The study, published in Cancer Immunology Research, a journal of the American Association for Cancer Research, tackles a question that immunologists have rarely been able to address directly in human tissue: does the way a T cell generates and uses energy determine whether it mounts an effective attack or slides into exhaustion? Exhaustion is a state in which a cell, activated too long and too continuously, stops responding to the threats it was designed to destroy. Checkpoint immunotherapy, such as antibodies against the PD-1 receptor, releases one of the brakes holding those cells back. For some patients the effect is dramatic; for many others it fails, and the reasons have remained stubbornly unclear.

Metabolism has long seemed a plausible place to look for answers. An immune cell’s capacity to act — to proliferate, to produce inflammatory signals, to kill tumor cells — is constrained by how it generates energy and building blocks. But probing that relationship in human tumors has been technically formidable. The standard laboratory method for measuring cellular metabolism requires a large, pure population of a single cell type, something that is nearly impossible to obtain from a biopsy. As first author Sujeetha A. Rajakumar, Ph.D., a former research associate in the Department of Otolaryngology–Head and Neck Surgery at Johns Hopkins Medicine, explains, what arrives from the clinic is a mixture, there is not much of it, and the cells researchers most want to study are often the rarest. Most of what the field knows about immune cell metabolism has therefore come from mouse tissue and cells grown in dishes, systems that do not always faithfully reflect what happens inside a patient.

The Johns Hopkins team circumvented this bottleneck by measuring each cell’s metabolic machinery alongside the surface markers that identify it. This approach allowed them to read three things from a single cell simultaneously: which cell type it is, what functional state it is in, and what metabolic profile it uses. They applied the method to several populations of tumor-infiltrating immune cells, including mucosal-associated invariant T (MAIT) cells, conventional CD8+ T cells, and innate lymphoid cells (ILCs). Because the technique works on scarce and mixed samples, it opened a window onto metabolic states that had previously been invisible in human tumor tissue.

The tumor samples came from patients enrolled in two phase II clinical trials at Johns Hopkins Medicine in which immunotherapy was administered before surgery. Participants received either the anti-PD-1 antibody nivolumab alone or nivolumab combined with an antibody against interleukin-8, a signaling protein that recruits immune cells to sites of inflammation and infection. Tissue was collected before immunotherapy began and again four weeks later at the time of surgery, giving the investigators a rare opportunity to observe how the immune and metabolic states of individual cells changed within the same patients over the course of treatment.

Three findings stood out. First, the team identified a population of T cells within these tumors that proved to be metabolically fitter and less exhausted than their neighbors, suggesting that not all tumor-infiltrating lymphocytes are equally depleted and that metabolic state tracks closely with function. Second, the more exhausted cells showed elevated levels of the enzyme glucose-6-phosphate dehydrogenase, or G6PD, the rate-limiting enzyme of a metabolic pathway those cells appear to rely on — making it a possible point of intervention. Third, a subset of innate lymphoid cells carried a metabolic profile associated with immune suppression, raising the possibility that these cells may actively pose an obstacle to checkpoint therapy rather than merely failing to help it.

To test whether the exhausted cells truly depend on the G6PD pathway, the researchers turned to laboratory cultures of tumor-infiltrating CD8+ T cells from a separate group of untreated patients. They sorted the cells according to their expression of CD39, a protein that can contribute to immunosuppression by limiting the activation of T cells. The cultures were then treated with a G6PD inhibitor, with an anti-PD-1 antibody, with both, or with neither. The combination treatment produced the largest gene expression changes in the most exhausted cells and increased their secretion of CD27, a marker of T-cell activation. In other words, the cells that seemed least reachable by conventional immunotherapy were the ones that changed the most when the metabolic pathway was blocked alongside checkpoint blockade.

Senior author Martin Alphonse, Ph.D., an assistant professor of dermatology at the Johns Hopkins University School of Medicine, frames the work around a deceptively simple question: take a piece of head and neck tumor tissue and you will find immune cells inside it whose sole purpose is to recognize something abnormal and destroy it — so what has happened to them? The answer emerging from this study is that part of what has happened is metabolic. Exhausted cells appear to have rewired their energy production in a way that can be mapped, and at least one node of that rewiring can be targeted in the laboratory to partially restore function. Rajakumar notes that when the pathway was blocked alongside checkpoint inhibitor treatment, the cells expected to be least reachable changed the most and became reactivated — evidence, she says, that the pathway is worth pursuing.

The clinical context makes the work consequential. Head and neck squamous cell carcinoma, which arises from the cells lining the mouth, throat and voicebox, is the seventh most common cancer worldwide, with roughly 890,000 new cases each year. With checkpoint inhibitors helping fewer than a quarter of these patients, any strategy that could expand the fraction of responders would address a major unmet need. Growing evidence has suggested that metabolic reprogramming influences whether a T cell mounts an effective response or becomes exhausted, but this study is among the relatively few to examine that link directly in human tumor tissue rather than in animal models or cell lines, and to do so across multiple immune cell types at single-cell resolution.

The researchers and their collaborators are careful to stress what the findings are and what they are not. Blocking G6PD in laboratory cultures reactivated exhausted cells, but no patient in the trials received a G6PD inhibitor, and the approach should not be considered a treatment itself. Alphonse emphasizes that these findings need confirmation in larger patient groups before anything can be built on them. The next steps, he says, are to reproduce the results in independent cohorts and to test whether interfering with this metabolic step has any effect in a living system, not just in a dish. Additional co-authors are Namya Nanda, Chloe Kim, Dustin Dikeman, Tanguy Y. Seiwert, Zubair Khan and Sewon Kang, all affiliated with Johns Hopkins Medicine. Study co-author Carole Fakhry, M.D., M.P.H., senior associate dean for clinical affairs at Johns Hopkins, underscores that such interdisciplinary, collaborative studies are critical to understanding how to make therapies more effective in the future, leveraging the translational capabilities of clinical trials to generate insights that laboratory work alone cannot provide. The work was supported by the Johns Hopkins Department of Dermatology, a Career Development Award from the Dermatology Foundation, the Department of Otolaryngology–Head and Neck Surgery, and the Bloomberg~Kimmel Institute for Cancer Immunotherapy. Alphonse and Rajakumar are inventors on two provisional patent applications related to the work, assigned to The Johns Hopkins University, which manages these relationships under its conflict-of-interest policies.

Subject of Research: Immunometabolic profiling of exhausted tumor-infiltrating T cells in head and neck squamous cell carcinoma

Article Title: Johns Hopkins investigators identify a metabolic weak point in exhausted immune cells in head and neck cancer

Article References: Johns Hopkins investigators identify a metabolic weak point in exhausted immune cells in head and neck cancer. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: head and neck cancer, T cell exhaustion, immunotherapy, checkpoint inhibitors, G6PD, tumor metabolism, CD8+ T cells, innate lymphoid cells, MAIT cells, nivolumab, single-cell profiling, Cancer Immunology Research

M cells are unusual epithelial cells found primarily over organized lymphoid structures such as Peyer’s patches. Their defining function is transcytosis: they capture particles, proteins and microorganisms at the intestinal surface and ferry them across the epithelial layer to immune cells below. This process gives the immune system access to samples of the gut environment without requiring widespread disruption of the barrier. M cells have a distinctive architecture that helps them perform this task. Compared with neighboring absorptive epithelial cells, they possess a thinner apical surface and a pocket-like basolateral compartment where immune cells can gather. These features make them gateways between the intestinal lumen and the immune tissue beneath it. The study by Cao, You, Wang and colleagues focuses attention on an additional possibility—that M cells are not merely delivery points. By organizing an epithelial niche, they may also influence which immune cells are maintained nearby and which molecular signals those cells produce.

Group 3 innate lymphoid cells, or ILC3s, are strategically suited to life at mucosal surfaces. They do not use antigen-specific receptors in the same way as T cells, but they can respond rapidly to cytokines and environmental cues. A major product of ILC3 activity is IL-22, a cytokine that acts primarily on epithelial and stromal cells rather than directly on most immune cells. When IL-22 binds to its receptor on epithelial cells, it can activate intracellular signaling pathways that alter barrier-associated gene expression, stimulate production of antimicrobial proteins and promote tissue repair. In the intestine, this creates a feedback system in which immune cells help epithelial cells withstand constant exposure to food molecules, resident microbes and potential pathogens. The biological importance of this circuit means that the location of ILC3s matters. Cells positioned close to the epithelium can deliver IL-22 where it is most useful, while epithelial cells can provide signals that influence ILC3 maintenance and function.

The new report is significant because it links that IL-22-producing immune compartment to the specialized epithelial landscape created by M cells. The title of the study identifies the central relationship: Peyer’s patch M cells “organize an epithelial niche” that sustains ILC3s and IL-22. In biological terms, a niche is not simply a physical location. It is a combination of neighboring cells, signaling molecules, extracellular structures and local nutrients that allows a cell population to survive, renew itself or retain a particular functional state. By describing an M-cell-organized niche, the researchers frame the intestinal epithelium as an active participant in immune organization. The implication is that M cells may help define the conditions under which ILC3s remain present and continue producing IL-22, thereby connecting luminal sampling with the epithelial defenses that protect the intestinal surface.

This concept could help resolve a longstanding problem in mucosal immunology: how the gut maintains a barrier that is both protective and permeable enough to support essential interactions with microbes. The intestine must exclude invasive organisms while tolerating an enormous community of beneficial bacteria and processing nutrients from the outside world. Peyer’s patches are central to this balancing act because they bring environmental sampling into close contact with organized immune tissue. M cells help initiate that sampling, while ILC3s and IL-22 contribute to the epithelial response. Putting these elements into one cellular framework suggests that immune surveillance and barrier defense are not separate operations. They may be coordinated through specialized microenvironments in which epithelial cells determine the placement and behavior of nearby innate immune cells. The finding therefore has relevance beyond one cell type: it illustrates how tissue architecture can shape immunity.

The study’s focus also highlights a broader principle in modern immunology. Immune cells are often discussed as if they operate independently, releasing cytokines in response to danger signals and then disappearing when the threat is gone. In living tissues, however, immune function depends heavily on cellular neighborhoods. Epithelial cells can present ligands, release growth and survival factors, alter metabolic conditions and create physical structures that guide immune-cell behavior. ILC3s are especially dependent on such local information because their rapid responses are governed by tissue-derived signals as well as by inflammatory cytokines. If M cells help establish the niche that sustains them, then changes in M-cell abundance, maturation or activity could potentially affect the local supply of IL-22. The supplied study identifies this relationship, but its broader importance lies in directing attention toward the tissue-level mechanisms that maintain mucosal immunity rather than focusing only on isolated molecular pathways.

The findings may eventually inform research into disorders in which epithelial defense and immune regulation become uncoupled. Excessive or poorly controlled IL-22 activity has been associated broadly with inflammatory processes in mucosal tissues, while inadequate IL-22 responses can leave epithelial surfaces more vulnerable to damage and infection. Any attempt to translate the new biology into therapies would require caution, because strengthening or suppressing one part of the circuit could have opposing effects depending on the disease context. Manipulating M cells, the signals that sustain ILC3s or the epithelial response to IL-22 might alter antigen sampling as well as barrier protection. The paper does not, on the basis of the supplied information, establish a treatment or demonstrate a clinical intervention. Its immediate contribution is mechanistic: it identifies an epithelial niche organized by M cells as a relevant setting for the persistence of ILC3s and IL-22 production, creating a framework for future work on intestinal immune balance.

The discovery also gives Peyer’s patches a more dynamic role in the public imagination. These structures are often introduced as sites where immune cells encounter material transported from the gut, but the reported relationship suggests that they are also carefully engineered interfaces. M cells can be viewed as sensors and couriers, moving material across the epithelium; ILC3s act as rapid-response regulators; and IL-22 functions as a molecular message that instructs epithelial cells to reinforce their defenses. The power of the system comes from proximity. Signals can be delivered rapidly because the relevant cells occupy the same specialized environment. As scientists continue mapping the cellular neighborhoods that govern immunity, such arrangements may prove common across the body’s barrier tissues. The study by Cao and colleagues makes the intestinal epithelium a striking example of that principle, showing how a cell built to sample the outside world may also help preserve the immune machinery needed to keep that world at bay.

Cao, W. H. J., You, Y., Wang, N., et al. (2026). Peyer’s patch M cells organize an epithelial niche that sustains group 3 innate lymphoid cells and IL-22. Nature Immunology, 27, 1829–1841. https://doi.org/10.1038/s41590-026-02606-3