as pMHC-decorated nanoparticles and soluble pMHC, to reprogram pathogenic T-cell response. We also explored CAR-T therapy strategies for autoimmune diseases, such as CAR-Treg, designed to precisely modulate pMHC-TCR signaling. Collectively, these precision interventions in immunological synapse assembly during autoimmune response are considered the basis for safer, antigen-specific immunotherapy capable of restoring self-tolerance without global immunosuppression.

PMID:42074260 | DOI:10.3390/ijms27083622

Anal Bioanal Chem. 2026 May 1. doi: 10.1007/s00216-026-06507-0. Online ahead of print.

ABSTRACT

Peptide-based immunotherapy is a promising cancer treatment due to its scalability and patient-centered approach; therefore, there is an increasing focus on discovering neoantigens or modified peptides which could elicit a better immune response. We recently found that the methionine sulfoxide variant of YMDGTMSQV, an immunogenic tyrosinase derived epitope, elicits a stronger immune response compared to the native one. Here, we address the separation of six MHC I-restricted tyrosinase-derived peptides methionine sulfoxide stereoisomers (YMNGTMSQV, YMDGTMSQV, YMQGTMSQV, YMDGVMSQV, FMNGTMSQV, FMDGTMSQV) using offline two-dimensional high-performance liquid chromatography coupled with UV/Vis-Circular Dichroism detection. For all analyzed peptides, using our methodology, we observed that placing the sulfoxide on the methionine in sixth position results in no enantiodiscrimination, suggesting the net contribution of the N-terminus tyrosine or phenylalanine π electrons in separation. We show how modifying the amino acids in the vicinities of the methionine-sulfoxide residues results in the ablation of the chiral discrimination. We also render our methodology analytical to semi-preparative level. We describe the stereoisomers stability and capture differences regarding their propensity towards oxidation, our results suggesting that the substitution of the N-terminus tyrosine to phenylalanine could be involved in this process. We analyzed the tandem mass spectrometry fragmentation patterns of the separated optic isomers and search for clues about their discrimination. Moreover, we found that the stereoisomers are similar recognized by specific HLA compared with the racemic variant. Our methodology could be valuable for potential applications in an enantiomer-specific peptide-based immunotherapy selection.

PMID:42065779 | DOI:10.1007/s00216-026-06507-0

Biophys J. 2026 Apr 25:S0006-3495(26)00313-9. doi: 10.1016/j.bpj.2026.04.028. Online ahead of print.

ABSTRACT

The strongest genetic risk factor for Behçet's disease, a relapsing inflammatory disorder marked by recurrent mucocutaneous ulcers and uveitis, is HLA-B^∗51:01, a class I major histocompatibility complex (MHC-I) allele that presents intracellular peptides to CD8⁺ T cells. The molecular mechanisms linking the peptide preferences of this allele to dysregulated immunity remain unclear, limiting efforts to design peptide-based modulators of antigen presentation. Here, we define HLA-B^∗51:01's peptide selection rules by mapping the "interaction fingerprint" of 36 self-peptides using an extensive set of all-atom molecular dynamics simulations. These uncovered a conserved hydrophobic-polar blueprint that is tuned by peptide length. In silico pulling experiments performed at high-speed atomic force microscopy-like loading rates suggest a three-tier hierarchy of mechanical resilience: 9-mers resist the highest forces, 8-mers exhibit intermediate resistance, and 10/11-mers rupture most easily. Our comprehensive analysis provides an atomistic framework for understanding the molecular mechanisms underlying HLA-B^∗51:01 pathobiology and offers quantitative parameters to guide the design of therapeutic peptides or small molecules to modulate antigen presentation in Behçet's disease.

PMID:42036944 | DOI:10.1016/j.bpj.2026.04.028

Expert Opin Drug Discov. 2026 Apr 24. doi: 10.1080/17460441.2026.2665791. Online ahead of print.

ABSTRACT

INTRODUCTION: Immunogenicity of therapeutic proteins is a major concern because it may compromise their clinical use and efficacy. Preclinical prediction of anti-drug antibody development using in vitro assays is therefore a challenge for candidate biologics.

AREAS COVERED: This review, based on a thorough literature search of the PubMed database up to December 2025, provides an overview of in vitro assays predicting biologic immunogenicity, including antigen internalization assay, dendritic cell activation assay, peptide-MHC II affinity measurement, MHC‑associated peptide proteomics (MAPPs) assay, and T cell activation/proliferation assays. The main features and applications of these assays are summarized, with special emphasis on their advantages and limitations.

EXPERT OPINION: Although in vitro immunogenicity assays are proposed to discriminate between low- and high-immunogenic biologics, they face numerous challenges. These include selecting the most appropriate test(s), lack of standardization in methods and technical parameters, defining positivity thresholds, high costs, the need for specialized equipment and trained personnel, the complexity and labor-intensive nature of assays, and the difficulty of translating in vitro results into clinical immunogenicity outcomes. Additional assay validation studies are undoubtedly required to better define the implementation and robustness of in vitro immunogenicity prediction for biologics, which could be advantageously combined with in silico approaches.

PMID:42030029 | DOI:10.1080/17460441.2026.2665791

MedComm (2020). 2026 Apr 21;7:e70742. doi: 10.1002/mco2.70742. eCollection 2026 May.

ABSTRACT

Immunotherapies have transformed the treatment of cancers and infectious diseases by harnessing the precision and adaptability of the immune system. Central to these advances is the major histocompatibility complex (MHC) system, with classical MHC-I molecules well documented for their role in immune surveillance. MHC-dependent therapies, including immune checkpoint blockade (ICB), T cell receptor (TCR)-engineered therapies, and cancer vaccines, have shown substantial clinical promise. However, their broader efficacy is hindered by the extreme polymorphism of classical MHC-I molecules, susceptibility to immune evasion, and frequent downregulation in many disease settings. In contrast, nonclassical MHC-I molecules, including HLA-E, HLA-F, HLA-G, CD1, and MR1, offer alternative therapeutic opportunities. Shaped by strong evolutionary conservation, these molecules exhibit limited polymorphism, specialized antigen repertoires, distinct trafficking behaviors, and the capability to engage both innate and adaptive immune cells. In this review, we synthesize current knowledge of the structural biology, antigen presentation pathways, receptor interactions, and immunoregulatory functions of nonclassical MHC-I molecules. We further highlight emerging therapeutic strategies, including immune checkpoint modulation, cargo-based ligands, conformation-specific biologics, vaccines, and cellular therapies, while critically evaluating translational challenges. By linking specialized structural and functional features to therapeutic design, this review provides a unified framework for exploiting nonclassical MHC-I molecules as next-generation targets in immunotherapy.

PMID:42027260 | PMC:PMC13100496 | DOI:10.1002/mco2.70742

Clin Cancer Res. 2026 Apr 22:OF1-OF13. doi: 10.1158/1078-0432.CCR-25-3349. Online ahead of print.

ABSTRACT

PURPOSE: The development of Bruton tyrosine kinase inhibitors (BTKi) and their introduction into clinical practice represents a major advance in the treatment of chronic lymphocytic leukemia (CLL). However, monotherapy with ibrutinib or other BTKis does not induce complete remissions or undetectable minimal residual disease even with extended therapy. Therefore, there is a need to understand the differences between ibrutinib-sensitive and -resistant CLL cells along with immune microenvironment to identify therapeutic approaches for controlling residual disease during BTKi treatment.

EXPERIMENTAL DESIGN: Here, we investigated the cellular heterogeneity of peripheral blood mononuclear cells from patients with CLL treated with ibrutinib using single-cell RNA sequencing.

RESULTS: We identified unique transcriptional heterogeneity within the B-cell cluster in the ibrutinib-sensitive and -resistant patients. Ibrutinib-sensitive cells showed enrichment of B-cell populations with upregulation of MHC I molecules and TNF family members. Additionally, we observed that inflammatory response and metabolism-related pathways were decreased, whereas cellular response to stress and DNA repair programs were increased in the ibrutinib-resistant samples. T cells in ibrutinib-resistant patients showed expansion of regulatory T cells and an exhausted CD8 effector T-cell compartment. Furthermore, CD14+ and CD16+ monocytes from ibrutinib-resistant patients preferentially expressed a gene expression program of antiviral immunity.

CONCLUSIONS: At single-cell level, our findings demonstrate a picture of transcriptional heterogeneity in the tumor compartment and immune milieu. Overall, these findings highlight transcriptional changes in circulating immune cells associated with ibrutinib resistance, suggesting that T-cell exhaustion and monocyte polarization accompany and may contribute to resistance during long-term BTKi therapy.

PMID:42018044 | DOI:10.1158/1078-0432.CCR-25-3349

EMBO Mol Med. 2026 Apr 17. doi: 10.1038/s44321-026-00424-6. Online ahead of print.

ABSTRACT

Immune suppression is one of the primary obstacles in neoantigen immunotherapy because tumors can rapidly adapt by reducing MHC-I expression or antigen presentation. Here, we developed a novel immunotherapy strategy that combined vaccination of neoantigens with MICB α3 antigen, by using bacterial outer membrane vesicles (OMVs) as a versatile vector and adjuvant. This approach aims to simultaneously induce a neoantigen-specific cellular immune response and an anti-MICB α3 humoral immune response, to enhance the recognition and killing of tumor cells by immune cells. This strategy significantly improves the infiltration of neoantigen-specific T cells and NK cells, and reverses immunosuppression across various preclinical models. Mechanistically, ILC1s characterized by high GZMA/GZMB expression represent the primary subset accumulating within tumors and are responsible for enhancing antitumor immunity, which can induce Gasdermin D cleavage in tumor cells to initiate tumor pyroptosis for a cascade of cancer-immunity cycle. Overall, this study demonstrated that combined neoantigens and shared MICB α3 antigen for tumor vaccination enhances immune efficacy by eliciting ILC1s-mediated tumor pyroptosis and support the rationale and clinical translation for cancer immunotherapy.

PMID:41998137 | DOI:10.1038/s44321-026-00424-6