Cell Death Signature in Gut Lining Predicts Inflammatory Bowel Disease Relapse

Inflammatory bowel disease, an umbrella term that covers Crohn’s disease and ulcerative colitis, is one of the most stubborn chronic conditions in modern medicine. Patients cycle through flares and remissions, often for decades, and clinicians have few reliable ways to know when a seemingly quiet gut is about to erupt again. A new study by Pang, Al-Ani and colleagues, highlighted in Cell Research by Ivan Zanoni of Harvard Medical School and Boston Children’s Hospital, now suggests that the answer may lie in how the cells lining the intestine choose to die. The work reveals that gut inflammation reprograms intestinal epithelial cells, making them susceptible to a necroptotic-to-apoptotic cell death axis that appears in nascent inflammatory bowel disease lesions and, remarkably, can be exploited to predict disease relapse before major inflammation is even visible.

To appreciate why this matters, it helps to understand that cell death is not a single process but a family of genetically programmed routines with very different consequences for the immune system. Pyroptosis, mediated by pore-forming gasdermin proteins, necroptosis, driven by the RIPK kinases and the pseudokinase MLKL, and ferroptosis, an iron-dependent form of lipid peroxidation, are the most inflammatory forms, spilling cellular contents that alarm neighboring tissue. Apoptosis, executed by caspase-3, caspase-6 and caspase-7, is by contrast mostly immunosilent, allowing cells to be quietly dismantled and cleared. Although cell death programs in intestinal epithelial cells are known to be major drivers of inflammatory bowel disease, it has remained unclear exactly which epithelial cells undergo which form of death, whether these processes can be therapeutically targeted, and whether they could serve as clinical markers of impending relapse.

The research team tackled these questions with unusual scale and rigor. They analyzed more than 900 biopsies as well as three-dimensional organoids grown from the gut tissue of controls and of inflammatory bowel disease patients with quiescent or mildly active disease, including individuals treated with biologics or small molecules, the so-called advanced therapies. From patients with Crohn’s disease and ulcerative colitis alike, the investigators collected noninflamed, marginally inflamed and inflamed biopsies. Transcriptomic analyses revealed something unexpected: even though many of these patients were clinically quiescent or already on advanced therapies, transcriptional signatures of tumor necrosis factor and interferons, together with apoptotic gene programs, were still dysregulated in their intestinal tissue.

Protein-level analyses reinforced the message. Western blotting of patient samples showed increased apoptotic and necroptotic signaling in both ulcerative colitis and Crohn’s disease, and this signaling correlated with the degree of inflammation. The spatial pattern was particularly telling. While necroptosis was elevated in noninflamed biopsies, apoptosis, whether occurring alone or alongside necroptotic markers, was found mostly in histologically inflamed samples. This ordering suggested a sequence: necroptosis precedes apoptosis during the development of lesions, with the two death programs marking different stages of the same pathological trajectory rather than representing independent phenomena.

Digging deeper with bioinformatic analyses, the authors identified a distinctive cluster of intestinal epithelial cells expressing NOS2, the gene encoding inducible nitric oxide synthase, together with ZBP1, a protein involved in multiple cell death complexes, and MLKL, the executioner of necroptosis. This cluster, which was also detectable in independent datasets, expressed genes typically associated with inflammatory macrophages, an unusual identity for epithelial cells. Spatial analyses then placed these cells precisely at the top of colonic crypts, and beneath them, in the lamina propria, the investigators found cells expressing tumor necrosis factor, coinciding with an increase in CD4-positive T cells expressing interferon gamma. In other words, the epithelial cells poised for death were sitting in an inflammatory niche saturated with the two cytokines most strongly implicated in inflammatory bowel disease.

To test whether this niche was functionally meaningful, the team established three-dimensional colonocyte organoids and exposed them to tumor necrosis factor and interferon gamma. The cytokine combination induced the inflammatory macrophage-like transcriptional program in the epithelial cells, along with necroptotic and apoptotic gene signatures. At the protein level, the researchers confirmed processing of caspase-3, caspase-8, caspase-9 and caspase-10, together with activation and cleavage of RIPK3 and MLKL. The organoids were undergoing mitochondrial apoptosis, although nonlethal necroptotic signaling was also detected, hinting that the two pathways can run in parallel within the same cells. Further mechanistic work showed that inducible nitric oxide synthase was necessary to license apoptosis, which was driven by the pro-apoptotic protein PUMA, tying the inflammatory chemistry of the gut directly to the cell’s decision to self-destruct.

The most clinically striking result came from longitudinal follow-up. The authors tracked their cohort of inflammatory bowel disease patients for 24 to 36 months and found a significant increase in the necroptotic marker phosphorylated RIPK3, and a trend toward increased apoptotic cleaved caspase-3, in patients who subsequently relapsed. These were patients who, at the time of the original analyses, showed no major signs of inflammation. A protein signature detectable in a biopsy could therefore flag, months in advance, which patients in remission are quietly heading toward a flare, potentially transforming how clinicians time treatment intensification, monitoring intervals and therapeutic withdrawals.

The study also carries important lessons for drug development. With regard to necroptosis, the authors found that the classical pattern of RIPK1, RIPK3 and MLKL activation was not consistently observed across all patients; instead, unique patterns were associated with different subgroups of individuals. This heterogeneity suggests that clinical trials of RIPK1 inhibitors would benefit from careful patient stratification, since a one-size-fits-all approach may obscure benefit in the subgroups whose biology actually depends on this pathway. Similarly, the precise identification of inducers of epithelial cell death, such as inducible nitric oxide synthase and PUMA, opens concrete targets for new therapeutic interventions aimed at promoting epithelial healing during disease.

Important questions remain open. Histological assessment of inflamed and noninflamed biopsies cannot yet predict whether a noninflamed piece of tissue is healing or harboring a future inflammatory lesion, so further studies are needed to prove the necroptotic-to-apoptotic axis in real time. The authors also suggested that necroptosis and apoptosis may occur simultaneously in the same cell, a process reminiscent of PANoptosis, a form of cell death characterized by the simultaneous activation of multiple death pathways, but visualization at the single-cell level will be needed to confirm this. There is also the question of pyroptosis. The authors identified activated gasdermin E, a pore-forming member of the gasdermin family, in their samples, and a recent separate study showed that type III interferons, which are particularly elevated in inflammatory bowel disease biopsies, correlate with ZBP1, activated caspase-8 and cleaved gasdermin C, and drive pyroptotic death of reparative stem cells that delays lesion repair. Whether the necroptotic-to-apoptotic pathway is integrated with pyroptotic programs, or whether cell type, location and timing separate these events, is now a central question for the field.

Culture systems add another layer of complexity. The identification of tumor necrosis factor plus interferon gamma as a potent driver of the necroptotic-to-apoptotic axis in three-dimensional organoids is notable, but under those experimental conditions the authors did not recapitulate the type III interferon-induced cell death or gasdermin C activation previously shown in two-dimensional organoid cultures, which are more differentiated and well defined. Tumor necrosis factor and interferon gamma have previously been found to induce pyroptosis together with apoptosis and necroptosis in the context of lung viral infections, while during acute respiratory distress syndrome type III interferons showed the capacity to induce apoptosis in mice and humans. Future studies will therefore need to address how different culture conditions, tissue origin across distinct regions of the intestinal tract, and specific cell subtypes shape the response to different inflammatory milieus and the selection of different death pathways. Even with those caveats, the study stands as an important foundation, both for a better mechanistic understanding of inflammatory bowel disease and for the development of improved intervention strategies, offering clinicians a potential early-warning system written in the language of dying cells.

Subject of Research: A necroptotic-to-apoptotic cell death axis in intestinal epithelial cells that predicts relapse in inflammatory bowel disease

Article Title: No time to die: cell death predicts IBD relapse

Article References: No time to die: cell death predicts IBD relapse. (n.d.). https://doi.org/10.1038/s41422-026-01304-x

Image Credits: AI Generated

DOI: 10.1038/s41422-026-01304-x

Keywords: inflammatory bowel disease, Crohn's disease, ulcerative colitis, necroptosis, apoptosis, pyroptosis, intestinal epithelial cells, TNF, interferon gamma, RIPK3, organoids, disease relapse