Abnormal epithelial cell-death signalling may persist during apparent IBD remission and could identify patients at greater risk of relapse, Australian researchers have found.
Patients with apparently inactive IBD may harbour abnormal epithelial cell-death signalling that predicts a subsequent flare, according to Australian research that could reshape concepts of deep remission.
The prospective study, published in Science, found increased necroptotic and apoptotic signalling in intestinal tissue from patients with Crohn’s disease and ulcerative colitis, including non-inflamed tissue and patients receiving advanced therapies.
Patients were followed for more than two years and researchers found that those with higher levels of this abnormal cell-death signalling were more likely to subsequently experience a clinical relapse.
The findings raise the possibility that molecular changes in the intestinal lining could one day help identify patients whose disease remains biologically active despite apparent remission and reveal new treatment targets aimed at achieving deeper and more durable remission.
The WEHI and the Royal Melbourne Hospital researchers analysed more than 900 intestinal biopsies from 80 people with and without IBD, integrating histology, immunoblotting, bulk and spatial transcriptomics, patient-derived intestinal organoids, and clinical data.
The multidisciplinary team included Associate Professor Britt Christensen and Dr Aysha Al-Ani from the RMH, together with Professor James Murphy, Professor James Vince, Dr Andre Samson, Professor Edwin Hawkins, Dr Jiyi Pang, and a broader team of researchers from WEHI and collaborating institutions.
“One of the frustrations in treating IBD is that a patient can be feeling well, their tests can look reassuring and their bowel can appear healed, but we still can’t be certain that the disease is truly switched off,” Professor Christensen said.
“What surprised us was that although many of the patients in our study had well-controlled disease and the majority were in endoscopic remission, we could still see increased cell-death signalling in the intestinal lining.
“It suggests there may be disease still smouldering beneath the surface That finding led us to ask whether these signals had any bearing on what happened to patients later.
“When we looked at their subsequent clinical course, patients with higher levels of this signalling were more likely to relapse.
“That opens up two really interesting possibilities. The first is whether we could eventually use these molecular changes to identify patients who are still at risk of a flare despite appearing to be in remission.
“The second is whether these pathways themselves could become treatment targets, allowing us to treat the disease that remains beneath apparent remission and help patients stay well for longer.”
Most patients in the study had mildly active disease by clinical, endoscopic, and histological measures, while 62% were receiving biologic or small-molecule therapies.
Despite this relatively well-controlled disease, necroptotic signalling was elevated in non-inflamed IBD biopsies taken away from mucosal inflammation.
Overall, 74 of 93 IBD samples assessed had either phosphorylated RIPK3, a marker of necroptotic signalling, or cleaved caspase-3, a marker of apoptosis, above the non-IBD mean.
The researchers said the findings suggested necroptotic signalling emerged early during lesion development, while apoptotic signalling became more prominent with established inflammation.
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Spatial transcriptomics further identified an inflammatory epithelial state that was already detectable in non-inflamed IBD tissue. A subpopulation of differentiated absorptive epithelial cells showed altered expression of genes including NOS2, MLKL, and ZBP1, with these cells expanding as inflammation increased.
Patient-derived organoid experiments implicated interferon-gamma and TNF as important drivers of the process. Together, the cytokines killed up to 80% of colonocytes in vitro and reproduced transcriptional and cell-death signalling features seen in patient biopsies.
The mechanistic work suggested inflammation drove mitochondrial apoptosis through different pathways in mature epithelial cells and intestinal stem cells. PUMA was implicated in stem-cell apoptosis, while inducible nitric oxide synthase appeared to promote apoptosis in colonocytes.
The clinical implications emerged when investigators followed patients for 24 to 36 months.
Of 52 patients enrolled in the longitudinal analysis, 22 were lost to follow-up, 14 remained stable without a change in therapy, and 16 experienced an inflammatory flare requiring corticosteroids or an escalation or switch in treatment.
Baseline CRP did not differ between patients who subsequently relapsed and those who remained stable. However, those who relapsed had more histological inflammation and higher levels of phosphorylated RIPK3 relative to non-IBD controls. Cleaved caspase-3 was also higher among patients who relapsed, although this difference was not statistically significant.
The findings were not yet ready to alter clinical monitoring, the researchers said. The relapse analysis was relatively small, and the study did not establish a validated biomarker threshold or show that treatment directed at these pathways prevents flares.
However, the researchers said that noncanonical epithelial cell-death signalling represented an early and graded feature of mucosal disease that could persist despite treatment and apparent remission.
“The ethos behind IBD therapy is to reduce the frequency and severity of flares, halt disease progression and improve patients’ lives,” said gastroenterologist Dr Al-Ani, whose PhD work was supported by a Crohn’s & Colitis Australia top-up scholarship.
“More sensitive molecular detection may help us keep patients in deep remission for longer and introduce new treatments.”
Future research will determine whether interrupting these pathways can protect intestinal epithelial and stem cells and help achieve a deeper and more durable state of remission.
Crohn’s & Colitis Australia CEO Leanne Raven said the findings addressed an important source of uncertainty for people living with IBD.
“For people living with IBD, being told you are in remission should bring reassurance, yet many people still live with the uncertainty of when the next flare might come. Research like this helps us understand what may be happening beneath the surface, even when someone appears to be well,” Ms Raven said.
“The hope is that research of this kind will ultimately give people greater confidence that remission can last — by helping clinicians identify those who remain at risk and opening the door to treatments that could keep disease under control for longer.”
