Single cell map helps predict childhood Crohn's severity and treatment response

by Emily Packer, eLife

edited by Lisa Lock, reviewed by Robert Egan

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Researchers have created a detailed map of childhood Crohn's disease before and after treatment to help understand disease progression. The study, published in eLife, is described by the editors as an important study that substantially advances understanding of pediatric Crohn's disease, mapping its cellular makeup and how patients respond to treatment. The editors add that the evidence is compelling, based on thorough analyses and underpinned by rigorous methodology.

Crohn's disease is an inflammatory bowel disease (IBD) that arises when the gastrointestinal tract's normal state is disrupted by chronic inflammation. Among IBDs, pediatric-onset Crohn's disease is particularly common, representing 25% of all IBD cases, and is debilitating because of its early onset and the lack of treatment options specifically for children. Treatment is tailored to each child's case but commonly includes steroids and immune-modulating drugs, and often antibodies that work against a molecule called tumor necrosis factor-alpha (TNFα).

"While targeting TNF is shared across many autoimmune and inflammatory conditions, it is not successful in all patients, and many go on to develop TNF-resistant disease," says co-first author Kyle Kimler, senior data scientist in the Cell Discovery Network at Boston Children's Hospital, Boston, U.S. "It's of tremendous importance to understand for which patients TNF therapy is not necessary, in which patients it may help to control disease, and which patients are not likely to benefit at all."

Kimler is co-first author of the study alongside Benjamin Doran, now a Ph.D. student at the University of Chicago; Alison Yu, formerly clinical research manager in the Division of Pediatric Hematology/Oncology at the Dana-Farber/Boston Children's Cancer and Blood Disorders Center; and Hengqi Betty Zheng, associate professor at Seattle Children's and the University of Washington School of Medicine, Seattle, U.S.

Building a cellular atlas

The team used powerful sequencing tools called single-cell RNA sequencing to analyze the cellular profiles of diagnostic human biopsies from the small intestines of 14 untreated children with Crohn's disease, repeat biopsies from eight of those children after treatment, and 13 biopsies from a control group of children with noninflammatory gastrointestinal disorders (functional gastrointestinal disorders, or FGID).

They were able to separate the groups of children treated with anti-TNFα agents into subgroups who either had a complete or partial response and could then relate these outcomes to the patients' cell states at diagnosis.

To aid their analysis, they developed a new publicly available bioinformatics tool called ARBOL (Spanish for "tree"), which repeatedly splits groups of data into smaller subgroups to create trees of cell "states." They used this to generate two fully described cellular atlases for childhood Crohn's (pediCD atlas) and FGID, consisting of 94,451 and 107,432 cells, respectively. From this, they were able to identify specific cell signatures that predict disease severity and treatment outcomes.

Cell signatures tied to severity

The specific changes in cell composition associated with more severe disease were an increase in proinflammatory immune cells—including T cells, cytotoxic natural killer cells, subsets of monocytes and macrophages—and a decrease in metabolically specialized subsets of cells that line the normal, healthy intestine. The team noted significant cell changes at diagnosis underlying clinically observed disease severity, which affected the decision whether to treat with anti-TNFα agents.

They then combined their pediCD atlas with follow-up treatment data from eight children and with a single-cell atlas from adults with Crohn's disease receiving treatment. This revealed that anti-TNF treatment pushes the childhood Crohn's cellular ecosystem toward the more severe, treatment-resistant disease state often found in adult Crohn's disease.

"Our study addresses a critical unmet need in the fields of IBD with the creation of an atlas of newly diagnosed untreated disease tissue, coupled with detailed clinical follow-ups to link diagnostic cell types to disease progression," says co-senior author Leslie Kean, director of the Stem Cell Transplant Center at Dana-Farber/Boston Children's Cancer and Blood Disorders Center, and the Robert A. Stranahan Professor of Pediatrics at Harvard Medical School, Boston, U.S.

Kean adds, "That the severity of pediatric Crohn's disease is not uniquely predicted by a singular cell subset or gene reflects the complex genetic and environmental factors that are implicated. But with this study, we have discovered precisely which changes in Crohn's disease cell composition anticipate both disease severity and treatment response."

Kean is co-senior author of the study alongside Jose Ordovas-Montanes, associate professor in the Division of Gastroenterology, Hepatology, and Nutrition at Boston Children's Hospital and Harvard Medical School, and Alex Shalek, director of the Institute for Medical Engineering and Science at the Massachusetts Institute of Technology, Cambridge, U.S.

Limits of a narrow cohort

The authors note some limitations to their work that are important to consider. For example, despite profiling more untreated patients than previous studies at single-cell resolution, the cohort size limits their analyses because of the strict inclusion/exclusion criteria used, the follow-up period, and the ability to capture untreated patients early in the diagnostic process.

They are therefore unable to directly correlate genetic and environmental influences, such as the enteric microbiome, infections and dietary factors, within the cohort. Additionally, the cohort is representative only of the demographics of FGID and IBD in Seattle.

As Ordovas-Montanes concludes, "It will be essential to understand how both FGID and IBD may present differently in patients across the world and the influences involved. Future studies will need to include multiple cohorts to help uncover more location-specific and generalizable insights into these diseases."

Publication details

Hengqi Betty Zheng et al, Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade, eLife (2026). DOI: 10.7554/elife.91792.3

Journal information: eLife

Clinical categories

PediatricsGastroenterologyChildren's healthCommon illnesses & Prevention Provided by eLife Who's behind this story?

Lisa Lock

BA art history, MA material culture. Former museum editor, paramedic, and transplant coordinator. Editing for Science X since 2021. Full profile →

Robert Egan

Bachelor's in mathematical biology, Master's in creative writing. Well-traveled with unique perspectives on science and language. Full profile →

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