In inflammatory bowel disease (IBD), the mucosal innate lymphoid cell (ILC) compartment is disturbed — proinflammatory ILC1 expand while mature NKp44+ ILC3 decline — and biological therapy (anti-TNF, vedolizumab, ustekinumab) partly restores this equilibrium. Creyns et al. (2020) left open how this restoration comes about and what it is worth clinically: whether it reflects direct drug action on ILCs or is a collateral consequence of mucosal healing; what selective IL-23 p19 blockade does to human ILCs in vivo; where circulating NKp44+ ILC3 in Crohn's disease come from; whether the changes hold in biologic-naive patients; whether baseline circulating ILCs predict treatment response; and whether the shifts functionally drive mucosal healing. These questions remain open.

Background

Inflammatory bowel disease (IBD) — comprising Crohn's disease (CD) and ulcerative colitis (UC) — is characterized by chronic relapsing intestinal inflammation driven by dysregulated adaptive and innate immunity. Modern treatment relies on biological therapies ('biologics'): monoclonal antibodies against tumor necrosis factor (anti-TNF), against the gut-homing integrin α4β7 (vedolizumab), and against the p40 subunit shared by interleukin-12 (IL-12) and IL-23 (ustekinumab). A newer class blocks only the IL-23-specific p19 subunit (risankizumab, mirikizumab, guselkumab, brazikumab), sparing IL-12. Innate lymphoid cells (ILCs) are lymphocytes that lack antigen-specific receptors yet secrete T-helper-like cytokines at mucosal barriers. ILC1 depend on the transcription factor T-bet and produce interferon-γ and TNF (proinflammatory); ILC3 depend on RORγt and produce IL-22 and IL-17, which sustain epithelial barrier integrity; NKp44, a natural cytotoxicity receptor, marks mature human ILC3 ('NCR+' ILC3). ILCs in the bloodstream are mostly immature, multilineage-competent precursors (Lim et al. 2017). Work before 2020 established the disease association: inflamed IBD mucosa contains more ILC1 and fewer NKp44+ ILC3 than healthy mucosa (Bernink et al. 2015; Forkel et al. 2019), and IL-12 and IL-23 drive ex vivo interconversion between human intestinal ILC1 and ILC3 (Bernink et al. 2015), which is why cytokine-targeting drugs were expected to act on these cells. Creyns et al. (2020) then provided the first in vivo comparison across three prospective IBD cohorts starting anti-TNF, vedolizumab, or ustekinumab: all three drugs partly restored the mucosal ILC1/NKp44+ ILC3 ratio (decrease of ILC1 with anti-TNF and vedolizumab, increase of NKp44+ ILC3 with all three), 15% of CD patients — but no UC patient or healthy control — had NKp44+ ILC3 in blood, and anti-TNF further raised these circulating cells over time. Paradoxically, the changes tracked therapeutic efficacy across drugs (strongest with vedolizumab and anti-TNF, weakest with the poorly performing ustekinumab cohort), prompting the authors to favor — without establishing — the interpretation that the shifts are a collateral effect of intestinal healing rather than a direct pharmacological effect, and to pose the mechanistic and translational questions that define this problem.

Problem Statement

The overarching objective is to determine how biological therapy reshapes the intestinal innate lymphoid cell compartment in inflammatory bowel disease — mechanistically, comparatively across drug classes, and translationally. The problem, as posed by the source study (Creyns et al. 2020), comprises six linked open questions: (1) Causality and mechanism: do the therapy-associated mucosal ILC subset shifts (decrease of proinflammatory ILC1, increase of homeostatic NKp44+ ILC3) result from a direct effect of the drug on ILCs — for example neutralization of membrane TNF on ILC1 by anti-TNF, or altered recruitment — or are they an indirect, collateral consequence of reduced mucosal inflammation and healing? (2) Origin and trafficking: what is the provenance of the NKp44+ ILC3 detected in the blood of a subset of Crohn's disease patients — spill-over from severely inflamed transmural gut tissue, de novo generation in other lymphoid organs, or altered trafficking dynamics during therapy? (3) Drug-class specificity and cytokine dependence: what are the in vivo effects of selective IL-23 p19 blockade (risankizumab, brazikumab, guselkumab, mirikizumab) on mature ILC3 and on ILC1, and how do they compare with p40 blockade (ustekinumab), so as to clarify the cytokine-specific regulation of human ILC subsets? (4) Generalisability: are the therapy-associated ILC changes reproducible in newly diagnosed or biologic-naive patients, rather than the refractory, pretreated cohort studied originally? (5) Prediction: can baseline circulating ILC subset composition predict response to biological therapy? (6) Functional consequences: do the therapy-associated ILC subset shifts functionally contribute to mucosal healing and to the clinical efficacy of biological therapy? The causal/mechanistic question (1) is the core of the problem, and questions (2)–(6) are linked extensions that may be pursued independently.

References

  1. Creyns B, Jacobs I, Verstockt B, Cremer J, Ballet V, Vandecasteele R, Vanuytsel T, Ferrante M, Vermeire S, Van Assche G, Ceuppens JL, Breynaert C. Biological Therapy in Inflammatory Bowel Disease Patients Partly Restores Intestinal Innate Lymphoid Cell Subtype Equilibrium. Frontiers in Immunology 11:1847 (2020). doi:10.3389/fimmu.2020.01847, https://doi.org/10.3389/fimmu.2020.01847
  2. Bernink JH, Krabbendam L, Germar K, de Jong E, Gronke K, Kofoed-Nielsen M, Munneke JM, Hazenberg MD, Villaudy J, Buskens CJ, Bemelman WA, Diefenbach A, Blom B, Spits H. Interleukin-12 and -23 Control Plasticity of CD127+ Group 1 and Group 3 Innate Lymphoid Cells in the Intestinal Lamina Propria. Immunity 43(1):146-160 (2015). doi:10.1016/j.immuni.2015.06.019, https://doi.org/10.1016/j.immuni.2015.06.019
  3. Forkel M, van Tol S, Höög C, Michaëlsson J, Almer S, Mjösberg J. Distinct Alterations in the Composition of Mucosal Innate Lymphoid Cells in Newly Diagnosed and Established Crohn's Disease and Ulcerative Colitis. Journal of Crohn's and Colitis 13(1):67-78 (2019). doi:10.1093/ecco-jcc/jjy119, https://doi.org/10.1093/ecco-jcc/jjy119
  4. Lim AI, Li Y, Lopez-Lastra S, Stadhouders R, Paul F, Casrouge A, Serafini N, Puel A, Bustamante J, Surace L, Masse-Ranson G, David E, Strick-Marchand H, Le Bourhis L, Cocchi M, Topazio D, Graziano P, Muscarella LA, Rogge L, Norel X, Sallenave JM, Allez M, Graf T, Hendriks RW, Casanova JL, Amit I, Yssel H, Di Santo JP. Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation. Cell 168(6):1086-1100.e10 (2017). doi:10.1016/j.cell.2017.02.021, https://doi.org/10.1016/j.cell.2017.02.021
  5. Mazzurana L, Bonfiglio F, Forkel M, D'Amato M, Halfvarson J, Mjösberg J. Crohn's Disease Is Associated With Activation of Circulating Innate Lymphoid Cells. Inflammatory Bowel Diseases 27(7):1128-1138 (2021). doi:10.1093/ibd/izaa316, https://doi.org/10.1093/ibd/izaa316
  6. Cao S, Fachi JL, Ma K, Ulezko Antonova A, Wang Q, Cai Z, Kaufman RJ, Ciorba MA, Deepak P, Colonna M. The IRE1α/XBP1 pathway sustains cytokine responses of group 3 innate lymphoid cells in inflammatory bowel disease. Journal of Clinical Investigation 134(13):e174198 (2024). doi:10.1172/JCI174198, https://doi.org/10.1172/JCI174198
  7. Onali S, di Petrillo A, Favale A, Pillai R, Fantini MC. Patients with Crohn's Disease Achieving Ustekinumab-Induced Remission Are Characterized by Increased Baseline IL-23 Receptor Expression on Lamina Propria Th1 Cells. Journal of Clinical Medicine 15(14):5434 (2026). doi:10.3390/jcm15145434, https://doi.org/10.3390/jcm15145434
  8. Bennstein SB, Uhrberg M. Circulating innate lymphoid cells (cILCs): Unconventional lymphocytes with hidden talents. Journal of Allergy and Clinical Immunology 154(3):523-536 (2024). doi:10.1016/j.jaci.2024.06.016, https://doi.org/10.1016/j.jaci.2024.06.016
  9. Horn V, Sonnenberg GF. Group 3 innate lymphoid cells in intestinal health and disease. Nature Reviews Gastroenterology & Hepatology 21(6):428-443 (2024). doi:10.1038/s41575-024-00906-3, https://doi.org/10.1038/s41575-024-00906-3
  10. Yao X, Ma K, Zhu Y, Cao S. Innate Lymphoid Cells in Inflammatory Bowel Disease. Cells 14(11):825 (2025). doi:10.3390/cells14110825, https://doi.org/10.3390/cells14110825
  11. Hao J, Guo X. Group 3 innate lymphoid cells: guardians of intestinal homeostasis. Trends in Immunology 47(5):359-374 (2026). doi:10.1016/j.it.2025.11.008, https://doi.org/10.1016/j.it.2025.11.008
  12. Diao J, Cao H, Zhou J, Shen J. Pathological reprogramming of innate immune cells drives resistance to biologics in inflammatory bowel diseases. Autoimmunity Reviews 25(7):104098 (2026). doi:10.1016/j.autrev.2026.104098, https://doi.org/10.1016/j.autrev.2026.104098