Nucleotide Adduct Binding MR1 and Activation of MR1-Restricted T Cells

Academic Background

MR1T cells, a recently discovered class of T cells, can recognize antigens presented by MHC class I-related molecule MR1 without microbial infection. These cells exhibit both helper and cytotoxic properties in vitro, but the endogenous antigens they recognize remain unclear, hindering the understanding of their physiological roles and therapeutic potential. This study aims to unveil the endogenous antigens of MR1T cells and address the ambiguity regarding the role of MR1T cells in biological and pathological conditions.

Source

The paper was written by Vacchini et al., with authors from institutions including Basel University Hospital and Basel University, ETH Zurich, University of Minnesota, and Mario Negri Institute for Pharmacological Research. The article was published in the journal Science Immunology on May 10, 2024.

Research Process

Research Steps

a) Detailed Research Process

The study utilized various genetic, pharmacological, and biochemical methods to explore the antigens recognized by MR1T cells. A genome-wide CRISPR-Cas9 gene knockout screening was conducted to explore key metabolic pathways in the process of MR1T cell recognition of target cells. The initial phase involved multiple rounds of killing with a prototype cytotoxic MR1T cell clone, TC5A87. Selected surviving cells enriched with specific single-guide RNA (sgRNA) sequences revealed 243 enriched sgRNAs and 5331 depleted sgRNAs, highlighting multiple genes associated with metabolic processes.

The screening results underwent binomial enrichment analysis through gene ontology (GO) term calculation, identifying 127 enriched gene targets and 650 depleted gene targets, mainly involving carbon synthesis, carbohydrate metabolism, and protein metabolism. Further research used a single-gene knockout reaction model (RECON3D) to predict the impact on the metabolic network, validating the importance of oxidative phosphorylation and purine metabolism in the process.

b) Major Findings

The study identified several genes and metabolites in the purine metabolism pathway, including adenosine deaminase (ADA), adenylosuccinate synthetase 1 (ADSSL1), and laccase domain-containing protein 1 (LACC1), related to MR1T cell activation. Knockout experiments of these genes showed that their absence significantly affects MR1T cell recognition and activation.

By adding synthetic nucleotides and nucleosides to cultured acute monocytic leukemia cells (THP-1), it was found that the absence of ADA and other members of purine metabolism significantly increases the response of MR1T cells to antigens, especially under synthetic nucleotide influence. Additionally, compounds like DADO, guanine, and guanosine at high concentrations increased the reactivity of some MR1T cell clones.

Synergistic Effect of Methylglyoxal and Purine Metabolism Pathways

Further screening data indicated that triose phosphate isomerase (TPI1) and the glycolytic pathway related to methylglyoxal production are associated. Knockout of TPI1 or inhibition with glyoxalase (GLO1) and glyoxalase domain-containing protein (GLOD4) showed that the accumulation of methylglyoxal significantly enhances MR1T cell activation. This result was further validated through various synthetic reactions and cytokine measurement experiments, demonstrating enhanced MR1T cell response under exposure to methylglyoxal and key enzyme inhibitors of purine metabolism.

Metabolite Binding to MR1

The study of MR1 binding nucleic acid derivatives revealed that changes in the purine metabolism pathway and oxidative phosphorylation are crucial for MR1 antigen presentation. Using high-performance liquid chromatography (HPLC) combined with high-resolution mass spectrometry (HRMS), it was discovered that carbon-based nucleotide adducts bind to the MR1 molecule and support MR1T cell activation. These molecules mainly include etheno-adenosine (ETHENO-A) and M1Ado/M1Ade adducts.

Clinical Relevance of MR1T Cell Recognition

The study employed synthetic MR1-ligand tetramers to identify and isolate MR1T cells from donor blood samples, finding MR1-m1Ado tetramer-positive T cells in both healthy individuals and non-small cell lung cancer patient samples. These T cells produced interferon-gamma (IFN-γ) upon encountering MR1-m1Ado antigens, further validating the importance of these antigens in physiological and pathological environments.

Research Conclusions

Scientific and Practical Value

The study reveals the recognition mechanism of MR1T cells and their specific recognition of metabolites, providing a new perspective on the role of MR1T cells in physiological and pathological environments. This discovery not only deepens the understanding of the immune recognition mechanism of MR1T cells but also lays a foundation for developing novel cancer interventions and immunotherapies.

Research Highlights

1. Newly Discovered Antigens: The study unveils new endogenous antigens of MR1T cells, filling a knowledge gap in the field.
2. Multidisciplinary Integration: The research utilized genetic, pharmacological, and biochemical methods, providing comprehensive and accurate data support.
3. Clinical Relevance: The findings were validated in both healthy individuals and cancer patient samples, demonstrating practical applications.

The next steps of the research will focus on understanding the physiological roles of MR1T cells and their potential in cancer treatment, as well as exploring broader applications and recognition mechanisms of MR1T cell antigens.

Summary

This paper deeply explores the origin and mechanism of action of MR1T cell antigens, providing new potential targets for immunotherapy. The results indicate that metabolic changes, particularly carbon-based nucleotide adducts, play a crucial role in MR1T cell recognition and response, laying a theoretical foundation for developing MR1T cell-targeted therapeutic strategies.