Investigators identify blood protein signature for non-invasive diagnosis of pediatric inflammatory bowel disease

by Mass General Brigham

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For children with suspected inflammatory bowel disease (IBD), a chronic, relapsing condition of the gastrointestinal tract, getting the right diagnosis relies on a combination of clinical evaluation, imaging, endoscopy and histopathology. Identifying reliable blood-based diagnostic tools remains an important unmet clinical need.

In a study published in eBioMedicine, researchers at Beth Israel Deaconess Medical Center (BIDMC) and Mass General Brigham for Children have used proteomics—the large-scale measurement of proteins in the blood—to identify distinct patterns of proteins that could accurately identify children with inflammatory bowel disease.

"Our findings measuring expression of 1,300 proteins in blood samples demonstrate the utility of blood proteomics in identifying disease-specific biomarkers and new noninvasive tests for differential diagnosis in pediatric IBD as well as defining the underlying pathophysiological mechanisms," said co-senior author Towia Libermann, Ph.D., director of the Genomics, Proteomics, Bioinformatics, and Systems Biology Center at BIDMC. "A validated blood-based diagnostic approach could help reduce diagnostic delays, minimize invasive procedures, and support earlier, more personalized treatment decisions for children with IBD."

"Noninvasive diagnostic tools can contribute to the diagnosis of inflammatory bowel disease but are not yet at the point of replacing standard clinical and pathologic data," said co-senior author Harland Winter, MD, co-director of the Center for Pediatric Inflammatory Bowel Disease at Mass General Brigham for Children. "Nevertheless, the data from these new proteomic platforms represent a much-needed advancement in the care of children with Crohn's disease and ulcerative colitis as we learn how best to not only treat diseases but also to personalize treatment."

Led by Libermann and Winter, the team analyzed blood samples from an initial group of 47 children with and without inflammatory bowel disease. Using a proteomics platform capable of measuring more than 1,000 proteins at once, the team identified a distinct protein pattern in children with IBD. These patterns reflect small shifts in the quantities and combinations of many proteins—signals that are difficult to detect when each marker is considered on its own.

While individual protein markers have long been studied in IBD, this broader approach allowed the researchers to identify a high-level pattern and then narrow it down to a smaller, more practical set. Libermann, Winter and colleagues identified 95 proteins elevated in children with IBD, along with 70 that helped distinguish its two main forms, ulcerative colitis and Crohn's disease. The team further narrowed the field to eight proteins using machine learning that showed strong diagnostic performance in their initial analysis.

To make the approach more practical for potential clinical use, the researchers then reduced the signal to four proteins and validated them using conventional, clinically available tests in two larger groups of 295 and 105 children, respectively. The four-protein test identified IBD with high accuracy, in the 80%–90% range. A separate four-protein test achieved more than 90% predictive performance in differentiating ulcerative colitis from Crohn's disease.

Beyond improved diagnostics, the newly identified protein patterns also offer insight into how inflammatory pathways are altered in children with inflammatory bowel disease, helping explain differences between Crohn's disease and ulcerative colitis and potentially informing future efforts to develop targeted therapies and precision medicine approaches.

Publication details

Mmeyeneabasi Omede et al, Serum proteomics in paediatric inflammatory bowel disease from a case–control study: biomarker discovery and ulcerative colitis–Crohn's disease differentiation, eBioMedicine (2026). DOI: 10.1016/j.ebiom.2026.106311

Journal information: EBioMedicine

Key medical concepts

Inflammatory Bowel DiseasesUlcerative ColitisCrohn's DiseaseProteomicsBiomarkers

Clinical categories

PediatricsGastroenterologyChildren's healthLaboratory medicineCommon illnesses & Prevention Provided by Mass General Brigham Who's behind this story?

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